Steven Jacobsen
Dr. Jacobsen studies mechanisms of epigenetic inheritance and gene regulation in both the model plant Arabidopsis thaliana and in mammalian stem cells. Our research involves genetic screens, genomics, epigenomics, and biochemistry. We also develop novel methods for CRISPR mediated genome editing.
Websites:
Research Interests:
Epigenetics, Epigenomics, Genetics, Gene regulation,Publications:
Boone BA, Mendoza CP, Behrendt NJ, Jacobsen SE. α-Crystalline Domains and Intrinsically Disordered Regions Can Work in Parallel to Induce Accumulation of MBD6 at Chromocenters in Arabidopsis thaliana. Epigenomes. 2024 Aug 28; 8(3). view on PubMed
McDonald BR, Picard CL, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. Nat Plants. 2024 08; 10(8):1246-1257. view on PubMed
Harris CJ, Zhong Z, Ichino L, Feng S, Jacobsen SE. H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment. Elife. 2024 May 30; 12. view on PubMed
Harris CJ, Zhong Z, Ichino L, Feng S, Jacobsen SE. H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment. bioRxiv. 2024 Mar 05. view on PubMed
Wang S, Wang M, Ichino L, Boone BA, Zhong Z, Papareddy RK, Lin EK, Yun J, Feng S, Jacobsen SE. MBD2 couples DNA methylation to transposable element silencing during male gametogenesis. Nat Plants. 2024 01; 10(1):13-24. view on PubMed
Yoon PH, Skopintsev P, Shi H, Chen L, Adler BA, Al-Shimary M, Craig RJ, Loi KJ, DeTurk EC, Li Z, Amerasekera J, Trinidad M, Nisonoff H, Chen K, Lahiri A, Boger R, Jacobsen S, Banfield JF, Doudna JA. Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes. Nucleic Acids Res. 2023 Dec 11; 51(22):12414-12427. view on PubMed
Wang Z, Castillo-González CM, Zhao C, Tong CY, Li C, Zhong S, Liu Z, Xie K, Zhu J, Wu Z, Peng X, Jacob Y, Michaels SD, Jacobsen SE, Zhang X. H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome. Nat Commun. 2023 11 18; 14(1):7484. view on PubMed
Boone BA, Ichino L, Wang S, Gardiner J, Yun J, Jami-Alahmadi Y, Sha J, Mendoza CP, Steelman BJ, van Aardenne A, Kira-Lucas S, Trentchev I, Wohlschlegel JA, Jacobsen SE. ACD15, ACD21, and SLN regulate the accumulation and mobility of MBD6 to silence genes and transposable elements. Sci Adv. 2023 11 17; 9(46):eadi9036. view on PubMed
Yan C, Han W, Zhou Q, Niwa K, Tang MJ, Burch JE, Zhang Y, Delgadillo DA, Sun Z, Wu Z, Jacobsen SE, Nelson H, Houk KN, Tang Y. Genome Mining from Agriculturally Relevant Fungi Led to a d-Glucose Esterified Polyketide with a Terpene-like Core Structure. J Am Chem Soc. 2023 11 22; 145(46):25080-25085. view on PubMed
Boone BA, Ichino L, Wang S, Gardiner J, Yun J, Jami-Alahmadi Y, Sha J, Mendoza CP, Steelman BJ, van Aardenne A, Kira-Lucas S, Trentchev I, Wohlschlegel JA, Jacobsen SE. ACD15, ACD21 and SLN regulate accumulation and mobility of MBD6 to silence genes and transposable elements. bioRxiv. 2023 Oct 06. view on PubMed
Mcdonald BR, Picard C, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. bioRxiv. 2023 Sep 25. view on PubMed
Venkei ZG, Gainetdinov I, Bagci A, Starostik MR, Choi CP, Fingerhut JM, Chen P, Balsara C, Whitfield TW, Bell GW, Feng S, Jacobsen SE, Aravin AA, Kim JK, Zamore PD, Yamashita YM. A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila. Nat Cell Biol. 2023 Oct; 25(10):1495-1505. view on PubMed
Yoon PH, Skopintsev P, Shi H, Chen LX, Adler BA, Al-Shimary M, Craig RJ, Li Z, Amerasekera J, Trinidad M, Nisonoff H, Chen K, Lahiri A, Boger R, Jacobsen S, Banfield JF, Doudna JA. Eukaryotic RNA-guided endonucleases evolved from a unique clade of bacterial enzymes. bioRxiv. 2023 Aug 10. view on PubMed
Han W, Wu Z, Zhong Z, Williams J, Jacobsen SE, Sun Z, Tang Y. Assessing the Biosynthetic Inventory of the Biocontrol Fungus Trichoderma afroharzianum T22. J Agric Food Chem. 2023 Aug 02; 71(30):11502-11519. view on PubMed
Li Z, Wang M, Zhong Z, Gallego-Bartolomé J, Feng S, Jami-Alahmadi Y, Wang X, Wohlschlegel J, Bischof S, Long JA, Jacobsen SE. The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation. Nat Commun. 2023 07 12; 14(1):4135. view on PubMed
Parkman JA, Barlow CD, Sheppert AP, Jacobsen S, Barksdale CA, Wayment AX, Newton MP, Burt SR, Michaelis DJ. Structural Analysis of Non-native Peptide-Based Catalysts Using 2D NMR-Guided MD Simulations. J Phys Chem A. 2023 Jul 06; 127(26):5602-5608. view on PubMed
Zhong Z, Xue Y, Harris CJ, Wang M, Li Z, Ke Y, Liu M, Zhou J, Jami-Alahmadi Y, Feng S, Wohlschlegel JA, Jacobsen SE. MORC proteins regulate transcription factor binding by mediating chromatin compaction in active chromatin regions. Genome Biol. 2023 04 26; 24(1):96. view on PubMed
Wang M, Zhong Z, Gallego-Bartolomé J, Feng S, Shih YH, Liu M, Zhou J, Richey JC, Ng C, Jami-Alahmadi Y, Wohlschlegel J, Wu K, Jacobsen SE. Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14. Nat Commun. 2023 03 28; 14(1):1736. view on PubMed
Xie G, Du X, Hu H, Li S, Cao X, Jacobsen SE, Du J. Structure and mechanism of the plant RNA polymerase V. Science. 2023 03 24; 379(6638):1209-1213. view on PubMed
Wang M, Zhong Z, Gallego-Bartolomé J, Li Z, Feng S, Kuo HY, Kan RL, Lam H, Richey JC, Tang L, Zhou J, Liu M, Jami-Alahmadi Y, Wohlschlegel J, Jacobsen SE. A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis. Nat Plants. 2023 03; 9(3):460-472. view on PubMed
Li Z, Zhong Z, Wu Z, Pausch P, Al-Shayeb B, Amerasekera J, Doudna JA, Jacobsen SE. Genome editing in plants using the compact editor CasΦ. Proc Natl Acad Sci U S A. 2023 01 24; 120(4):e2216822120. view on PubMed
Li Z, Wang M, Zhong Z, Gallego-Bartolomé J, Feng S, Jami-Alahmadi Y, Wang X, Wohlschlegel J, Bischof S, Long JA, Jacobsen SE. The MOM1 complex recruits the RdDM machinery via MORC6 to establish de novo DNA methylation. bioRxiv. 2023 Jan 10. view on PubMed
Veley KM, Elliott K, Jensen G, Zhong Z, Feng S, Yoder M, Gilbert KB, Berry JC, Lin ZD, Ghoshal B, Gallego-Bartolomé J, Norton J, Motomura-Wages S, Carrington JC, Jacobsen SE, Bart RS. Improving cassava bacterial blight resistance by editing the epigenome. Nat Commun. 2023 01 05; 14(1):85. view on PubMed
Zhong Z, Feng S, Mansfeld BN, Ke Y, Qi W, Lim YW, Gruissem W, Bart RS, Jacobsen SE. Haplotype-resolved DNA methylome of African cassava genome. Plant Biotechnol J. 2023 02; 21(2):247-249. view on PubMed
Al-Shayeb B, Skopintsev P, Soczek KM, Stahl EC, Li Z, Groover E, Smock D, Eggers AR, Pausch P, Cress BF, Huang CJ, Staskawicz B, Savage DF, Jacobsen SE, Banfield JF, Doudna JA. Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors. Cell. 2022 11 23; 185(24):4574-4586.e16. view on PubMed
Ichino L, Picard CL, Yun J, Chotai M, Wang S, Lin EK, Papareddy RK, Xue Y, Jacobsen SE. Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen. Cell Rep. 2022 11 22; 41(8):111699. view on PubMed
Zhong Z, Wang Y, Wang M, Yang F, Thomas QA, Xue Y, Zhang Y, Liu W, Jami-Alahmadi Y, Xu L, Feng S, Marquardt S, Wohlschlegel JA, Ausin I, Jacobsen SE. Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis. Nat Commun. 2022 11 15; 13(1):6970. view on PubMed
Lim YW, Mansfeld BN, Schläpfer P, Gilbert KB, Narayanan NN, Qi W, Wang Q, Zhong Z, Boyher A, Gehan J, Beyene G, Lin ZD, Esuma W, Feng S, Chanez C, Eggenberger N, Adiga G, Alicai T, Jacobsen SE, Taylor NJ, Gruissem W, Bart RS. Mutations in DNA polymerase δ subunit 1 co-segregate with CMD2-type resistance to Cassava Mosaic Geminiviruses. Nat Commun. 2022 07 07; 13(1):3933. view on PubMed
Hernández-García J, Diego-Martin B, Kuo PH, Jami-Alahmadi Y, Vashisht AA, Wohlschlegel J, Jacobsen SE, Blázquez MA, Gallego-Bartolomé J. Comprehensive identification of SWI/SNF complex subunits underpins deep eukaryotic ancestry and reveals new plant components. Commun Biol. 2022 06 06; 5(1):549. view on PubMed
Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Harris JC, Wu Z, Zhai J, Yang M, Li S, Jacobsen SE, Du J. A SYBR Gold-based Label-free in vitro Dicing Assay. Bio Protoc. 2022 Apr 05; 12(7):e4382. view on PubMed
Gardiner J, Ghoshal B, Wang M, Jacobsen SE. CRISPR-Cas-mediated transcriptional control and epi-mutagenesis. Plant Physiol. 2022 03 28; 188(4):1811-1824. view on PubMed
Potok ME, Zhong Z, Picard CL, Liu Q, Do T, Jacobsen CE, Sakr O, Naranbaatar B, Thilakaratne R, Khnkoyan Z, Purl M, Cheng H, Vervaet H, Feng S, Rayatpisheh S, Wohlschlegel JA, O'Malley RC, Ecker JR, Jacobsen SE. The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis. Proc Natl Acad Sci U S A. 2022 01 18; 119(3). view on PubMed
Desai VP, Chouaref J, Wu H, Pastor WA, Kan RL, Oey HM, Li Z, Ho J, Vonk KKD, San Leon Granado D, Christopher MA, Clark AT, Jacobsen SE, Daxinger L. The role of MORC3 in silencing transposable elements in mouse embryonic stem cells. Epigenetics Chromatin. 2021 10 27; 14(1):49. view on PubMed
Kojima-Kita K, Kuramochi-Miyagawa S, Nakayama M, Miyata H, Jacobsen SE, Ikawa M, Koseki H, Nakano T. MORC3, a novel MIWI2 association partner, as an epigenetic regulator of piRNA dependent transposon silencing in male germ cells. Sci Rep. 2021 10 14; 11(1):20472. view on PubMed
Wang Q, Xue Y, Zhang L, Zhong Z, Feng S, Wang C, Xiao L, Yang Z, Harris CJ, Wu Z, Zhai J, Yang M, Li S, Jacobsen SE, Du J. Mechanism of siRNA production by a plant Dicer-RNA complex in dicing-competent conformation. Science. 2021 Nov 26; 374(6571):1152-1157. view on PubMed
Cable J, Ronald PC, Voytas D, Zhang F, Levy AA, Takatsuka A, Arimura SI, Jacobsen SE, Toki S, Toda E, Gao C, Zhu JK, Boch J, Van Eck J, Mahfouz M, Andersson M, Fridman E, Weiss T, Wang K, Qi Y, Jores T, Adams T, Bagchi R. Plant genome engineering from lab to field-a Keystone Symposia report. Ann N Y Acad Sci. 2021 12; 1506(1):35-54. view on PubMed
Xue Y, Zhong Z, Harris CJ, Gallego-Bartolomé J, Wang M, Picard C, Cao X, Hua S, Kwok I, Feng S, Jami-Alahmadi Y, Sha J, Gardiner J, Wohlschlegel J, Jacobsen SE. Arabidopsis MORC proteins function in the efficient establishment of RNA directed DNA methylation. Nat Commun. 2021 07 13; 12(1):4292. view on PubMed
Ghoshal B, Picard CL, Vong B, Feng S, Jacobsen SE. CRISPR-based targeting of DNA methylation in Arabidopsis thaliana by a bacterial CG-specific DNA methyltransferase. Proc Natl Acad Sci U S A. 2021 06 08; 118(23). view on PubMed
Ichino L, Boone BA, Strauskulage L, Harris CJ, Kaur G, Gladstone MA, Tan M, Feng S, Jami-Alahmadi Y, Duttke SH, Wohlschlegel JA, Cheng X, Redding S, Jacobsen SE. MBD5 and MBD6 couple DNA methylation to gene silencing through the J-domain protein SILENZIO. Science. 2021 Jun 03. view on PubMed
Liu W, Gallego-Bartolomé J, Zhou Y, Zhong Z, Wang M, Wongpalee SP, Gardiner J, Feng S, Kuo PH, Jacobsen SE. Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase. Nat Commun. 2021 05 25; 12(1):3130. view on PubMed
Bourguet P, Picard CL, Yelagandula R, Pélissier T, Lorkovic ZJ, Feng S, Pouch-Pélissier MN, Schmücker A, Jacobsen SE, Berger F, Mathieu O. The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation. Nat Commun. 2021 05 11; 12(1):2683. view on PubMed
Zhang Z, Wang H, Wang Y, Xi F, Wang H, Kohnen MV, Gao P, Wei W, Chen K, Liu X, Gao Y, Han X, Hu K, Zhang H, Zhu Q, Zheng Y, Liu B, Ahmad A, Hsu YH, Jacobsen SE, Gu L. Whole-genome characterization of chronological age-associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth. Plant J. 2021 04; 106(2):435-453. view on PubMed
Choi CP, Tay RJ, Starostik MR, Feng S, Moresco JJ, Montgomery BE, Xu E, Hammonds MA, Schatz MC, Montgomery TA, Yates JR, Jacobsen SE, Kim JK. SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans. Elife. 2021 02 15; 10. view on PubMed
Zhong Z, Feng S, Duttke SH, Potok ME, Zhang Y, Gallego-Bartolomé J, Liu W, Jacobsen SE. DNA methylation-linked chromatin accessibility affects genomic architecture in Arabidopsis. Proc Natl Acad Sci U S A. 2021 02 02; 118(5). view on PubMed
Ghoshal B, Vong B, Picard CL, Feng S, Tam JM, Jacobsen SE. A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation in Arabidopsis thaliana. PLoS Genet. 2020 Dec; 16(12):e1008983. view on PubMed
Bourguet P, López-González L, Gómez-Zambrano Á, Pélissier T, Hesketh A, Potok ME, Pouch-Pélissier MN, Perez M, Da Ines O, Latrasse D, White CI, Jacobsen SE, Benhamed M, Mathieu O. DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis. Genome Biol. 2020 11 25; 21(1):283. view on PubMed
Feng S, Zhong Z, Wang M, Jacobsen SE. Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing. Epigenetics Chromatin. 2020 10 07; 13(1):42. view on PubMed
Pausch P, Al-Shayeb B, Bisom-Rapp E, Tsuchida CA, Li Z, Cress BF, Knott GJ, Jacobsen SE, Banfield JF, Doudna JA. CRISPR-CasΦ from huge phages is a hypercompact genome editor. Science. 2020 07 17; 369(6501):333-337. view on PubMed
Gardiner J, Zhao JM, Chaffin K, Jacobsen SE. Promoter and Terminator Optimization for DNA Methylation Targeting in Arabidopsis. Epigenomes. 2020 Jun 12; 4(2). view on PubMed
Wang Y, Zhong Z, Zhang Y, Xu L, Feng S, Rayatpisheh S, Wohlschlegel JA, Wang Z, Jacobsen SE, Ausin I. NAP1-RELATED PROTEIN1 and 2 negatively regulate H2A.Z abundance in chromatin in Arabidopsis. Nat Commun. 2020 06 08; 11(1):2887. view on PubMed
Liu Q, Bischof S, Harris CJ, Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE. The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis. Nat Commun. 2020 06 03; 11(1):2798. view on PubMed
Nicolau M, Picault N, Descombin J, Jami-Alahmadi Y, Feng S, Bucher E, Jacobsen SE, Deragon JM, Wohlschlegel J, Moissiard G. 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 Genet. 2020 04; 16(4):e1008324. view on PubMed
Venkei ZG, Choi CP, Feng S, Chen C, Jacobsen SE, Kim JK, Yamashita YM. A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage. PLoS Genet. 2020 03; 16(3):e1008648. view on PubMed
Wongpalee SP, Liu S, Gallego-Bartolomé J, Leitner A, Aebersold R, Liu W, Yen L, Nohales MA, Kuo PH, Vashisht AA, Wohlschlegel JA, Feng S, Kay SA, Zhou ZH, Jacobsen SE. CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Nat Commun. 2019 09 02; 10(1):3916. view on PubMed
Kim H, Yen L, Wongpalee SP, Kirshner JA, Mehta N, Xue Y, Johnston JB, Burlingame AL, Kim JK, Loparo JJ, Jacobsen SE. The Gene-Silencing Protein MORC-1 Topologically Entraps DNA and Forms Multimeric Assemblies to Cause DNA Compaction. Mol Cell. 2019 08 22; 75(4):700-710.e6. view on PubMed
Potok ME, Wang Y, Xu L, Zhong Z, Liu W, Feng S, Naranbaatar B, Rayatpisheh S, Wang Z, Wohlschlegel JA, Ausin I, Jacobsen SE. Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition. Nat Commun. 2019 07 26; 10(1):3352. view on PubMed
Nohales MA, Liu W, Duffy T, Nozue K, Sawa M, Pruneda-Paz JL, Maloof JN, Jacobsen SE, Kay SA. Multi-level Modulation of Light Signaling by GIGANTEA Regulates Both the Output and Pace of the Circadian Clock. Dev Cell. 2019 06 17; 49(6):840-851.e8. view on PubMed
Chen M, Liu Q, Gao SS, Young AE, Jacobsen SE, Tang Y. Genome mining and biosynthesis of a polyketide from a biofertilizer fungus that can facilitate reductive iron assimilation in plant. Proc Natl Acad Sci U S A. 2019 03 19; 116(12):5499-5504. view on PubMed
Papikian A, Liu W, Gallego-Bartolomé J, Jacobsen SE. Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems. Nat Commun. 2019 02 13; 10(1):729. view on PubMed
Gallego-Bartolomé J, Liu W, Kuo PH, Feng S, Ghoshal B, Gardiner J, Zhao JM, Park SY, Chory J, Jacobsen SE. Co-targeting RNA Polymerases IV and V Promotes Efficient De Novo DNA Methylation in Arabidopsis. Cell. 2019 02 21; 176(5):1068-1082.e19. view on PubMed
Harris CJ, Jacobsen SE. ADCP1: a novel plant H3K9me2 reader. Cell Res. 2019 01; 29(1):6-7. view on PubMed
Chen D, Liu W, Zimmerman J, Pastor WA, Kim R, Hosohama L, Ho J, Aslanyan M, Gell JJ, Jacobsen SE, Clark AT. The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation. Cell Rep. 2018 12 26; 25(13):3591-3602.e5. view on PubMed
Harris CJ, Scheibe M, Wongpalee SP, Liu W, Cornett EM, Vaughan RM, Li X, Chen W, Xue Y, Zhong Z, Yen L, Barshop WD, Rayatpisheh S, Gallego-Bartolome J, Groth M, Wang Z, Wohlschlegel JA, Du J, Rothbart SB, Butter F, Jacobsen SE. A DNA methylation reader complex that enhances gene transcription. Science. 2018 12 07; 362(6419):1182-1186. view on PubMed
Stoddard CI, Feng S, Campbell MG, Liu W, Wang H, Zhong X, Bernatavichute Y, Cheng Y, Jacobsen SE, Narlikar GJ. A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase. Mol Cell. 2019 01 03; 73(1):73-83.e6. view on PubMed
Yan Y, Liu Q, Jacobsen SE, Tang Y. 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 Rep. 2018 11; 19(11). view on PubMed
Li X, Harris CJ, Zhong Z, Chen W, Liu R, Jia B, Wang Z, Li S, Jacobsen SE, Du J. Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation. Proc Natl Acad Sci U S A. 2018 09 11; 115(37):E8793-E8802. view on PubMed
Orozco LD, Farrell C, Hale C, Rubbi L, Rinaldi A, Civelek M, Pan C, Lam L, Montoya D, Edillor C, Seldin M, Boehnke M, Mohlke KL, Jacobsen S, Kuusisto J, Laakso M, Lusis AJ, Pellegrini M. Epigenome-wide association in adipose tissue from the METSIM cohort. Hum Mol Genet. 2018 07 15; 27(14):2586. view on PubMed
Yan Y, Liu Q, Zang X, Yuan S, Bat-Erdene U, Nguyen C, Gan J, Zhou J, Jacobsen SE, Tang Y. Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action. Nature. 2018 07; 559(7714):415-418. view on PubMed
Orozco LD, Farrell C, Hale C, Rubbi L, Rinaldi A, Civelek M, Pan C, Lam L, Montoya D, Edillor C, Seldin M, Boehnke M, Mohlke KL, Jacobsen S, Kuusisto J, Laakso M, Lusis AJ, Pellegrini M. Epigenome-wide association in adipose tissue from the METSIM cohort. Hum Mol Genet. 2018 05 15; 27(10):1830-1846. view on PubMed
Pastor WA, Liu W, Chen D, Ho J, Kim R, Hunt TJ, Lukianchikov A, Liu X, Polo JM, Jacobsen SE, Clark AT. TFAP2C regulates transcription in human naive pluripotency by opening enhancers. Nat Cell Biol. 2018 05; 20(5):553-564. view on PubMed
Gallego-Bartolomé J, Gardiner J, Liu W, Papikian A, Ghoshal B, Kuo HY, Zhao JM, Segal DJ, Jacobsen SE. Targeted DNA demethylation of the Arabidopsis genome using the human TET1 catalytic domain. Proc Natl Acad Sci U S A. 2018 02 27; 115(9):E2125-E2134. view on PubMed
Liu W, Duttke SH, Hetzel J, Groth M, Feng S, Gallego-Bartolome J, Zhong Z, Kuo HY, Wang Z, Zhai J, Chory J, Jacobsen SE. RNA-directed DNA methylation involves co-transcriptional small-RNA-guided slicing of polymerase V transcripts in Arabidopsis. Nat Plants. 2018 03; 4(3):181-188. view on PubMed
Zhang Y, Harris CJ, Liu Q, Liu W, Ausin I, Long Y, Xiao L, Feng L, Chen X, Xie Y, Chen X, Zhan L, Feng S, Li JJ, Wang H, Zhai J, Jacobsen SE. Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation in Arabidopsis. Proc Natl Acad Sci U S A. 2018 01 30; 115(5):E1069-E1074. view on PubMed
Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. Correction: In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. Elife. 2017 08 31; 6. view on PubMed
Weiser NE, Yang DX, Feng S, Kalinava N, Brown KC, Khanikar J, Freeberg MA, Snyder MJ, Csankovszki G, Chan RC, Gu SG, Montgomery TA, Jacobsen SE, Kim JK. MORC-1 Integrates Nuclear RNAi and Transgenerational Chromatin Architecture to Promote Germline Immortality. Dev Cell. 2017 05 22; 41(4):408-423.e7. view on PubMed
Wollmann H, Stroud H, Yelagandula R, Tarutani Y, Jiang D, Jing L, Jamge B, Takeuchi H, Holec S, Nie X, Kakutani T, Jacobsen SE, Berger F. The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana. Genome Biol. 2017 05 18; 18(1):94. view on PubMed
Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE. Corrigendum: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2017 03 02; 543(7643):136. view on PubMed
Chen D, Liu W, Lukianchikov A, Hancock GV, Zimmerman J, Lowe MG, Kim R, Galic Z, Irie N, Surani MA, Jacobsen SE, Clark AT. Germline competency of human embryonic stem cells depends on eomesodermin. Biol Reprod. 2017 01 01; 97(6):850-861. view on PubMed
Feng W, Hale CJ, Over RS, Cokus SJ, Jacobsen SE, Michaels SD. Large-scale heterochromatin remodeling linked to overreplication-associated DNA damage. Proc Natl Acad Sci U S A. 2017 01 10; 114(2):406-411. view on PubMed
Lahmy S, Pontier D, Bies-Etheve N, Laudié M, Feng S, Jobet E, Hale CJ, Cooke R, Hakimi MA, Angelov D, Jacobsen SE, Lagrange T. Evidence for ARGONAUTE4-DNA interactions in RNA-directed DNA methylation in plants. Genes Dev. 2016 12 01; 30(23):2565-2570. view on PubMed
Ausin I, Feng S, Yu C, Liu W, Kuo HY, Jacobsen EL, Zhai J, Gallego-Bartolome J, Wang L, Egertsdotter U, Street NR, Jacobsen SE, Wang H. DNA methylome of the 20-gigabase Norway spruce genome. Proc Natl Acad Sci U S A. 2016 12 13; 113(50):E8106-E8113. view on PubMed
Li S, Yen L, Pastor WA, Johnston JB, Du J, Shew CJ, Liu W, Ho J, Stender B, Clark AT, Burlingame AL, Daxinger L, Patel DJ, Jacobsen SE. Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin. Proc Natl Acad Sci U S A. 2016 08 30; 113(35):E5108-16. view on PubMed
Bewick AJ, Ji L, Niederhuth CE, Willing EM, Hofmeister BT, Shi X, Wang L, Lu Z, Rohr NA, Hartwig B, Kiefer C, Deal RB, Schmutz J, Grimwood J, Stroud H, Jacobsen SE, Schneeberger K, Zhang X, Schmitz RJ. On the origin and evolutionary consequences of gene body DNA methylation. Proc Natl Acad Sci U S A. 2016 08 09; 113(32):9111-6. view on PubMed
Groth M, Moissiard G, Wirtz M, Wang H, Garcia-Salinas C, Ramos-Parra PA, Bischof S, Feng S, Cokus SJ, John A, Smith DC, Zhai J, Hale CJ, Long JA, Hell R, Díaz de la Garza RI, Jacobsen SE. MTHFD1 controls DNA methylation in Arabidopsis. Nat Commun. 2016 06 13; 7:11640. view on PubMed
Hale CJ, Potok ME, Lopez J, Do T, Liu A, Gallego-Bartolome J, Michaels SD, Jacobsen SE. Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana. PLoS Genet. 2016 06; 12(6):e1006092. view on PubMed
Harris CJ, Husmann D, Liu W, Kasmi FE, Wang H, Papikian A, Pastor WA, Moissiard G, Vashisht AA, Dangl JL, Wohlschlegel JA, Jacobsen SE. Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes. PLoS Genet. 2016 05; 12(5):e1005998. view on PubMed
Li S, Yang Z, Du X, Liu R, Wilkinson AW, Gozani O, Jacobsen SE, Patel DJ, Du J. Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette. Structure. 2016 Mar 01; 24(3):486-94. view on PubMed
Pastor WA, Chen D, Liu W, Kim R, Sahakyan A, Lukianchikov A, Plath K, Jacobsen SE, Clark AT. Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. Cell Stem Cell. 2016 Mar 03; 18(3):323-329. view on PubMed
Wang H, Beyene G, Zhai J, Feng S, Fahlgren N, Taylor NJ, Bart R, Carrington JC, Jacobsen SE, Ausin I. CG gene body DNA methylation changes and evolution of duplicated genes in cassava. Proc Natl Acad Sci U S A. 2015 Nov 03; 112(44):13729-34. view on PubMed
Zhai J, Bischof S, Wang H, Feng S, Lee TF, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson IR, Meyers BC, Ausin I, Jacobsen SE. A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis. Cell. 2015 Oct 08; 163(2):445-55. view on PubMed
Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol. 2015 Sep; 16(9):519-32. view on PubMed
Yazdi PG, Pedersen BA, Taylor JF, Khattab OS, Chen YH, Chen Y, Jacobsen SE, Wang PH. Increasing Nucleosome Occupancy Is Correlated with an Increasing Mutation Rate so Long as DNA Repair Machinery Is Intact. PLoS One. 2015; 10(8):e0136574. view on PubMed
Yazdi PG, Pedersen BA, Taylor JF, Khattab OS, Chen YH, Chen Y, Jacobsen SE, Wang PH. Nucleosome Organization in Human Embryonic Stem Cells. PLoS One. 2015; 10(8):e0136314. view on PubMed
Pastor WA, Stroud H, Nee K, Liu W, Pezic D, Manakov S, Lee SA, Moissiard G, Zamudio N, Bourc'his D, Aravin AA, Clark AT, Jacobsen SE. Erratum: MORC1 represses transposable elements in the mouse male germline. Nat Commun. 2015 Jul 10; 6:7604. view on PubMed
Zhang S, Zhou B, Kang Y, Cui X, Liu A, Deleris A, Greenberg MV, Cui X, Qiu Q, Lu F, Wohlschlegel JA, Jacobsen SE, Cao X. C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. Cell Discov. 2015; 1. view on PubMed
Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. Elife. 2015 Apr 07; 4:e06205. view on PubMed
Zhong X, Hale CJ, Nguyen M, Ausin I, Groth M, Hetzel J, Vashisht AA, Henderson IR, Wohlschlegel JA, Jacobsen SE. Domains rearranged methyltransferase3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis. Proc Natl Acad Sci U S A. 2015 Jan 20; 112(3):911-6. view on PubMed
Song XJ, Kuroha T, Ayano M, Furuta T, Nagai K, Komeda N, Segami S, Miura K, Ogawa D, Kamura T, Suzuki T, Higashiyama T, Yamasaki M, Mori H, Inukai Y, Wu J, Kitano H, Sakakibara H, Jacobsen SE, Ashikari M. Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. Proc Natl Acad Sci U S A. 2015 Jan 06; 112(1):76-81. view on PubMed
Pastor WA, Stroud H, Nee K, Liu W, Pezic D, Manakov S, Lee SA, Moissiard G, Zamudio N, Bourc'his D, Aravin AA, Clark AT, Jacobsen SE. MORC1 represses transposable elements in the mouse male germline. Nat Commun. 2014 Dec 12; 5:5795. view on PubMed
Groth M, Stroud H, Feng S, Greenberg MV, Vashisht AA, Wohlschlegel JA, Jacobsen SE, Ausin I. SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation. Proc Natl Acad Sci U S A. 2014 Dec 09; 111(49):17666-71. view on PubMed
Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE. Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell. 2014 Sep 04; 55(5):694-707. view on PubMed
Tsagaratou A, Äijö T, Lio CW, Yue X, Huang Y, Jacobsen SE, Lähdesmäki H, Rao A. Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation. Proc Natl Acad Sci U S A. 2014 Aug 12; 111(32):E3306-15. view on PubMed
Du J, Johnson LM, Groth M, Feng S, Hale CJ, Li S, Vashisht AA, Wohlschlegel JA, Patel DJ, Jacobsen SE. Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol Cell. 2014 Aug 07; 55(3):495-504. view on PubMed
Yelagandula R, Stroud H, Holec S, Zhou K, Feng S, Zhong X, Muthurajan UM, Nie X, Kawashima T, Groth M, Luger K, Jacobsen SE, Berger F. The histone variant H2A.W defines heterochromatin and promotes chromatin condensation in Arabidopsis. Cell. 2014 Jul 03; 158(1):98-109. view on PubMed
Sequeira-Mendes J, Aragüez I, Peiró R, Mendez-Giraldez R, Zhang X, Jacobsen SE, Bastolla U, Gutierrez C. The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States. Plant Cell. 2014 Jun; 26(6):2351-2366. view on PubMed
Zhong X, Du J, Hale CJ, Gallego-Bartolome J, Feng S, Vashisht AA, Chory J, Wohlschlegel JA, Patel DJ, Jacobsen SE. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell. 2014 May 22; 157(5):1050-60. view on PubMed
Moissiard G, Bischof S, Husmann D, Pastor WA, Hale CJ, Yen L, Stroud H, Papikian A, Vashisht AA, Wohlschlegel JA, Jacobsen SE. Transcriptional gene silencing by Arabidopsis microrchidia homologues involves the formation of heteromers. Proc Natl Acad Sci U S A. 2014 May 20; 111(20):7474-9. view on PubMed
Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, Zhong X, Marson G, Pellegrini M, Segal DJ, Patel DJ, Jacobsen SE. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. 2014 03 06; 507(7490):124-128. view on PubMed
Huang Y, Chavez L, Chang X, Wang X, Pastor WA, Kang J, Zepeda-Martínez JA, Pape UJ, Jacobsen SE, Peters B, Rao A. Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc Natl Acad Sci U S A. 2014 Jan 28; 111(4):1361-6. view on PubMed
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel DJ, Jacobsen SE. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014 Jan; 21(1):64-72. view on PubMed
Greenberg MV, Deleris A, Hale CJ, Liu A, Feng S, Jacobsen SE. Interplay between active chromatin marks and RNA-directed DNA methylation in Arabidopsis thaliana. PLoS Genet. 2013 Nov; 9(11):e1003946. view on PubMed
Widman N, Feng S, Jacobsen SE, Pellegrini M. Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation. Epigenetics. 2014 Feb; 9(2):236-42. view on PubMed
Li-Byarlay H, Li Y, Stroud H, Feng S, Newman TC, Kaneda M, Hou KK, Worley KC, Elsik CG, Wickline SA, Jacobsen SE, Ma J, Robinson GE. RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee. Proc Natl Acad Sci U S A. 2013 Jul 30; 110(31):12750-5. view on PubMed
Chen PY, Ganguly A, Rubbi L, Orozco LD, Morselli M, Ashraf D, Jaroszewicz A, Feng S, Jacobsen SE, Nakano A, Devaskar SU, Pellegrini M. Intrauterine calorie restriction affects placental DNA methylation and gene expression. Physiol Genomics. 2013 Jul 15; 45(14):565-76. view on PubMed
Law JA, Du J, Hale CJ, Feng S, Krajewski K, Palanca AM, Strahl BD, Patel DJ, Jacobsen SE. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature. 2013 Jun 20; 498(7454):385-9. view on PubMed
Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang GL, Meyers BC, Jacobsen SE. Plants regenerated from tissue culture contain stable epigenome changes in rice. Elife. 2013 Mar 19; 2:e00354. view on PubMed
Vincent JJ, Huang Y, Chen PY, Feng S, Calvopiña JH, Nee K, Lee SA, Le T, Yoon AJ, Faull K, Fan G, Rao A, Jacobsen SE, Pellegrini M, Clark AT. Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell Stem Cell. 2013 Apr 04; 12(4):470-8. view on PubMed
Xu Y, Wang Y, Stroud H, Gu X, Sun B, Gan ES, Ng KH, Jacobsen SE, He Y, Ito T. A matrix protein silences transposons and repeats through interaction with retinoblastoma-associated proteins. Curr Biol. 2013 Feb 18; 23(4):345-50. view on PubMed
Stroud H, Greenberg MV, Feng S, Bernatavichute YV, Jacobsen SE. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell. 2013 Jan 17; 152(1-2):352-64. view on PubMed
Deleris A, Stroud H, Bernatavichute Y, Johnson E, Klein G, Schubert D, Jacobsen SE. Loss of the DNA methyltransferase MET1 Induces H3K9 hypermethylation at PcG target genes and redistribution of H3K27 trimethylation to transposons in Arabidopsis thaliana. PLoS Genet. 2012; 8(11):e1003062. view on PubMed
Caro E, Stroud H, Greenberg MV, Bernatavichute YV, Feng S, Groth M, Vashisht AA, Wohlschlegel J, Jacobsen SE. The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation-independent manner. PLoS Genet. 2012; 8(10):e1002995. view on PubMed
Du J, Zhong X, Bernatavichute YV, Stroud H, Feng S, Caro E, Vashisht AA, Terragni J, Chin HG, Tu A, Hetzel J, Wohlschlegel JA, Pradhan S, Patel DJ, Jacobsen SE. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell. 2012 Sep 28; 151(1):167-80. view on PubMed
Colomé-Tatché M, Cortijo S, Wardenaar R, Morgado L, Lahouze B, Sarazin A, Etcheverry M, Martin A, Feng S, Duvernois-Berthet E, Labadie K, Wincker P, Jacobsen SE, Jansen RC, Colot V, Johannes F. Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation. Proc Natl Acad Sci U S A. 2012 Oct 02; 109(40):16240-5. view on PubMed
Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol. 2012 Sep; 19(9):870-5. view on PubMed
Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y, Wang GL, Meyers BC, Jacobsen SE, Pellegrini M. Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci U S A. 2012 Jul 24; 109(30):12040-5. view on PubMed
Stroud H, Hale CJ, Feng S, Caro E, Jacob Y, Michaels SD, Jacobsen SE. DNA methyltransferases are required to induce heterochromatic re-replication in Arabidopsis. PLoS Genet. 2012 Jul; 8(7):e1002808. view on PubMed
Talbert PB, Ahmad K, Almouzni G, Ausió J, Berger F, Bhalla PL, Bonner WM, Cande WZ, Chadwick BP, Chan SW, Cross GA, Cui L, Dimitrov SI, Doenecke D, Eirin-López JM, Gorovsky MA, Hake SB, Hamkalo BA, Holec S, Jacobsen SE, Kamieniarz K, Khochbin S, Ladurner AG, Landsman D, Latham JA, Loppin B, Malik HS, Marzluff WF, Pehrson JR, Postberg J, Schneider R, Singh MB, Smith MM, Thompson E, Torres-Padilla ME, Tremethick DJ, Turner BM, Waterborg JH, Wollmann H, Yelagandula R, Zhu B, Henikoff S. A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin. 2012 Jun 21; 5:7. view on PubMed
Ausin I, Greenberg MV, Simanshu DK, Hale CJ, Vashisht AA, Simon SA, Lee TF, Feng S, Española SD, Meyers BC, Wohlschlegel JA, Patel DJ, Jacobsen SE. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A. 2012 May 29; 109(22):8374-81. view on PubMed
Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, Husmann D, Zhan Y, Lajoie BR, McCord RP, Hale CJ, Feng W, Michaels SD, Frand AR, Pellegrini M, Dekker J, Kim JK, Jacobsen SE. MORC family ATPases required for heterochromatin condensation and gene silencing. Science. 2012 Jun 15; 336(6087):1448-51. view on PubMed
Pontvianne F, Blevins T, Chandrasekhara C, Feng W, Stroud H, Jacobsen SE, Michaels SD, Pikaard CS. Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes Dev. 2012 May 01; 26(9):945-57. view on PubMed
Kinoshita T, Jacobsen SE. Opening the door to epigenetics in PCP. Plant Cell Physiol. 2012 May; 53(5):763-5. view on PubMed
Stroud H, Otero S, Desvoyes B, Ramírez-Parra E, Jacobsen SE, Gutierrez C. Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2012 Apr 03; 109(14):5370-5. view on PubMed
Foret S, Kucharski R, Pellegrini M, Feng S, Jacobsen SE, Robinson GE, Maleszka R. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A. 2012 Mar 27; 109(13):4968-73. view on PubMed
Hale CJ, Jacobsen SE. Plant biology: Equal-parenting policy. Nature. 2012 Jan 22; 482(7383):42-4. view on PubMed
Ausin I, Greenberg MV, Li CF, Jacobsen SE. The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis. Epigenetics. 2012 Jan 01; 7(1):29-33. view on PubMed
Sim JJ, Shi J, Calara F, Rasgon S, Jacobsen S, Kalantar-Zadeh K. Association of plasma renin activity and aldosterone-renin ratio with prevalence of chronic kidney disease: the Kaiser Permanente Southern California cohort. J Hypertens. 2011 Nov; 29(11):2226-35. view on PubMed
Law JA, Vashisht AA, Wohlschlegel JA, Jacobsen SE. SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV. PLoS Genet. 2011 Jul; 7(7):e1002195. view on PubMed
Chen PY, Feng S, Joo JW, Jacobsen SE, Pellegrini M. A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biol. 2011 Jul 06; 12(7):R62. view on PubMed
Stroud H, Feng S, Morey Kinney S, Pradhan S, Jacobsen SE. 5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells. Genome Biol. 2011 Jun 20; 12(6):R54. view on PubMed
Kinney SM, Chin HG, Vaisvila R, Bitinaite J, Zheng Y, Estève PO, Feng S, Stroud H, Jacobsen SE, Pradhan S. Tissue-specific distribution and dynamic changes of 5-hydroxymethylcytosine in mammalian genomes. J Biol Chem. 2011 Jul 15; 286(28):24685-93. view on PubMed
Greenberg MV, Ausin I, Chan SW, Cokus SJ, Cuperus JT, Feng S, Law JA, Chu C, Pellegrini M, Carrington JC, Jacobsen SE. Identification of genes required for de novo DNA methylation in Arabidopsis. Epigenetics. 2011 Mar; 6(3):344-54. view on PubMed
Costas C, de la Paz Sanchez M, Stroud H, Yu Y, Oliveros JC, Feng S, Benguria A, López-Vidriero I, Zhang X, Solano R, Jacobsen SE, Gutierrez C. Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks. Nat Struct Mol Biol. 2011 Mar; 18(3):395-400. view on PubMed
Rajakumara E, Law JA, Simanshu DK, Voigt P, Johnson LM, Reinberg D, Patel DJ, Jacobsen SE. 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 Dev. 2011 Jan 15; 25(2):137-52. view on PubMed
Yuan B, Zhang J, Wang H, Xiong L, Cai Q, Wang T, Jacobsen S, Pradhan S, Wang Y. 6-Thioguanine reactivates epigenetically silenced genes in acute lymphoblastic leukemia cells by facilitating proteasome-mediated degradation of DNMT1. Cancer Res. 2011 Mar 01; 71(5):1904-11. view on PubMed
Feng S, Jacobsen SE. Epigenetic modifications in plants: an evolutionary perspective. Curr Opin Plant Biol. 2011 Apr; 14(2):179-86. view on PubMed
Feng S, Rubbi L, Jacobsen SE, Pellegrini M. Determining DNA methylation profiles using sequencing. Methods Mol Biol. 2011; 733:223-38. view on PubMed
Deleris A, Greenberg MV, Ausin I, Law RW, Moissiard G, Schubert D, Jacobsen SE. Involvement of a Jumonji-C domain-containing histone demethylase in DRM2-mediated maintenance of DNA methylation. EMBO Rep. 2010 Dec; 11(12):950-5. view on PubMed
Feng S, Jacobsen SE, Reik W. Epigenetic reprogramming in plant and animal development. Science. 2010 Oct 29; 330(6004):622-7. view on PubMed
Henderson IR, Deleris A, Wong W, Zhong X, Chin HG, Horwitz GA, Kelly KA, Pradhan S, Jacobsen SE. 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 Genet. 2010 Oct 28; 6(10):e1001182. view on PubMed
Jacob Y, Stroud H, Leblanc C, Feng S, Zhuo L, Caro E, Hassel C, Gutierrez C, Michaels SD, Jacobsen SE. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature. 2010 Aug 19; 466(7309):987-91. view on PubMed
Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Krämer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M. Relationship between nucleosome positioning and DNA methylation. Nature. 2010 Jul 15; 466(7304):388-92. view on PubMed
Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA, Jacobsen SE. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol. 2010 May 25; 20(10):951-6. view on PubMed
Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE. Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8689-94. view on PubMed
Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010 Mar; 11(3):204-20. view on PubMed
Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010 Feb 25; 463(7284):1101-5. view on PubMed
Henderson IR, Chan SR, Cao X, Johnson L, Jacobsen SE. Accurate sodium bisulfite sequencing in plants. Epigenetics. 2010 Jan 01; 5(1):47-9. view on PubMed
Ausin I, Mockler TC, Chory J, Jacobsen SE. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat Struct Mol Biol. 2009 Dec; 16(12):1325-7. view on PubMed
Pradhan S, Chin HG, Estève PO, Jacobsen SE. SET7/9 mediated methylation of non-histone proteins in mammalian cells. Epigenetics. 2009 Aug 16; 4(6):383-7. view on PubMed
Miura K, Agetsuma M, Kitano H, Yoshimura A, Matsuoka M, Jacobsen SE, Ashikari M. A metastable DWARF1 epigenetic mutant affecting plant stature in rice. Proc Natl Acad Sci U S A. 2009 Jul 07; 106(27):11218-23. view on PubMed
Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 2009; 10(6):R62. view on PubMed
Jacob Y, Feng S, LeBlanc CA, Bernatavichute YV, Stroud H, Cokus S, Johnson LM, Pellegrini M, Jacobsen SE, Michaels SD. ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol. 2009 Jul; 16(7):763-8. view on PubMed
Law JA, Jacobsen SE. Molecular biology. Dynamic DNA methylation. Science. 2009 Mar 20; 323(5921):1568-9. view on PubMed
Estève PO, Chin HG, Benner J, Feehery GR, Samaranayake M, Horwitz GA, Jacobsen SE, Pradhan S. Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proc Natl Acad Sci U S A. 2009 Mar 31; 106(13):5076-81. view on PubMed
Widman N, Jacobsen SE, Pellegrini M. Determining the conservation of DNA methylation in Arabidopsis. Epigenetics. 2009 Feb 16; 4(2):119-24. view on PubMed
Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK. Criteria for annotation of plant MicroRNAs. Plant Cell. 2008 Dec; 20(12):3186-90. view on PubMed
Kim JK, Estève PO, Jacobsen SE, Pradhan S. UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells. Nucleic Acids Res. 2009 Feb; 37(2):493-505. view on PubMed
Johnson LM, Law JA, Khattar A, Henderson IR, Jacobsen SE. SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet. 2008 Nov; 4(11):e1000280. view on PubMed
Kraft E, Bostick M, Jacobsen SE, Callis J. ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Plant J. 2008 Dec; 56(5):704-15. view on PubMed
Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One. 2008 Sep 08; 3(9):e3156. view on PubMed
Hashimoto H, Horton JR, Zhang X, Bostick M, Jacobsen SE, Cheng X. The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix. Nature. 2008 Oct 09; 455(7214):826-9. view on PubMed
Henderson IR, Jacobsen SE. Sequencing sliced ends reveals microRNA targets. Nat Biotechnol. 2008 Aug; 26(8):881-2. view on PubMed
Henderson IR, Jacobsen SE. Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev. 2008 Jun 15; 22(12):1597-606. view on PubMed
Jones AM, Chory J, Dangl JL, Estelle M, Jacobsen SE, Meyerowitz EM, Nordborg M, Weigel D. The impact of Arabidopsis on human health: diversifying our portfolio. Cell. 2008 Jun 13; 133(6):939-43. view on PubMed
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008 Mar 13; 452(7184):215-9. view on PubMed
Li CF, Henderson IR, Song L, Fedoroff N, Lagrange T, Jacobsen SE. Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana. PLoS Genet. 2008 Feb; 4(2):e27. view on PubMed
Oh JJ, Boctor BN, Jimenez CA, Lopez R, Koegel AK, Taschereau EO, Phan DT, Jacobsen SE, Slamon DJ. Promoter methylation study of the H37/RBM5 tumor suppressor gene from the 3p21.3 human lung cancer tumor suppressor locus. Hum Genet. 2008 Feb; 123(1):55-64. view on PubMed
El-Shami M, Pontier D, Lahmy S, Braun L, Picart C, Vega D, Hakimi MA, Jacobsen SE, Cooke R, Lagrange T. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 2007 Oct 15; 21(20):2539-44. view on PubMed
Zhang X, Germann S, Blus BJ, Khorasanizadeh S, Gaudin V, Jacobsen SE. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol. 2007 Sep; 14(9):869-71. view on PubMed
Bostick M, Kim JK, Estève PO, Clark A, Pradhan S, Jacobsen SE. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science. 2007 Sep 21; 317(5845):1760-4. view on PubMed
Henderson IR, Jacobsen SE. Epigenetic inheritance in plants. Nature. 2007 May 24; 447(7143):418-24. view on PubMed
Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007 May; 5(5):e129. view on PubMed
Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A. 2007 Mar 13; 104(11):4536-41. view on PubMed
Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol. 2007 Feb 20; 17(4):379-84. view on PubMed
Chan SW, Zhang X, Bernatavichute YV, Jacobsen SE. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol. 2006 Nov; 4(11):e363. view on PubMed
Cole DC, Manas ES, Stock JR, Condon JS, Jennings LD, Aulabaugh A, Chopra R, Cowling R, Ellingboe JW, Fan KY, Harrison BL, Hu Y, Jacobsen S, Jin G, Lin L, Lovering FE, Malamas MS, Stahl ML, Strand J, Sukhdeo MN, Svenson K, Turner MJ, Wagner E, Wu J, Zhou P, Bard J. Acylguanidines as small-molecule beta-secretase inhibitors. J Med Chem. 2006 Oct 19; 49(21):6158-61. view on PubMed
Peng P, Chan SW, Shah GA, Jacobsen SE. Plant genetics: increased outcrossing in hothead mutants. Nature. 2006 Sep 28; 443(7110):E8; discussion E8-9. view on PubMed
Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 2006 Oct; 16(10):1276-88. view on PubMed
Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006 Sep 22; 126(6):1189-201. view on PubMed
Li CF, Pontes O, El-Shami M, Henderson IR, Bernatavichute YV, Chan SW, Lagrange T, Pikaard CS, Jacobsen SE. An ARGONAUTE4-containing nuclear processing center colocalized with Cajal bodies in Arabidopsis thaliana. Cell. 2006 Jul 14; 126(1):93-106. view on PubMed
Pontes O, Li CF, Costa Nunes P, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell. 2006 Jul 14; 126(1):79-92. view on PubMed
Chan SW, Henderson IR, Zhang X, Shah G, Chien JS, Jacobsen SE. RNAi, DRD1, and histone methylation actively target developmentally important non-CG DNA methylation in arabidopsis. PLoS Genet. 2006 Jun 02; 2(6):e83. view on PubMed
Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet. 2006 Jun; 38(6):721-5. view on PubMed
Sung S, He Y, Eshoo TW, Tamada Y, Johnson L, Nakahigashi K, Goto K, Jacobsen SE, Amasino RM. Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat Genet. 2006 Jun; 38(6):706-10. view on PubMed
Mylne JS, Barrett L, Tessadori F, Mesnage S, Johnson L, Bernatavichute YV, Jacobsen SE, Fransz P, Dean C. LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc Natl Acad Sci U S A. 2006 Mar 28; 103(13):5012-7. view on PubMed
Chin HG, Patnaik D, Estève PO, Jacobsen SE, Pradhan S. Catalytic properties and kinetic mechanism of human recombinant Lys-9 histone H3 methyltransferase SUV39H1: participation of the chromodomain in enzymatic catalysis. Biochemistry. 2006 Mar 14; 45(10):3272-84. view on PubMed
Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang X, Golic KG, Jacobsen SE, Bestor TH. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science. 2006 Jan 20; 311(5759):395-8. view on PubMed
Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol. 2005; 6(11):R90. view on PubMed
Chan SW, Henderson IR, Jacobsen SE. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet. 2005 May; 6(5):351-60. view on PubMed
Zemach A, Li Y, Wayburn B, Ben-Meir H, Kiss V, Avivi Y, Kalchenko V, Jacobsen SE, Grafi G. DDM1 binds Arabidopsis methyl-CpG binding domain proteins and affects their subnuclear localization. Plant Cell. 2005 May; 17(5):1549-58. view on PubMed
Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol. 2005 Jan 26; 15(2):154-9. view on PubMed
Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. Applications of DNA tiling arrays for whole-genome analysis. Genomics. 2005 Jan; 85(1):1-15. view on PubMed
Johnson L, Mollah S, Garcia BA, Muratore TL, Shabanowitz J, Hunt DF, Jacobsen SE. Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res. 2004; 32(22):6511-8. view on PubMed
Patnaik D, Chin HG, Estève PO, Benner J, Jacobsen SE, Pradhan S. Substrate specificity and kinetic mechanism of mammalian G9a histone H3 methyltransferase. J Biol Chem. 2004 Dec 17; 279(51):53248-58. view on PubMed
Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I, Jenuwein T, Khorasanizadeh S, Jacobsen SE. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 2004 Oct 27; 23(21):4286-96. view on PubMed
Morris KV, Chan SW, Jacobsen SE, Looney DJ. Small interfering RNA-induced transcriptional gene silencing in human cells. Science. 2004 Aug 27; 305(5688):1289-92. view on PubMed
Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol. 2004 Jul 13; 14(13):1214-20. view on PubMed
Jackson JP, Johnson L, Jasencakova Z, Zhang X, PerezBurgos L, Singh PB, Cheng X, Schubert I, Jenuwein T, Jacobsen SE. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma. 2004 Mar; 112(6):308-15. view on PubMed
Chan SW, Zilberman D, Xie Z, Johansen LK, Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. Science. 2004 Feb 27; 303(5662):1336. view on PubMed
Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004 May; 2(5):E104. view on PubMed
Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol. 2003 Dec 16; 13(24):2212-7. view on PubMed
Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Fischer RL, Kakutani T. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science. 2004 Jan 23; 303(5657):521-3. view on PubMed
Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol. 2003 Mar 04; 13(5):421-6. view on PubMed
Zilberman D, Cao X, Jacobsen SE. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation. Science. 2003 Jan 31; 299(5607):716-9. view on PubMed
Soppe WJ, Jasencakova Z, Houben A, Kakutani T, Meister A, Huang MS, Jacobsen SE, Schubert I, Fransz PF. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 2002 Dec 02; 21(23):6549-59. view on PubMed
Schauer SE, Jacobsen SE, Meinke DW, Ray A. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 2002 Nov; 7(11):487-91. view on PubMed
Johnson L, Cao X, Jacobsen S. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr Biol. 2002 Aug 20; 12(16):1360-7. view on PubMed
Cao X, Jacobsen SE. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A. 2002 Dec 10; 99 Suppl 4:16491-8. view on PubMed
Choi Y, Gehring M, Johnson L, Hannon M, Harada JJ, Goldberg RB, Jacobsen SE, Fischer RL. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis. Cell. 2002 Jul 12; 110(1):33-42. view on PubMed
Cao X, Jacobsen SE. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol. 2002 Jul 09; 12(13):1138-44. view on PubMed
Jackson JP, Lindroth AM, Cao X, Jacobsen SE. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature. 2002 Apr 04; 416(6880):556-60. view on PubMed
Jacobsen SE, Sakai H, Finnegan EJ, Cao X, Meyerowitz EM. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr Biol. 2000 Feb 24; 10(4):179-86. view on PubMed
Jacobsen SE, Running MP, Meyerowitz EM. Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. Development. 1999 Dec; 126(23):5231-43. view on PubMed
