233. Brandon A. Boone, Cristy P. Mendoza, Noah J. Behrendt and Steven E. Jacobsen. (2024) α-Crystalline Domains and Intrinsically Disordered Regions Can Work in Parallel to Induce Accumulation of MBD6 at Chromocenters in Arabidopsis thaliana.
Epigenomes,8:33.
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232. Xin Zang, Undramaa Bat-Erdene, Weixue Huang, Zhongshou Wu, Steve E. Jacobsen, Yi Tang, and Jiahai Zhou. (2024) Structural bases of dihydroxy acid dehydratase inhibition and biodesign for self-resistance.
BioDesign Research, DOI:10.34133/bdr.0046. Pages 1-21.
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231. Bayley R. McDonald, Colette L. Picard, Ian M. Brabb, Marina I. Savenkova, Robert J. Schmitz, Steven E. Jacobsen, and Sascha H. Duttke. (2024) Enhancers associated with unstable RNAs are rare in plants.
Nature Plants, 10: 1246–1257.
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230. C. Jake Harris, Zhenhui Zhong, Lucia Ichino, Suhua Feng, and Steven E Jacobsen. (2024) H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment.
eLife, 12: RP89353.
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229. Shuya Wang, Ming Wang, Lucia Ichino, Brandon A Boone, Zhenhui Zhong, Ranjith K Papareddy, Evan K Lin, Jaewon Yun, Suhua Feng, Steven E Jacobsen. (2024) MBD2 couples DNA methylation to transposable element silencing during male gametogenesis.
Nature Plants, doi: 10.1038/s41477-023-01599-3.
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228. Brandon A. Boone, Lucia Ichino, Shuya Wang, Jason Gardiner, Jaewon Yun, Yasaman Jami-Alahmadi, Jihui Sha, Cristy P. Mendoza, Bailey J. Steelman, Aliya van Aardenne, Sophia Kira-Lucas, Isabelle Trentchev, James A. Wohlschlegel, and Steven E Jacobsen. (2023) ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements.
Science Advances, 9(46):eadi9036. doi: 10.1126/sciadv.adi9036.
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227. Zhen Wang, Claudia M Castillo-González, Changjiang Zhao, Chun-Yip Tong, Changhao Li, Songxiao Zhong, Zhiyang Liu, Kaili Xie, Jiaying Zhu, Zhongshou Wu, Xu Peng, Yannick Jacob, Scott D Michaels, Steven E Jacobsen, Xiuren Zhang. (2023) H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome.
Nature Communications, 14:7484.
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226. Chunsheng Yan, Wenyu Han, Qingyang Zhou, Kanji Niwa, Melody J Tang, Jessica E Burch, Yalong Zhang, David A Delgadillo, Zuodong Sun, Zhongshou Wu, Steven E Jacobsen, Hosea Nelson, K N Houk, Yi Tang. (2023) Genome Mining from Agriculturally Relevant Fungi Led to a d-Glucose Esterified Polyketide with a Terpene-like Core Structure.
Journal of The American Chemical Society, 145:25080-25085.
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225. Zsolt G Venkei, Ildar Gainetdinov, Ayca Bagci, Margaret R Starostik, Charlotte P Choi, Jaclyn M Fingerhut, Peiwei Chen, Chiraag Balsara, Troy W Whitfield, George W Bell, Suhua Feng, Steven E Jacobsen, Alexei A Aravin, John K Kim, Phillip D Zamore, Yukiko M Yamashita. (2023) A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila.
Nature Cell Biology, 25: 1495-1505.
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224. Peter H. Yoon, Petr Skopintsev, Honglue Shi, LinXing Chen, Benjamin A. Adler, Muntathar Al-Shimary, Rory J. Craig, Kenneth J. Loi, Evan C. DeTurk, Zheng Li, Jasmine Amerasekera, Marena Trinidad, Hunter Nisonoff, Kai Chen, Ar ushi Lahiri, Ron Boger, Steve Jacobsen, Jillian F. Banfield and Jennifer A. Doudna. (2023) Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes
Nucleic Acids Research, 51:12414–12427.
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223. Wenyu Han, Zhongshou Wu, Zhenhui Zhong, Jason Williams, Steven E Jacobsen, Zuodong Sun, Yi Tang. (2023) Assessing the Biosynthetic Inventory of the Biocontrol Fungus Trichoderma afroharzianum T22.
Journal of Agricultural Food Chemistry, 71:11502-11519.
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222. Zheng Li, Ming Wang, Zhenhui Zhong, Javier Gallego-Bartolome, Suhua Feng, Yasaman Jami-Alahmadi, Xinyi Wang, James A. Wohlschlegel, Sylvain Bischof, Jeff A. Long, and Steven E. Jacobsen. (2023) The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation.
Nature Communications, 14, 1-16.
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221. Zhenhui Zhong, Yan Xue, C. Jake Harris, Ming Wang, Zheng Li, Yunqing Ke, Mukun Liu, Jessica Zhou, Yasaman Jami-Alahmadi, Suhua Feng, James A. Wohlschlegel and Steven E. Jacobsen. (2023) MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions.
Genome Biology, 24:96.
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220. Ming Wang, Zhenhui Zhong, Javier Gallego-Bartolomé, Suhua Feng, Yuan-Hsin Shih, Mukun Liu, Jessica Zhou, John Curtis Richey, Charmaine Ng, Yasaman Jami-Alahmadi, James Wohlschlegel, Keqiang Wu & Steven E. Jacobsen. (2023) Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14.
Nature Communications, 14:1736.
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219. Guohui Xie, Xuan Du, Hongmiao Hu, Sisi Li, Xiaofeng Cao, Steven E. Jacobsen, Jiamu Du.(2023) Structure and mechanism of the plant RNA polymerase V.
Science, 379:1209-1213.
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218. Ming Wang, Zhenhui Zhong & Steven E. Jacobsen (2023) Targeted gene silencing by diverse epigenetic pathways.
Nature Plants, 9:383-384.
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217. Ming Wang, Zhenhui Zhong, Javier Gallego-Bartolomé, Zheng Li, Suhua Feng, Hsuan Yu Kuo, Ryan L. Kan, Hoiyan Lam, John Curtis Richey, Linli Tang, Jessica Zhou, Mukun Liu, Yasaman Jami-Alahmadi, James Wohlschlegel & Steven E. Jacobsen. (2023) A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis.
Nature Plants, 9:460-472.
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216. Zheng Li, Zhenhui Zhong, Zhongshou Wu, Patrick Pausch, Basem Al-Shayeb, Jasmine Amerasekera, Jennifer A. Doudna, and Steven E. Jacobsen (2023) Genome editing in plants using the compact editor CasΦ.
Proceedings of the National Academy of Sciences, 120 (4): e2216822120.
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215. KiraM. Veley, Kiona Elliott, Greg Jensen, Zhenhui Zhong, Suhua Feng, Marisa Yoder, Kerrigan B. Gilbert, Jeffrey C. Berry, Zuh-Jyh Daniel Lin, Basudev Ghoshal, Javier Gallego-Bartolomé, Joanna Norton, Sharon Motomura-Wages, James C. Carrington, Steven E. Jacobsen & Rebecca S. Bart. (2023) Improving cassava bacterial blight resistance by editing the epigenome.
Nature Communications, 14:85.
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214. Zhenhui Zhong, Suhua Feng, Ben N. Mansfeld, Yunqing Ke, Weihong Qi, Yi-Wen Lim, Wilhelm Gruissem, Rebecca S. Bart and Steven E. Jacobsen. (2022) Haplotype-resolved DNA methylome of African cassava genome.
Plant Biotechnology Journal, pp. 1-3.
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213. Basem Al-Shayeb, Petr Skopintsev, Katarzyna M Soczek, Elizabeth C Stahl, Zheng Li, Evan Groover, Dylan Smock, Amy R Eggers, Patrick Pausch, Brady F Cress, Carolyn J Huang, Brian Staskawicz, David F Savage, Steven E Jacobsen, Jillian F Banfield, Jennifer A Doudna. (2022) Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors.
Cell, 185:4574-4586
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212. Zhenhui Zhong, Yafei Wang, Ming Wang, Fan Yang, Quentin Angelo Thomas, Yan Xue, Yaxin Zhang, Wanlu Liu, Yasaman Jami-Alahmadi, Linhao Xu, Suhua Feng, Sebastian Marquardt, James A. Wohlschlegel, Israel Ausin, and Steven E. Jacobsen. (2022) Histone chaperone ASF1 mediates H3.3-H4deposition in Arabidopsis.
Nature Communications, 13:6970
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211. Lucia Ichino, Colette L. Picard, Jaewon Yun, Meera Chotai, Shuya Wang, Evan K. Lin, Ranjith K. Papareddy, Yan Xue, and Steven E. Jacobsen. (2022) Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen.
Cell Reports, 41, 111699
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210. Yi-Wen Lim, Ben N. Mansfeld, Pascal Schläpfer, Kerrigan B. Gilbert, Narayanan N. Narayanan, Weihong Qi, Qi Wang, Zhenhui Zhong, Adam Boyher, Jackson Gehan, Getu Beyene, Zuh-Jyh Daniel Lin, Williams Esuma, Suhua Feng, Christelle Chanez, Nadine Eggenberger, Gerald Adiga, Titus Alicai, Steven E. Jacobsen, Nigel J. Taylor, Wilhelm Gruissem and Rebecca S. Bart. (2022) Mutations in DNA polymerase δ subunit 1 cosegregate with CMD2-type resistance to Cassava Mosaic Geminiviruses.
Nature Communications, 13:3933
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209. Jorge Hernández-García, Borja Diego-Martin, Peggy Hsuanyu Kuo, Yasaman Jami-Alahmadi, Ajay A. Vashisht, James Wohlschlegel, Steven E. Jacobsen, Miguel A. Blázquez and Javier Gallego-Bartolomé. (2022) Comprehensive identification of SWI/SNF complex subunits underpins deep eukaryotic ancestry and reveals new plant components.
Communications Biology, (2022)5:549
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208. Qian Wang, Yan Xue, Laixing Zhang3, Zhenhui Zhong, Suhua Feng, Changshi Wang, Lifan Xiao, Zhenlin Yang, C. Jake Harris, Zhe Wu, Jixian Zhai, Maojun Yang, Sisi Li, Steven E. Jacobsen and Jiamu Du. (2022) A SYBR Gold-based Label-free in vitro Dicing Assay.
Bio-Protocol, 12(07):4382.
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207. Jason Gardiner, Basudev Ghoshal, Ming Wang and Steven E. Jacobsen. (2022) CRISPR–Cas-mediated transcriptional control and epi-mutagenesis.
Plant Physiology, 188:1811-1824.
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206. Magdalena E. Potok, Zhenhui Zhong, Colette L. Picard, Qikun Liu, Truman Do, Cassidy E. Jacobsen, Ocean Sakr, Bilguudei Naranbaatar, Ruwan Thilakaratne, Zhanna Khnkoyan, Megan Purl, Harrison Cheng, Helena Vervaet, Suhua Feng, Shima Rayatpisheh, James A. Wohlschlegel, Ronan C. O’Malley, Joseph R. Ecker, and Steven E. Jacobsen. (2022) The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis.
Proceedings of the National Academy of Sciences, e2115570119.
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205. Qian Wang, Yan Xue, Laixing Zhang, Zhenhui Zhong, Suhua Feng, Changshi Wang, Lifan Xiao, Zhenlin Yang, C Jake Harris, Zhe Wu, Jixian Zhai, Maojun Yang, Sisi Li, Steven E Jacobsen, Jiamu Du. (2021) Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation.
Science, 374:1152-1157.
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204. Kanako Kojima-Kita, Satomi Kuramochi-Miyagawa, Manabu Nakayama, Haruhiko Miyata, Steven E Jacobsen, Masahito Ikawa, Haruhiko Koseki, Toru Nakano. (2021) MORC3, a novel MIWI2 association partner, as an epigenetic regulator of piRNA dependent transposon silencing in male germ cells.
Scientific Reports, 11:20472.
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203. Varsha P Desai, Jihed Chouaref, Haoyu Wu, William A Pastor, Ryan L Kan, Harald M Oey, Zheng Li, Jamie Ho, Kelly K D Vonk, David San Leon Granado, Michael A Christopher, Amander T Clark, Steven E Jacobsen, Lucia Daxinger. (2021) The role of MORC3 in silencing transposable elements in mouse embryonic stem cells.
Epigenetics and Chromatin, 14:49.
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202. Jennifer Cable, Pamela C Ronald, Daniel Voytas, Feng Zhang, Avraham A Levy, Ayumu Takatsuka, Shin-Ichi Arimura, Steven E Jacobsen, Seiichi Toki, Erika Toda, Caixia Gao, Jian-Kang Zhu, Jens Boch, Joyce Van Eck, Magdy Mahfouz, Mariette Andersson, Eyal Fridman, Trevor Weiss, Kan Wang, Yiping Qi, Tobias Jores, Tom Adams, Rammyani Bagchi. (2021) Plant genome engineering from lab to field-a Keystone Symposia report.
Ann N Y Acad Sci., doi: 10.1111/nyas.14675.
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201. Yan Xue, Zhenhui Zhong, C. Jake Harris, Javier Gallego-Bartolomé, Ming Wang, Colette Picard, Xueshi Cao, Shan Hua, Ivy Kwok, Suhua Feng, Yasaman Jami-Alahmadi, Jihui Sha, Jason Gardiner, James Wohlschlegel & Steven E. Jacobsen. (2021) Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation.
Nature Communications, 12:4292.
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200. Lucia Ichino, Brandon A Boone, Luke Strauskulage, C Jake Harris, Gundeep Kaur, Matthew A Gladstone, Maverick Tan, Suhua Feng, Yasaman Jami Alahmadi, Sascha H Duttke, James A Wohlschlegel, Xiaodong Cheng, Sy Redding and Steven E Jacobsen. (2021) MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO.
Science, 372:1434-1439.
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199. Basudev Ghoshal, Colette L. Picard, Brandon Vong, Suhua Feng, and Steven E. Jacobsen. (2021) CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase.
Proceedings of the National Academy of Sciences, 118 (23): e2125016118.
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198.Wanlu Liu, Javier Gallego-Bartolomé, Yuxing Zhou, Zhenhui Zhong, Ming Wang, Somsakul Pop Wongpalee, Jason Gardiner, Suhua Feng, Peggy Hsuanyu Kuo and Steven E. Jacobsen. (2021) Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase.
Nature Communications, 12:3130.
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197.Pierre Bourguet, Colette L. Picard, Ramesh Yelagandula, Thierry Pélissier, Zdravko J. Lorković, Suhua Feng, Marie-Noëlle Pouch-Pélissier, Anna Schmücker, Steven E. Jacobsen, Frédéric Berger & Olivier Mathieu. (2021) The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation.
Nature Communications, 12:2683.
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196. Charlotte P Choi, Rebecca J Tay, Margaret R Starostik, Suhua Feng, James J Moresco, Brooke E Montgomery, Emily Xu, Maya A Hammonds, Michael C Schatz, Taiowa A Montgomery, John R Yates 3rd, Steven E Jacobsen, John K Kim. (2021) SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans.
Elife, 10:e60681.
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195. Zeyu Zhang, Huihui Wang, Yongsheng Wang, Feihu Xi, Huiyuan Wang, Markus V. Kohnen, Pengfei Gao, Wentao Wei, Kai Chen, Xuqing Liu, Yubang Gao, Ximei Han, Kaiqiang Hu, Hangxiao Zhang, Qiang Zhu , Yushan Zheng, Bo Liu, Ayaz Ahmad, Yau-Heiu Hsu, Steven E. Jacobsen, and Lianfeng Gu. (2021) Whole-genome characterization of chronological age associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth.
The Plant Journal, 106:435-453.
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194. Zhenhui Zhong, Suhua Feng,, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolome, Wanlu Liu, and Steven E. Jacobsen. (2021) DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis.
Proceedings of the National Academy of Sciences, 118 (5): e2023347118.
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193. Basudev Ghoshal, Brandon Vong, Colette L. Picard, Suhua Feng, Janet M. Tam, Steven E. Jacobsen. (2020) A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation in Arabidopsis thaliana.
PLOS Genetics, 16 (12): e1008983.
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192. Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E. Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I. White, Steven E. Jacobsen, Moussa Benhamed and Olivier Mathieu*. (2020) DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis.
Genome Biology, 21:283.
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191. Suhua Feng, Zhenhui Zhong, Ming Wang and Steven E. Jacobsen. (2020) Efficient and accurate determination of genome‑wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl Sequencing.
Epigenetics & Chromatin, Vol 13, Article number 42.
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190. Patrick Pausch*, Basem Al-Shayeb*, Ezra Bisom-Rapp, Connor A. Tsuchida, Zheng Li, Brady F. Cress, Gavin J. Knott, Steven E. Jacobsen, Jillian F. Banfield, Jennifer A. Doudna. (2020) CRISPR-CasΦ from huge phages is a hypercompact genome editor.
Science, 6501: 333-337.
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189. Jason Gardiner, Jenny M. Zhao, Kendall Chaffin and Steven E. Jacobsen. (2020) Promoter and Terminator Optimization for DNA Methylation Targeting in Arabidopsis.
Epigenomes, 4(2):9.
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188. Yafei Wang, Zhenhui Zhong, Yaxin Zhang, Linhao Xu, Suhua Feng, Shima Rayatpisheh, James A. Wohlschlegel, Zonghua Wang, Steven E. Jacobsen and Israel Ausin. (2020) NAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in Arabidopsis.
Nature Communications, 11:2887.
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187. Qikun Liu, Sylvain Bischof, C. Jake Harris, Zhenhui Zhong, Lingyu Zhan, Calvin Nguyen, Andrew Rashoff, William D. Barshop, Fei Sun, Suhua Feng, Magdalena Potok, Javier Gallego-Bartolome, Jixian Zhai, James A. Wohlschlegel, Michael F. Carey, Jeffrey A. Long and Steven E. Jacobsen. (2020) The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis.
Nature Communications, 11:2798.
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186. Melody Nicolau, Nathalie Picault, Julie Descombin, YasamanJami-Alahmadi, Suhua Feng, Etienne Bucher, Steven E. Jacobsen, Jean-Marc Deragon, James Wohlschlegel, Guillaume Moissiard. (2020) The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thaliana.
PLOS Genetics, 16(4):e1008324.
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185. Zsolt G.Venkei, Charlotte P. Choi, Suhua Feng, Cuie Chen, Steven E. Jacobsen, John K. Kim, Yukiko M.Yamashita. (2020) A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage.
PLOS Genetics, 16(3): e1008648.
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184. Somsakul Pop Wongpalee, Shiheng Liu, Javier Gallego-Bartolomé, Alexander Leitner, Ruedi Aebersold, Wanlu Liu, Linda Yen, Maria A. Nohales, Peggy Hsuanyu Kuo, Ajay A. Vashisht, James A. Wohlschlegel, Suhua Feng, Steve A. Kay, Z. Hong Zhou and Steven E. Jacobsen. (2019) CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation.
Nature Communications, 10: 3916.
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183. HyeongJun Kim, Linda Yen, Somsakul P. Wongpalee, Jessica A. Kirshner, Nicita Mehta, Yan Xue, Jonathan B. Johnston, Alma L. Burlingame, John K. Kim, Joseph J. Loparo and Steve E. Jacobsen. (2019) The Gene-Silencing Protein MORC-1 Topologically Entraps DNA and Forms Multimeric Assemblies to Cause DNA Compaction.
Molecular Cell, 75: 700-710.
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182. Magdalena E. Potok, Yafei Wang, Linhao Xu, Zhenhui Zhong, Wanlu Liu, Suhua Feng, Bilguudei Naranbaatar, Shima Rayatpisheh, Zonghua Wang, James A. Wohlschlegel, Israel Ausin and Steven E. Jacobsen. (2019) Arabidopsis SWR1-associated protein methyl-CpGbinding domain 9 is required for histone H2A.Z deposition.
Nature Communications, 10: 3352.
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181. Maria A. Nohales, Wanlu Liu, Tomas Duffy, Kazunari Nozue, Mariko Sawa, Jose L. Pruneda-Paz, Julin N. Maloof, Steven E. Jacobsen, and Steve A. Kay. (2019) Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock.
Developmental Cell, 49: 840-851.
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180. Mengbin Chen, Qikun Liu, Shu-Shan Gao, Abbegayle E. Young, Steven E. Jacobsen, and Yi Tang. (2019) Genome mining and biosynthesis of a polyketide from a biofertilizer fungus that can facilitate reductive iron assimilation in plant.
Proceedings of the National Academy of Sciences, 116: 5499-5504.
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179. Javier Gallego-Bartolomé, Wanlu Liu, Peggy Hsuanyu Kuo, Suhua Feng, Basudev Ghoshal, Jason Gardiner, Jenny Miao-Chi Zhao, Soo Young Park, Joanne Chory, Steven E. Jacobsen. (2019) Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis.
Cell, 176: 1068–1082.
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178. Ashot Papikian, Wanlu Liu, Javier Gallego-Bartolomé, and Steven E. Jacobsen. (2019) Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems.
Nature Communications, 10: 729.
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177. Caitlin I. Stoddard, Suhua Feng, Melody G. Campbell, Wanlu Liu, Haifeng Wang, Xuehua Zhong, Yana Bernatavichute, Yifan Cheng, Steven E. Jacobsen, and Geeta J. Narlikar. (2019) A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase.
Molecular Cell, 73: 73-83.
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176. Di Chen, Wanlu Liu, Jill Zimmerman, William A. Pastor, Rachel Kim, Linzi Hosohama, Jamie Ho, Marianna Aslanyan, Joanna J. Gell, Steven E. Jacobsen, Amander T. Clark. (2018) The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation.
Cell Reports, 25: 3591-3602.
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175. C. Jake Harris, Marion Scheibe, Somsakul Pop Wongpalee, Wanlu Liu, Evan M. Cornett, Robert M. Vaughan, Xueqin Li, Wei Chen, Yan Xue, Zhenhui Zhong, Linda Yen, William D. Barshop, Shima Rayatpisheh, Javier Gallego-Bartolome, Martin Groth, Zonghua Wang, James A. Wohlschlegel, Jiamu Du, Scott B. Rothbart, Falk Butter, and Steven E. Jacobsen. (2018) A DNA methylation reader complex that enhances gene transcription.
Science, 6419: 1182-1186.
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174. C. Jake Harris and Steven E. Jacobsen. (2018) ADCP1: a novel plant H3K9me2 reader.
Cell Research, 0:1-2.
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173. Yan Yan, Qikun Liu, Steven E Jacobsen, and Yi Tang. (2018) The impact and prospect of natural product discovery in agriculture: New technologies to explore the diversity of secondary metabolites in plants and microorganisms for applications in agriculture.
EMBO Reports, 19, e46824.
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172. Xueqin Li, C. Jake Harris, Zhenhui Zhong, Wei Chen, Rui Liu, Bei Jia, Zonghua Wang, Sisi Li, Steven E. Jacobsen, and Jiamu Du. (2018) Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation.
Proceedings of the National Academy of Sciences, (37), E8793-E8802.
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171. Luz D. Orozco, Colin Farrel, Christopher Hale, Liudmilla Rubbi, Arturo Rinaldi, Mete Civelek, Calvin Pan, Larry Lam, Dennis Montoya, Chantle Edillor, Marcus Seldin, Michael Boehnke, Karen L. Mohlke, Steven E. Jacobsen, Johanna Kuusisto, Markku Laakso, Aldons J. Lusis, and Matteo Pellegrini. (2018) Epigenome-wide association in adipose tissue from the METSIM cohort.
Human Molecular Genetics, 27:10, 1830–1846.
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170. Yan Yan, Qikun Liu, Xin Zang, Shuguang Yuan, Undramaa Bat-Erdene, Calvin Nguyen, Jianhua Gan, Jiahai Zhou, Steven E. Jacobsen, and Yi Tang. (2018) Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action.
Nature, 559, 415–418.
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168. Javier Gallego-Bartolomé, Jason Gardiner, Wanlu Liu, Ashot Papikian, Basudev Ghoshal, Hsuan Yu Kuo, Jenny Miao-Chi Zhao, David J. Segal, and Steven E. Jacobsen. (2018) Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain.
Proceedings of the National Academy of Sciences, 115(9): E2125-E2134.
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167. Wanlu Liu, Sascha H. Duttke, Jonathan Hetzel, Martin Groth, Suhua Feng, Javier Gallego-Bartolome, Zhenhui Zhong, Hsuan Yu Kuo, Zonghua Wang, Jixian Zhai, Joanne Chory, and Steven E. Jacobsen. (2018) RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis.
Nature Plants, 4, 181-188.
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166. Yu Zhang, C. Jake Harris, Qikun Liu, Wanlu Liu, Israel Ausin, Yanping Long, Lidan Xiao, Li Feng, Xu Chen, Yubin Xie, Xinyuan Chen, Lingyu Zhan, Suhua Feng, Jingyi Jessica Li, Haifeng Wang, Jixian Zhai, and Steven E. Jacobsen. (2018) Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis.
Proc. Nat. Acad. Sci. U. S. A., 115:E1069-E1074.
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165. Di Chen, Wanlu Liu, Anastasia Lukianchikov, Grace V. Hancock, Jill Zimmerman, Matthew G. Lowe, Rachel Kim, Zoran Galic, Naoko Irie, M. Azim Surani, Steven E. Jacobsen, and Amander T. Clark. (2017) Germline competency of human embryonic stem cells depends on eomesodermin.
Biology of Reproduction, 97(6), 850–861.
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164. Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen, and Frederic Berger. (2017) The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana.
Genome Biology, 18(1):94.
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163. Natasha E. Weiser, Danny X. Yang, Suhua Feng, Natallia Kalinava, Kristen C. Brown, Jayshree Khanikar, Mallory A. Freeberg, Martha J. Snyder, Gyorgyi Csankovszki, Raymond C. Chan, Sam G. Gu, Taiowa A. Montgomery, Steven E. Jacobsen, and John K. Kim. (2017) MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality.
Developmental Cell, 41(4):408-423.e7.
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162. Wei Feng, Christopher J. Hale, Ryan S. Over, Shawn J. Cokus, Steven E. Jacobsen, and Scott D. Michaels. (2017) Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage.
Proc. Nat. Acad. Sci. U. S. A., 114(2): 406-411.
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161. Sylvie Lahmy, Dominique Pontier, Natacha Bies-Etheve, Michele Laudie, Suhua Feng, Edouard Jobet, Christopher J. Hale, Richard Cooke, Mohamed-Ali Hakimi, Dimitar Angelov, Steven E. Jacobsen, and Thierry Lagrange. (2016) Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants.
Genes & Development, 30(23):2565-2570.
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160. Israel Ausin, Suhua Feng, Chaowei Yu, Wanlu Liu, Hsuan Yu Kuo, Elise L. Jacobsen, Jixian Zhai, Javier Gallego-Bartolome, Lin Wang, Ulrika Egertsdotter, Nathaniel R. Street, Steven E. Jacobsen, and Haifeng Wang. (2016) DNA methylome of the 20-gigabase Norway spruce genome.
Proc. Nat. Acad. Sci. U. S. A., doi/10.1073/pnas.1618019113.
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159. Sisi Li, Linda Yen, William A. Pastor, Jonathan B. Johnston, Jiamu Du, Colin Shew, Wanlu Liu, Jamie Ho, Bryan Stender, Amander T. Clark, Alma L. Burlingame, Lucia Daxinger, Dinshaw J. Patel, and Steven E. Jacobsen. (2016) Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin.
Proc. Nat. Acad. Sci. U. S. A., 113:E5108-E5116.
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158. Adam J. Bewick, Lexiang Ji, Chad E. Niederhuth, Eva-Maria Willing, Brigitte T. Hofmeister, Xiuling Shi, Li Wang, Zefu Lu, Nicholas A. Rohr, Benjamin Hartwig, Christiane Kiefer, Roger B. Deal, Jeremy Schmutz, Jane Grimwood, Hume Stroud, Steven E. Jacobsen, Korbinian Schneeberger, Xiaoyu Zhang, and Robert J. Schmitz. (2016) On the origin and evolutionary consequences of gene body DNA methylation.
Proc. Nat. Acad. Sci. U. S. A.,113:9111-9116.
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157. Martin Groth, Guillaume Moissiard, Markus Wirtz, Haifeng Wang, Carolina Garcia-Salinas, Perla A. Ramos-Parra, Sylvain Bischof, Suhua Feng, Shawn J. Cokus, Amala John, Danielle C. Smith, Jixian Zhai, Christopher J. Hale, Jeff A. Long, Ruediger Hell, Rocio I. Diaz de la Garza & Steven E. Jacobsen. (2016) MTHFD1 controls DNA methylation in Arabidopsis.
Nature Communications, 7:11640.
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156. Christopher J. Hale, Magdalena E. Potok, Jennifer Lopez, Truman Do, Ao Liu, Javier Gallego-Bartolome, Scott D. Michaels, Steven E. Jacobsen. (2016) Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana.
PLOS Genetics, DOI:10.1371/journal.pgen.1006092.
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155. C. Jake Harris, Dylan Husmann, Wanlu Liu, Farid El Kasmi, Haifeng Wang, Ashot Papikian, William A. Pastor, Guillaume Moissiard, Ajay A. Vashisht, Jeffery L. Dang, James A. Wohlschlegel, Steven E. Jacobsen. (2016) Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes.
PLOS Genetics,12(5):e1005998 DOI:10.1371/journal.pgen.1005998.
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154. William A. Pastor, Di Chen, Wanlu Liu, Rachel Kim, Anna Sahakyan, Anastasia Lukianchikov, Kathrin Plath, Steven E. Jacobsen, and Amander T. Clark. (2016) Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory.
Cell Stem Cell 18:323-329.
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153. Sisi Li, Zhenlin Yang, Xuan Du, Rui Liu, Alex W. Wilkinson, Or Gozani, Steven E. Jacobsen, Dinshaw J. Patel, and Jiamu Du. (2016) Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette.
Structure 24:486-494.
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152. Mala Samaranayake, Pierre-Olivier Esteve, Hang Gyeong Chin, George R. Feehery, Mihika Pradhan, Steven E. Jacobsen, Michael F. Carey, and Sriharsa Pradhan. (2015) Transcription coupled DNA methylation mediated by RNA Pol II and DNMT1.
Epigenetic Diagnosis & Therapy, 1:000-000.
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151. Haifeng Wang, Getu Beyene, Jixian Zhai, Suhua Feng, Noah Fahlgren, Nigel J. Taylor, Rebecca Bart, James C. Carrington, Steven E. Jacobsen, and Israel Ausin. (2015) CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proc. Nat. Acad. Sci. U. S. A.,
112:13729-13734
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150. Jixian Zhai, Sylvain Bischof, Haifeng Wang, Suhua Feng, Tzuu-fen Lee, Chong Teng, Xinyuan Chen, Soo Young Park, Linshan Liu, Javier Gallego-Bartolome, Wanlu Liu, Ian R. Henderson, Blake C. Meyers, Israel Ausin, and Steven E. Jacobsen. (2015) A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis.
Cell, 163:445-455.
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149. Puya G. Yazdi, Brian A. Pedersen, Jared F. Taylor, Omar S. Khattab, Yu-Han Chen, Yumay Chen, Steven E. Jacobsen, Ping H. Wang. (2015) Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact.
PLOS ONE, DOI:10.1371/journal.pone.0136574.
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148. Puya G. Yazdi, Brian A. Pedersen, Jared F. Taylor, Omar S. Khattab, Yu-Han Chen, Yumay Chen, Steven E. Jacobsen, Ping H. Wang. (2015) Nucleosome Organization in Human Embryonic Stem Cells.
PLOS ONE, DOI:10.1371/journal.pone.0136314.
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147. Jiamu Du, Lianna M. Johnson, Steven E. Jacobsen and Dinshaw J. Patel. (2015) DNA methylation pathways and their crosstalk with histone methylation.
Nature Reviews Molecular Cell Biology, 16:519-532.
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145. Shuaibin Zhang, Bing Zhou, Yanyuan Kang, Xia Cui, Ao Liu, Angelique Deleris, Maxim VC Greenberg, Xiekui Cui, Qi Qiu, Falong Lu, James A Wohlschlegel, Steven E Jacobsen and Xiaofeng Cao. (2015) C-terminal domains of histone demethylase JMJ14 interact with a pair of NAC transcription factors to mediate specific chromatin association. Cell Discovery, 1:15003. PDFSupplementaryFiguresTables
144. Xuehua Zhong, Christopher J. Hale, Minh Nguyen, Israel Ausin, Martin Groth, Jonathan Hetzel, Ajay A. Vashisht, Ian R. Henderson, James A. Wohlschlegel, and Steven E. Jacobsen. (2015) DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA
polymerase V transcript abundance in Arabidopsis.
Proc. Nat. Acad. Sci. U. S. A., 112:911-916.
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143. Xian Jun Song, Takeshi Kuroha, Madoka Ayano, Tomoyuki Furuta, Keisuke Nagai, Norio Komeda, Shuhei Segami, Kotaro Miura, Daisuke Ogawa, Takumi Kamura, Takamasa Suzuki, Tetsuya Higashiyama, Masanori Yamasaki, Hitoshi Mori, Yoshiaki Inukai, Jianzhong Wu, Hidemi Kitano, Hitoshi Sakakibara, Steven E. Jacobsen, and Motoyuki Ashikari. (2015) Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. Proc. Nat. Acad. Sci. U. S. A.,
112:76-81.
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141. Martin Groth, Hume Stroud, Suhua Feng, Maxim V. C. Greenberg, Ajay A. Vashisht, James A. Wohlschlegel, Steven E. Jacobsen, and Israel Ausin. (2014) SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation.
Proc. Nat. Acad. Sci. U. S. A., 111:17666-17671.
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140. Suhua Feng, Shawn J. Cokus, Veit Schubert, Jixian Zhai, Matteo Pellegrini, and Steven E. Jacobsen. (2014) Genome-wide Hi-C Analyses in Wild-Type and Mutants Reveal High-Resolution Chromatin Interactions in Arabidopsis.
Molecular Cell, 55: 694-707.
PDFLink to full resolution images Files S1-S6
139. Jiamu Du, Lianna M. Johnson, Martin Groth, Suhua Feng, Christopher J. Hale, Sisi Li, Ajay A. Vashisht, Javier Gallego-Bartolome, James A. Wohlschlegel, Dinshaw J. Patel, and Steven E. Jacobsen. (2014) Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE.
Molecular Cell, 55:495-504.
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138. Ageliki Tsagaratou, Tarmo Aijo, Chan-Wang J. Lio, Xiaojing Yue, Yun Huang, Steven E. Jacobsen, Harri Lahdesmaki, and Anjana Rao. (2014) Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation.
Proc. Nat. Acad. Sci. U. S. A., 111:E3306-3315.
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137. Joana Sequeira-Mendes, Irene Araguez, Ramon Peiro, Raul Mendez-Giraldez, Xiaoyu Zhang, Steven E. Jacobsen, Ugo Bastolla, Crisanto Gutierrez. (2014) The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States.
The Plant Cell, 26:2351-2366.
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136. Ramesh Yelagandula, Hume Stroud, Sarah Holec, Keda Zhou, Suhua Feng, Xuehua Zhong, Uma M. Muthurajan, Xin Nie, Tomokazu Kawashima, Martin Groth, Karolin Luger, Steven E. Jacobsen, and Frederic Berger. (2014) The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis.
Cell, 158:98-109.
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135. Xuehua Zhong, Jiamu Du, Christopher J. Hale, Javier Gallego-Bartolome, Suhua Feng, Ajay A. Vashisht, Joanne Chory, James A. Wohlschlegel, Dinshaw J. Patel and Steven E. Jacobsen. (2014) Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
Cell, 157:1050-1060.
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134. Guillaume Moissiard, Sylvain Bischof, Dylan Husmann, William A. Pastor, Christopher J. Hale, Linda Yen, Hume Stroud, Ashot Papikian, Ajay A. Vashisht, James A. Wohlschlegel, and Steven E. Jacobsen. (2014) Transcriptional gene silencing by Arabidopsis microrchidia homologues involves the formation of heteromers.
Proc. Nat. Acad. Sci. U. S. A., 111:7474-7479.
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133. Yun Huang, Lukas Chavez, Xing Chang, Xue Wang, William A. Pastor, Jinsuk Kang, Jorge A. Zepeda-Martinez, Utz J. Pape, Steven E. Jacobsen, Bjoern Peters, and Anjana Rao. (2014) Distinct roles of the methycytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells.
Proc. Nat. Acad. Sci. U. S. A., 111: 1361-1366.
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132. Lianna M. Johnson, Jiamu Du, Christopher J. Hale, Sylvain Bischof, Suhua Feng, Ramakrishna K. Chodavarapu, Xuehua Zhong, Giuseppe Marson, Matteo Pellegrini, David J. Segal, Dinshaw J. Patel and Steven E. Jacobsen. (2014) SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation.
Nature, 507:124-128 .
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131. Hume Stroud, Truman Do, Jiamu Du, Xuehua Zhong, Suhua Feng, Lianna Johnson, Dinshaw J. Patel, Steven E. Jacobsen. (2014) Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis.
Nat Struct Mol Biol., 21:64-72.
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130. Nicolas Widman, Suhua Feng, Steven E. Jacobsen, Matteo Pellegrini. (2014) Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation.
Epigenetics, 9:236-242.
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129. Maxim V. C. Greenberg, Angelique Deleris, Christopher J. Hale, Ao Liu, Suhua Feng, Steven E. Jacobsen. (2013) Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thaliana.
PLoS Genetics: DOI: 10.1371.
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128. Hongmei Li-Byarlay, Yang Li, Hume Stroud, Suhua Feng, Thomas C. Newman, Megan Kaneda, Kirk K. Hou, Kim C. Worley, Christine G. Elsik, Samuel A. Wickline, Steven E. Jacobsen, Jian Ma, and, Gene E. Robinson. (2013) RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee.
Proc Natl Acad Sci U S A., 110:12750-12755.
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127. Pao-Yang Chen, Amit Ganguly, Liudmilla Rubbi, Luz Orozco, Marco Morselli, Davin Ashraf, Artur Jaroszewicz, Suhua Feng, Steven E. Jacobsen, Atsushi Nakano, Sherin Devaskar, and Matteo Pellegrini. (2013) Intrauterine calorie restriction affects placental DNA Methylation and gene expression.
Physiol Genomics, 45:565-576.
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126. Julie A. Law, Jiamu Du, Christopher J. Hale, Suhua Feng, Krzysztof Krajewski, Ana Marie S. Palanca, Brian D. Strahl, Dinshaw J. Patel & Steven E. Jacobsen. (2013) Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
Nature, 498, 385-389.
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125. John J. Vincent, Yun Huang, Pao-Yang Chen, Suhua Feng, Joseph H. Calvopina, Kevin Nee, Serena A. Lee, Thuc Le, Alexander J. Yoon, Kym Faull, Guoping Fan, Anjana Rao, Steven E. Jacobsen, Matteo Pellegrini and Amander T. Clark. (2013) Stage-specific roles for Tet1 and Tet2 in DNA demethylation in primordial germ cells.
Cell Stem Cell, 12:470-478.
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124. Hume Stroud, Bo Ding, Stacey A Simon, Suhua Feng, Maria Bellizzi, Matteo Pellegrini, Guo-Liang Wang, Blake C Meyers, Steven E Jacobsen. (2013) Plants regenerated from tissue culture contain stable epigenome changes in rice.
eLife, 2:e00354. DOI: 10.7554/eLife.00354. 14 pages.
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123. Yifeng Xu, Yizhong Wang, Hume Stroud, Xiaofeng Gu, Bo Sun, Eng-Seng Gan, Kian-Hong Ng, Steven E. Jacobsen, Yuehui He, and Toshiro Ito. (2013) A Matrix Protein Silences Transposons and Repeats through Interaction with Retinoblastoma-Associated Proteins.
Current Biology, 23, 345-350.
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122. Hume Stroud, Maxim V.C. Greenberg, Suhua Feng, Yana V. Bernatavichute, Steven E. Jacobsen. (2013) Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome.
Cell, 152: 352-364.
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121. Angelique Deleris, Hume Stroud, Yana Bernatavichute, Elizabeth Johnson, Gregor Klein, Daniel Schubert, Steven E. Jacobsen. (2012) Loss of the DNA Methyltransferase MET1 Induces H3K9 Hypermethylation at PcG Target Genes and Redistribution of H3K27 Trimethylation to Transposons in Arabidopsis thaliana.
PLoS Genetics, 8:e1003062, 1-13.
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120. Elena Caro, Hume Stroud, Maxim V. C. Greenberg, Yana V. Bernatavichute, Suhua Feng, Martin Groth, Ajay A. Vashisht, James Wohlschlegel, Steve E. Jacobsen. (2012) The SET-Domain Protein SUVR5 Mediates H3K9me2 Deposition and Silencing at Stimulus Response Genes in a DNA Methylation Independent Manner.
PLoS Genetics, 8:e1002995, 1-12.
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119. Maria Colomé-Tatché, Sandra Cortijo, René Wardenaar, Lionel Morgado, Benoit Lahouze, Alexis Sarazin, Mathilde Etcheverry, Antoine Martin, Suhua Feng, Evelyne Duvernois-Berthet, Karine Labadie, Patrick Wincker, Steven E. Jacobsen, Ritsert C. Jansen, Vincent Colot, and Frank Johannes. (2012) Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation.
Proc. Nat. Acad. Sci. U. S. A., 109: 16240-16245.
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118. Jiamu Du, Xuehua Zhong, Yana V. Bernatavichute, Hume Stroud, Suhua Feng, Elena Caro, Ajay A. Vashisht, Jolyon Terragni, Hang Gyeong Chin, Andy Tu, Jonathan Hetzel, James A. Wohlschlegel, Sriharsa Pradhan, Dinshaw J. Patel, and Steven E. Jacobsen. (2012) Dual Binding of Chromomethylase Domains to H3K9me2-containing Nucleosomes Directs DNA Methylation in Plants.
Cell, 151, 167-180.
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117. Xuehua Zhong, Christopher J. Hale, Julie A. Law, Lianna M. Johnson, Suhua Feng, Andy Tu, and Steven E. Jacobsen. (2012) DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons.
Nature Structural and Molecular Biology, 19: 870-875.
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116. The EPIC Planning Committee: Fred Berger, XiaoFeng Cao, Vicki Chandler, Liz Dennis, Rob Martienssen, Blake Meyers, Craig Pikaard, Jim Peacock, Eric Richards, Doris Wagner, Detlef Weigel, Vincent Colot, Roger Deal, Caroline Dean, Joe Ecker, Mary Gehring, Zhizhong Gong, Brian Gregory, Gutierrez Rodrigo, Jose Gutierrez-Marcos, Mitsuyasu Hasebe, Il-Doo Hwang, Steven E. Jacobsen, Tetsuji Kakutani, Jiayang Li, Scott Michaels, Yoo-Sun Noh, Nick Provart, Matt Vaughn. (2012) Reading the Second Code:Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment.
The Plant Cell, 24: 2257-2261.
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115. Paul B. Talbert, Kami Ahmad, Genevieve Almouzni, Juan Ausio, Frederic Berger, Prem L. Bhalla, William M. Bonner, W. Zacheus Cande, Brian P. Chadwick, Simon W L Chan, George A M Cross, Liwang Cui, Stefan I. Dimitrov, Detlef Doenecke, Jose M. Eirin-Lopez, Martin A. Gorovsky, Sandra B. Hake, Barbara A. Hamkalo, Sarah Holec, Steven E. Jacobsen, Kinga Kamieniarz, Saadi Khochbin, Andreas G. Ladurner, David Landsman, John A. Latham, Benjamin Loppin, Harmit S. Malik, William F. Marzluff, John R. Pehrson, Jan Postberg, Robert Schneider, Mohan B. Singh, M. Mitchell Smith, Eric Thompson, Maria-Elena Torres Padilla, David John Tremethick, Bryan M. Turner, Jakob Harm Waterborg, Heike Wollmann, Ramesh Yelagandula, Bing Zhu and Steven Henikoff. (2012) A unified phylogeny-based nomenclature for histone variants.
Epigenetics & Chromatin, 5:7 (19 pages).
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114. Hume Stroud, Christopher J. Hale, Suhua Feng, Elena Caro, Yannick Jacob, Scott D. Michaels, and Steven E. Jacobsen. (2012) DNA Methyltransferases Are Required to Induce Heterochromatic Re-Replication in Arabidopsis.
PLoS Genetics, 8: e1002808, 1-7.
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113. Ramakrishna K. Chodavarapu, Suhua Feng, Bo Ding, Stacey A. Simon, David Lopez, Yulin Jia, Guo-Liang Wang, Blake C. Meyers, Steven E. Jacobsen, and Matteo Pellegrini. (2012) Transcriptome and methylome interactions in rice hybrids.
Proc. Nat. Acad. Sci. U. S. A., 109: 12040-12045.
PDFTableS1TableS2TableS3TableS4TableS5TableS6TableS7TableS8
112. Guillaume Moissiard, Shawn J. Cokus, Joshua Cary, Suhua Feng, Allison C. Billi, Hume Stroud, Dylan Husmann, Ye Zhan, Bryan R. Lajoie, Rachel Patton McCord, Christopher J. Hale, Wei Feng, Scott D. Michaels, Alison R. Frand, Matteo Pellegrini, Job Dekker, John K. Kim, and Steven E. Jacobsen. (2012) MORC Family ATPases Required for Heterochromatin Condensation and Gene Silencing.
Science, 336:1448-1451.
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111. Israel Ausin, Maxim V. C. Greenberg, Dhirendra K. Simanshu, Christopher J. Hale, Ajay A. Vashisht, Stacey A. Simon, Tzuu-fen Lee, Suhua Feng, Sophia D. Espanola, Blake C. Meyers, James A. Wohlschlegel, Dinshaw J. Patel, and Steven E. Jacobsen. (2012) INVOLVED IN DE NOVO 2 containing complex involved in RNA-directed DNA methylation in Arabidopsis.
Proc. Nat. Acad. Sci. U. S. A., 109: 8374-8381.
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110. Tetsu Kinoshita and Steven E. Jacobsen. (2012) Opening the Door to Epigenetics in PCP.
Plant Cell Physiology, 53:763-765.
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109. Frederic Pontvianne, Todd Blevins, Chinmayi Chandrasekhara, Wei Feng, Hume Stroud, Steven E. Jacobsen, Scott D. Michaels, and Craig S. Pikaard. (2012) Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis.
Genes and Development, 26:945-957.
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108. Hume Stroud, Sofía Otero, Bénédicte Desvoyes, Elena Ramírez-Parra, Steven E. Jacobsen, and Crisanto Gutierrez. (2012) Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana.
Proc. Nat. Acad. Sci. U. S. A., 109:5370-5375.
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107. Sylvain Foret, Robert Kucharski, Matteo Pellegrini, Suhua Feng, Steven E. Jacobsen, Gene E. Robinson, and Ryszard Maleszka. (2012) DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.
Proc. Nat. Acad. Sci. U. S. A., 109: 4968-4973
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106. Christopher J. Hale and Steven E. Jacobsen (2012). Plant biology: Equal-parenting policy.
Nature, 482:42-44.
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105. Israel Ausin, Maxim V.C. Greenberg, Carey Fei Li, and Steven E. Jacobsen. (2012) The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis.
Epigenetics, 7:29-33.
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104. Julie A. Law, Ajay A. Vashisht, James A. Wohlschlegel, Steven E. Jacobsen. (2011) SHH1, a Homeodomain Protein Required for DNA Methylation, As Well As RDR2, RDM4, and Chromatin Remodeling Factors, Associate with RNA Polymerase IV.
PLoS Genetics, 7, e1002195.
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103. Hume Stroud, Suhua Feng, Shannon Morey Kinney, Sriharsa Pradhan and Steven E. Jacobsen. (2011) 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells.
Genome Biology, 12:R54.
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102. Pao-Yang Chen, Suhua Feng, Jong Wha J. Joo, Steven E. Jacobsen and Matteo Pellegrini. (2011) A comparative analysis of DNA methylation across human embryonic stem cell lines.
Genome Biology, 12, R62. PDFSupplementalInfo TableS2 TableS3 TableS4 TableS5 TableS6 TableS7
101. Bifeng Yuan, Jing Zhang, Hongxia Wang, Lei Xiong, Qian Cai, Tina Wang, Steven Jacobsen, Sriharsa Pradhan, and Yinsheng Wang. (2011) 6-Thioguanine reactivates epigenetically silenced genes in acute lymphoblastic leukemia cells by facilitating proteasome-mediated degradation of DNMT1.
Cancer Research, 71, 1904-1911.
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100. Shannon Morey Kinney, Hang Gyeong Chin, Jurate Bitinaite, Yu Zheng, Pierre Olivier Esteve, Romualdas Vaisvila, Suhua Feng, Hume Stroud, Steven E. Jacobsen and Sriharsa Pradhan. (2011) Tissue Specific Distribution and Dynamic Changes of 5 hydroxymethylcytosine in Mammalian Genome.
Journal of Biological Chemistry, 286, 24685-24693.
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99. Suhua Feng and Steven E. Jacobsen. (2011) Epigenetic modifications in plants: an evolutionary perspective.
Current Opinion in Plant Biology, 14, 179-186.
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98. Suhua Feng, Liudmilla Rubbi, Steven E. Jacobsen, and Matteo Pellegrini. (2011) Determining DNA Methylation Profiles Using Sequencing.
In, "High-Throughput Next Generation Sequencing: Methods and Applications". Young Min Kwon and Steven C. Ricke (eds.) Methods in Molecular Biology, 733, 223-238.
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97. Maxim V.C. Greenberg, Israel Ausin, Simon W.L. Chan, Shawn J. Cokus, Josh T. Cuperus, Suhua Feng, Julie A. Law, Carolyn Chu, Matteo Pellegrini, James C. Carrington and Steven E. Jacobsen. (2011) Identification of genes required for
de novo DNA methylation in Arabidopsis. Epigenetics, 6, 344-354.
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96. Eerappa Rajakumara, Julie A. Law, Dhirendra K. Simanshu, Philipp Voigt, Lianna M. Johnson, Danny Reinberg, Dinshaw J. Patel, and Steven E. Jacobsen. (2011) A dual flip out mechanism for 5mC recognition by the
Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes and Development, 25:137-152.
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95. Celina Costas, Maria de la Paz Sanchez, Hume Stroud, Yanchun Yu, Juan Carlos Oliveros, Suhua Feng, Alberto Benguria, Irene López-Vidriero, Xiaoyu Zhang, Roberto Solano, Steven E. Jacobsen and Crisanto Gutierrez. (2011) Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks.
Nature Structural and Molecular Biology, 18(3):395-400.
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94. Angelique Deleris, Maxim V.C. Greenberg, Israel Ausin, Rona W.Y. Law, Guillaume Moissiard, Daniel Schubert and Steven E. Jacobsen. (2010) Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA Methylation.
EMBO Reports, 11, 950-955.
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93. Suhua Feng, Steven E. Jacobsen, Wolf Reik. (2010) Epigenetic Reprogramming in Plant and Animal Development.
Science, 330:622-627.
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92. Ian R. Henderson, Angelique Deleris, William Wong, Xuehua Zhong, Hang Gyeong Chin, Gregory A. Horwitz, Krystyna A. Kelly, Sriharsa Pradhan, Steven E. Jacobsen. (2010) The De Novo Cytosine Methyltransferase DRM2 Requires Intact UBA Domains and a Catalytically Mutated Paralog DRM3 during RNA–Directed DNA Methylation in Arabidopsis thaliana.
PLoS Genetics, (6) 10: e1001182.
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91. Yannick Jacob, Hume Stroud, Chantal LeBlanc, Suhua Feng, Luting Zhuo, Elena Caro, Christiane Hassel, Crisanto Gutierrez, Scott D. Michaels and Steven E. Jacobsen. (2010) Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases.
Nature, 466:987-993.
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90. Ramakrishna K. Chodavarapu, Suhua Feng, Yana V. Bernatavichute, Pao-Yang Chen, Hume Stroud, Yanchun Yu, Jonathan Hetzel, Frank Kuo, Jin Kim, Shawn J. Cokus, David Casero, Maria Bernal, Peter Huijser, Amander T. Clark, Ute Krämer, Sabeeha S. Merchant, Xiaoyu Zhang, Steven E. Jacobsen, and Matteo Pellegrini. (2010) Relationship between nucleosome positioning and DNA methylation.
Nature, 466:388-392.
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89. Julie A. Law, Israel Ausin, Lianna M. Johnson, Ajay A. Vashisht, Jian-Kang Zhu, James A. Wohlschlegel, and Steven E. Jacobsen. (2010) A Protein Complex Required for Polymerase V Transcripts and RNA Directed DNA Methylation in Arabidopsis.
Current Biology, 20:951–956.
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88. Suhua Feng, Shawn J. Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G. Goll, Jonathan Hetzel, Jayati Jain, Steven H. Strauss, Marnie E. Halpern, Chinweike Ukomadu, Kirsten C. Sadler, Sriharsa Pradhan, Matteo Pellegrini, and Steven E. Jacobsen. (2010) Conservation and divergence of methylation patterning in plants and animals.
Proc. Nat. Acad. Sci. U. S. A., 107:8689–8694.
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87. Julie A. Law and Steven E. Jacobsen. (2010) Establishing, maintaining, and modifying DNA methylation patterns in plants and animals.
Nature Reviews Genetics, 11: 204-220.
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86. Christian Popp, Wendy Dean, Suhua Feng, Shawn J. Cokus, Simon Andrews, Matteo Pellegrini, Steven E. Jacobsen and Wolf Reik. (2010) Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency.
Nature, 463: 1101-1105.
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85. Ian R. Henderson, Simon R. Chan, Xiaofeng Cao, Lianna Johnson and Steven E. Jacobsen. (2010) Accurate sodium bisulfite sequencing in plants.
Epigenetics, 5:1, 47-49.
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84. Israel Ausin, Todd C. Mockler, Joanne Chory and Steven E. Jacobsen. (2009) IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana.
Nature Structural and Molecular Biology, 16: 1325-1327.
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83. Sriharsa Pradhan, Hang Gyeong Chin, Pierre-Olivier Estève and Steven E. Jacobsen. (2009) SET7/9 mediated methylation of non-histone proteins in mammalian cells.
Epigenetics, 4: 383-387.
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82. Kotaro Miura, Masakazu Agetsuma, Hidemi Kitano, Atsushi Yoshimura, Makoto Matsuoka, Steven E. Jacobsen and Motoyuki Ashikari. (2009) A metastable DWARF1 epigenetic mutant affecting plant stature in rice.
Proc. Nat. Acad. Sci. U. S. A., 106: 11218-11223.
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81. Yannick Jacob, Suhua Feng, Chantal A. LeBlanc, Yana V. Bernatavichute, Hume Stroud, Shawn Cokus, Lianna M. Johnson, Matteo Pellegrini, Steven E. Jacobsen and Scott D. Michaels. (2009) ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing.
Nature Structural and Molecular Biology, 16: 763-769.
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80. Xiaoyu Zhang, Yana V Bernatavichute, Shawn Cokus, Matteo Pellegrini and Steven E Jacobsen. (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana.
Genome Biology, 10: R62, R62.1-R62.14
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79. Pierre-Olivier Estève, Hang Gyeong Chin, Jack Benner, George R. Feehery, Mala Samaranayake, Gregory A. Horwitz, Steven E. Jacobsen and Sriharsa Pradhan. (2009) Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells.
Proc. Nat. Acad. Sci. U. S. A., 106: 5076-5081.
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78. Nicolas Widman, Steven E. Jacobsen and Matteo Pellegrini. (2009) Determining the conservation of DNA methylation in Arabidopsis.
Epigenetics, 4: 119-124.
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77. Julie A. Law and Steven E. Jacobsen. (2009) Molecular Biology: Dynamic DNA methylation.
Science, 323: 1568-1569.
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76. Jong Kyong Kim, Pierre Esteve, Steven E. Jacobsen and Sriharsa Pradhan (2009) UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells.
Nucleic Acids Research, 37: 493-505.
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75. Blake C. Meyers, Michael J. Axtell, Bonnie Bartel, David P. Bartel, David Baulcombe, John L. Bowman, Xiaofeng Cao, James C. Carrington, Xuemei Chen, Pamela J. Green, Sam Griffiths-Jones, Steven E. Jacobsen, Allison C. Mallory, Robert A. Martienssen, R. Scott Poethig, Yijun Qi, Herve Vaucheret, Olivier Voinnet,Yuichiro Watanabe, Detlef Weigel, and Jian-Kang Zhu (2008). Criteria for Annotation of Plant MicroRNAs.
The Plant Cell, 20: 3186-3190.
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74. Lianna M. Johnson, Julie A. Law, Anuj Khattar, Ian R. Henderson, Steven E. Jacobsen. (2008) SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation.
PLoS Genetics, 4(11), e1000280.
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73. Hideharu Hashimoto, John R. Horton, Xing Zhang, Magnolia Bostick, Steven E. Jacobsen & Xiaodong Cheng. (2008) The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
Nature, 455: 826-829.
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72. Yana V. Bernatavichute, Xiaoyu Zhang, Shawn Cokus, Matteo Pellegrini & Steven E. Jacobsen. (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in
Arabidopsis thaliana. PLoS ONE, 3, e3156.
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71. Edward Kraft, Magnolia Bostick, Steven E. Jacobsen & Judy Callis. (2008) ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases.
Plant Journal, 56:704-715.
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70. Ian R. Henderson & Steven E. Jacobsen (2008) Sequencing sliced ends reveals microRNA targets.
Nature Biotechnology, 26: 881-882.
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69. Ian R. Henderson & Steven E. Jacobsen. (2008) Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading.
Genes and Development, 22: 1597–1606.
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68. Alan M. Jones, Joanne Chory, Jeffery L. Dangl, Mark Estelle, Steven E. Jacobsen, Elliot M. Meyerowitz, Magnus Nordborg & Detlef Weigel. (2008) The Impact of Arabidopsis on Human Health: Diversifying Our Portfolio.
Cell, 133: 939-943.
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67. Shawn J. Cokus, Suhua Feng, Xiaoyu Zhang, Zugen Chen, Barry Merriman, Christian D. Haudenschild, Sriharsa Pradhan, Stanley F. Nelson, Matteo Pellegrini & Steven E. Jacobsen. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
Nature, 452: 215-219.
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66. Carey F. Li, Ian R. Henderson, Liang Song, Nina Federoff, Thierry Lagrange, and Steven E. Jacobsen. (2008) Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana.
PLoS Genetics 4(2) article e27.
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65. Juliana J. Oh, Baher N. Boctor, Cynthia A. Jimenez, Roberto Lopez, Ashley K. Koegel, Eileen O. Taschereau, Diana T. Phan, Steven E. Jacobsen, Dennis J. Slamon. (2008) Promoter methylation study of the H37/RBM5 tumor suppressor gene from the 3p21.3 human lung cancer tumor suppressor locus.
Human Genetics 123: 55-64.
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64. Mahmoud El-Shami, Dominique Pontier, Sylvie Lahmy, Laurence Braun, Claire Picart, Danielle Vega, Mohamed-Ali Hakimi, Steven E. Jacobsen, Richard Cooke, Thierry Lagrange. (2007) Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components.
Genes and Development 21: 2539-2544.
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63. Magnolia Bostick, Jong Kyong Kim, Pierre-Olivier Estève, Amander Clark, Sriharsa Pradhan, Steven E. Jacobsen. (2007) UHRF1 plays a role in maintaining DNA methylation in mammalian cells.
Science 317: 1760-1764.
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62. Xiaoyu Zhang, Sophie Germann, Bartlomiej J. Blus, Sepideh Khorasanizadeh, Valerie Gaudin and Steven E. Jacobsen. (2007) The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation.
Nature Structural and Molecular Biology 14: 869-871.
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61. Ian R. Henderson and Steven E. Jacobsen. (2007) Epigenetic inheritance in plants.
Nature 447: 418-424.
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60. Xiaoyu Zhang, Oliver Clarenz, Shawn Cokus, Yana V. Bernatavichute, Matteo Pellegrini, Justin Goodrich, and Steven E. Jacobsen. (2007) Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis.
PLoS Biology 5(5): 1026-1035 (article e129).
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59. Xiaoyu Zhang, Ian R. Henderson, Cheng Lu, Pamela J. Green and Steven E. Jacobsen. (2007) The Role of RNA Polymerase IV in Small RNA Metabolism.
Proceedings of the National Academy of Sciences 104: 4536-4541.
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58. Lianna M. Johnson, Magnolia Bostick, Xiaoyu Zhang, Edward Kraft, Ian Henderson, Judy Callis and Steven E. Jacobsen. (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation.
Current Biology 17: 379-384.
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57. Xiaoyu Zhang and Steven E. Jacobsen. (2006) Genetic Analysis of DNA methyltransferases in Arabidopsis.
Cold Spring Harbor Symposia on Quantitative Biology 71: 439-447.
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56. Simon W. L. Chan, Xiaoyu Zhang, Yana V. Bernatavichute, Steve E. Jacobsen. (2006) Two-step recruitment of RNA-directed DNA methylation to tandem repeats.
PLoS Biology 4(11): 1923-1933 (article e363)
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55. Peng Peng, Simon W. L. Chan, Govind Shah, Steve E. Jacobsen. (2006) Plant genetics: increased outcrossing in hothead mutants.
Nature 443: E8-E8 doi:10.1038/nature05251
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54. Cheng Lu, Karthik Kulkarni, Frédéric F. Souret, Ramesh MuthuValliappan, Shivakundan Singh Tej, R. Scott Poethig, Ian R. Henderson, Steven E. Jacobsen, Wenzhong Wang, Pamela J. Green, and Blake C. Meyers (2006) MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant.
Genome Research 16: 1276-1288
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53. Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W. L. Chan, Huaming Chen, Ian R. Henderson, Paul Shinn, Matteo Pellegrini, Steve E. Jacobsen and Joseph R. Ecker. (2006) Genome-wide High-Resolution Mapping and Functional Analysis of DNA Methylation in Arabidopsis.
Cell 126(6): 1189-201.
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52. Olga Pontes, Carey Fei Li, Pedro Costa Nunes, Jeremy Haag, Thomas Ream, Alexa Vitins, Steven E. Jacobsen and Craig S. Pikkard. (2006) The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center.
Cell 126: 79-92.
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51. Carey Fei Li, Olga Pontes, Mahmoud El-Shami, Ian R. Henderson, Yana V. Bernatavichute, Simon W. L. Chan, Thierry Lagrange, Craig S. Pikaard, and Steven E. Jacobsen. (2006) An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana.
Cell 126: 93-106.
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50. Simon W. L. Chan, Ian R. Henderson, Xiaoyu Zhang, Govind Shah, Jason S. C. Chien, and Steven E. Jacobsen. (2006) RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in Arabidopsis.
PLoS Genetics 2(6): 791-797 (article e83)
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49. Ian R Henderson, Xiaoyu Zhang, Cheng Lu, Lianna Johnson, Blake C Meyers, Pamela J Green and Steven E Jacobsen. (2006) Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning.
Nature Genetics 38: 721-725.
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48. Sibum Sung, Yuehui He, Tifani W. Eshoo, Yosuke Tamada, Lianna Johnson, Kenji Nakahigashi, Koji Goto, Steve E. Jacobsen, and Richard M. Amasino. (2006) Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1.
Nature Genetics 38: 706-710.
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47. Joshua S. Mylne, Lynne Barrett, Federico Tessadori, Stéphane Mesnage, Lianna Johnson, Yana V. Bernatavichute, Steven E. Jacobsen, Paul Fransz and Caroline Dean. (2006) LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC.
Proc. Nat. Acad. Sci. U. S. A. 103: 5012-5017.
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46. Hang Gyeong Chin, Debasis Patnaik, Pierre-Olivier Estève, Steven E. Jacobsen, and Sriharsa Pradhan. (2006) Catalytic properties and kinetic mechanism of human recombinant Lys-9 histone H3 methyltransferase SUV39H1: participation of the chromodomain in enzymatic catalysis.
Biochemistry 10: 3272-3284.
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45. Mary Grace Goll, Finn Kirpekar, Keith A. Maggert, Jeffrey A. Yoder, Chih-Lin Hsieh, Xiaoyu Zhang, Kent G. Golic, Steven E. Jacobsen, Timothy H. Bestor. (2006) Methylation of tRNA-Asp by the DNA Methyltransferase Homolog Dnmt2.
Science 311: 395-398.
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44. Robert K Tran, Daniel Zilberman, Cecilia de Busto, Renata F Ditt, Jorja G Henikoff, Anders M Lindroth, Jeffrey Delrow, Tom Boyle, Samson Kwong, Terri D Bryson, Steven E Jacobsen and Steven Henikoff. (2005) Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis.
Genome Biology 6: R90.
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43. Assaf Zemach, Yan Li, Bess Wayburn, Hagit Ben-Meir, Vladimir Kiss, Yigal Avivi, Vyacheslav Kalchenko, Steven E. Jacobsen, and Gideon Grafi. (2005) DDM1 binds Arabidopsis Methyl-CpG Binding Domain proteins and affects their subnuclear localization.
Plant Cell 17: 1549-1558.
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42. Simon W. L. Chan, Ian R. Henderson, and Steven E. Jacobsen. (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana.
Nature Reviews Genetics 6: 351-360.
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41. Robert K. Tran, Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen and Steven Henikoff. (2005) DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.
Current Biology 15: 154-159.
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40. Todd C. Mockler, Simon Chan, Ambika Sundaresan, Huaming Chen, Steven E. Jacobsen and Joseph R. Ecker. (2005) Applications of DNA Tiling Arrays for Whole-Genome Analysis.
Genomics 85: 1-15.
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39. Lianna Johnson, Sahanna Molla, Benjamin A. Garcia, Tara L. Muratore, Jeffrey Shabanowitz, Donald F. Hunt and Steven E. Jacobsen. (2004) Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications.
Nucleic Acids Research 32: 6511-6518.
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38. Debasis Patnaik, Hang Gyeong Chin, Pierre-Olivier Esteve, Jack Benner, Steven E. Jacobsen, and Sriharsa Pradhan. (2004) Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase.
Journal of Biological Chemistry 279:53248-53258.
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37. Anders M Lindroth, David Shultis, Zuzana Jasencakova, Jörg Fuchs, Lianna Johnson, Daniel Schubert, Debasis Patnaik, Sriharsa Pradhan, Justin Goodrich, Ingo Schubert, Thomas Jenuwein, Sepideh Khorasanizadeh, and Steven E Jacobsen. (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3.
EMBO 23: 4286-4296.
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36. Kevin V. Morris, Simon W. L. Chan, Steven E. Jacobsen, and David J. Looney. (2004) Small interfering RNA-induced transcriptional gene silencing in human cells.
Science 305: 1289-1292.
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35. Daniel Zilberman, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington and Steven E. Jacobsen. (2004) Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.
Current Biology 14: 1214-1220.
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34. James P. Jackson, Lianna Johnson, Zuzana Jasencakova, Xing Zhang, Laura Perez-Burgos, Prim B. Singh, Xiaodong Cheng, Ingo Schubert, Thomas Jenuwein, Steven E. Jacobsen. (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana.
Chromosoma 112: 308-315.
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33. Zhixin Xie, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau, Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington. (2004) Genetic and Functional Diversification of Small RNA Pathways in Plants.
PLoS Biology 2: 642-652.
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32. Simon W.-L. Chan, Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. (2004) RNA silencing genes control de novo DNA methylation.
Science 303: 1336.
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31. Tetsu Kinoshita, Asuka Miura, Yeonhee choi, Yuki Kinoshita, Xiaofeng Cao, Steven E. Jacobsen, Robert L. Fischer and Tetsuji Kakutani. (2004) One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation.
Science 303: 521-523.
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30. Xiaofeng Cao, Werner Aufsatz, Daniel Zilberman, M. Florian Mette, Michael S. Huang, Marjori Matzke and Steven E. Jacobsen. (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA Methylation.
Current BiologyPDF SupplementalInfo
29. Masaomi Kato, Asuka Miura, Judith Bender, Steven E. Jacobsen, and Tetsuji Kakutani. (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis.
Current Biology 13: 421-426.
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28. Daniel Zilberman, Xiaofeng Cao and Steven E. Jacobsen. (2003) ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation.
Science 299: 716-719.
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27. Wim J.J. Soppe, Zuzana Jasencakova, Andreas Houben, Tetsuji Kakutani, Armin Meister, Michael S. Huang, Steven E. Jacobsen, Ingo Schubert, and Paul F. Fransz. (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis.
EMBO 21: 6549-6559.
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26. Stephen E. Schauer, Steven E. Jacobsen, David W. Meinke, and Animesh Ray. (2002) DICER-LIKE1: Blind men and elephants in Arabidopsis development.
Trends in Plant Science 7: 487-491.
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25. Lianna M. Johnson, Xiaofeng Cao and Steven E. Jacobsen. (2002) Interplay between two epigenetic marks: DNA methylation and histone H3 lysine 9 methylation.
Current Biology 12: 1360-1367.
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24. Xiaofeng Cao and Steven E. Jacobsen. (2002) Locus specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes.
Proc. Nat. Acad. Sci. U. S. A. 99: 16491-16498.
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23. Yeonhee Choi, Mary Gehring, Lianna Johnson, Mike Hannon, John J. Harada, Robert B. Goldberg, Steven E. Jacobsen, Robert L. Fischer. (2002) DEMETER, a DNA Glycosylase Domain Protein, Is Required for Endosperm Gene Imprinting and Seed Viability in Arabidopsis.
Cell 110: 33-42.
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22. Xiaofeng Cao and Steven E. Jacobsen. (2002) Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing.
Current Biology 12: 1138-1144.
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21. James P. Jackson, Anders M. Lindroth, Xiaofeng Cao, Steven E. Jacobsen. (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase.
Nature 416: 556-560.
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20. Nancy A. Eckardt, Takashi Araki, Christoph Benning, Pilar Cubas, Justin Goodrich, Steven E. Jacobsen, Patrick Masson, Eiji Nambara, Rudiger Simon, Shauna Somerville, and Geoff Wasteneys. (2001) Arabidopsis Research 2001.
Plant Cell, 13: 1973-1982.
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19. Cindy Sue Malone, Maurine D. Miner, Jeanette R. Doerr, James P. Jackson, Steven E. Jacobsen, Randolph Wall, and Michael Teitell. (2001) CmC(A/T)GG DNA Methylation in Mature B Cell Lymphoma Gene Silencing.
PNAS 98: 10404-10409.
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18. Anders Lindroth, Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire M. McCallum, Steven Henikoff, Steven E. Jacobsen. (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
Science 292: 2077-2080.
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17. Naoki Kishimoto, Hajime Sakai, James Jackson, Steven E. Jacobsen, Elliot M. Meyerowitz, Elisabeth S. Dennis and E. Jean Finnegan. (2001) Site specificity of the METI DNA methyltransferase demonstrated through hypermethylation of the SUPERMAN locus.
Plant Molecular Biology 46: 171-183.
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16. Wim J.J. Soppe, Steven E. Jacobsen, Carlos Alonso-Blanco, James Jackson, Tetsuji Kakutani, Maarten Koornneef and Anton J.M. Peeters. (2000) The late flowering phenotype of fwa mutants is caused by gain of function epi-alleles at a homeodomain gene.
Molecular Cell 6: 791-802.
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15. Hajime Sakai, Beth A. Krizek, Steven E. Jacobsen, and Elliot M. Meyerowitz. (2000) Regulation of SUP Expression Identifies Multiple Regulators Involved in Arabidopsis Floral Meristem Development.
Plant Cell 12: 1607-1618.
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14. Xiaofeng Cao, Nathan M. Springer, Michael G. Muszynski, Ronald L. Phillips, Shawn Kaeppler, and Steven E. Jacobsen. (2000) Conserved plant genes with similarity to mammalian de novo DNA methyltransferases.
PNAS 97: 4979-4984.
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13. Steven E. Jacobsen, Hajime Sakai, E. Jean Finnegan, Xiaofeng Cao and Elliot. M. Meyerowitz. (2000) Ectopic methylation of flower-specific genes in Arabidopsis.
Current Biology 10: 179-186.
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12. Steven E. Jacobsen, Mark P. Running, and Elliot M. Meyerowitz. (1999) Disruption of an RNA helicase/ RNAse III homologue in Arabidopsis causes unregulated cell division in floral meristems.
Development 126: 5231-5243.
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11. Steven E. Jacobsen. (1999) Gene silencing: Maintaining methylation patterns.
Current Biology 9: R617-R619.
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10. Steven E. Jacobsen and Elliot M. Meyerowitz. (1997) Hypermethylated SUPERMAN epigenetic alleles in Arabidopsis.
Science 277: 1100-1103.
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9. Steven E. Jacobsen, Neil E. Olszewski, and Elliot M. Meyerowitz. (1998) SPINDLY's role in the gibberellin response pathway. In "Control of Plant Development: Genes and Signals".
Symp Soc Exp Biol. 51: 73-8.
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8. Steven E. Jacobsen, Kalli A. Binkowski and Neil E. Olszewski. (1996) SPINDLY, a tetratricopeptide repeat protein involved in gibberellin signal transduction in Arabidopsis.
Proc. Nat. Acad. Sci. U. S. A. 93: 9292-9296.
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7. Steven E. Clark, Steven E. Jacobsen, Joshua Z. Levin, and Elliot M. Meyerowitz. (1996) The CLAVATA and SHOOT MERISTEMLESS loci competitively regulate meristem activity in Arabidopsis.
Development 122: 1567-1575.
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6. Karen M. Leon-Kloosterziel, Marta Alvarez Gil, Gerda J. Ruijs, Steven E. Jacobsen, Neil E. Olszewski, Steven H. Schwartz, Jan A. D. Zeevaart, and Maarten Koornneef. (1996) Isolation and characterization of abscisic acid-deficient Arabidopsis mutants at two new loci.
The Plant Journal 10: 655-661.
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5. Steven E. Jacobsen and Neil E. Olszewski. (1996) Gibberellins regulate the abundance of RNAs with sequence similarity to proteinase inhibitors, dioxygenases, and dehydrogenases.
Planta 198: 78-86.
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4. Steven E. Jacobsen, Shi Lifang, Zhanguo Xin, and Neil E. Olszewski. (1994) Gibberellin-induced changes in the translatable mRNA populations of stamens and shoots of gibberellin-deficient tomato.
Planta 192: 372-378.
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3. Steven E. Jacobsen and Neil E. Olszewski. (1993) Mutations at the SPINDLY locus of Arabidopsis alter gibberellin signal transduction.
Plant Cell 5: 887-896.
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2. Steven E. Jacobsen and Neil E. Olszewski. (1991) Characterization of the arrest in anther development associated with gibberellin deficiency of the gib-1 mutant of tomato.
Plant Physiology 97: 409-414.
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1. Steven E. Jacobsen and Russell W. Wallace. (1986) Life cycle and population dynamics of Yellow Foxtail in established alfalfa.
Proc. of the Western Society of Weed Science 39: 179-185.
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