Henikoff Lab

Henikoff Lab

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Publications

2025

  • Henikoff S, Zheng Y, Paranal RM, Xu Y, Greene JE, Henikoff JG, Russell ZR, Szulzewsky F, Thirimanne HN, Kugel S, Holland EC, Ahmad K.Science. 2025 Jan 2;387(6735):737-743. doi: 10.1126/science.ads2169. Epub 2025 Feb 13. Abstract | Full text version | News article
  • Henikoff S, Dent SYR, Mostoslavsky R, Wang T, Comai L 2025 Current insights in Epigenetics and Epigenomics. Frontiers in Epigenetics and Epigenomics 3, 1566501. Full text version

2024

  • Janssens DH, Duran M, Otto DJ, Kirkey D, Yi JS, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S. MLL oncoprotein levels influence leukemia lineage identities. Nat Commun 2024 Oct 29;15(1):9341. doi: 10.1038/s41467-024-53399-8. Abstract | Full text version
  • Fiorenza S, Zheng Y, Purushe J, Bock TJ, Sarthy J, Janssens DH, Sheih AS, Kimble EL, Kirchmeier D, Phi TD, Gauthier J, Hirayama AV, Riddell SR, Wu Q, Gottardo R, Maloney DG, Yang JYH, Henikoff S, Turtle CJ. Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion. Nat Commun. 2024 Sep 27;15(1):8309. doi: 10.1038/s41467-024-52503-2. Abstract | Full text version
  • Dekker J & 4D Nucleome Consortium. An integrated view of the structure and function of the human 4D nucleome. bioRxiv. 2024 Oct 27:2024.09.17.613111. doi: 10.1101/2024.09.17.613111  Abstract | Full text version
  • Showman S, Talbert PB, Xu Y, Henikoff S. Protocol to measure centromeric array size changes using droplet digital PCR-based quantification of higher-order repeats. STAR Protoc. 2024 Jul 27;5(3):103218. Abstract |  Full text version
  • Neefjes J, Gurova K, Sarthy J, Szabó, G, Henikoff S. Chromatin as an old and new anticancer target. Trends in Cancer. doi: 10.1016/j.trecan.2024.05.005 Abstract | Full text version
  • Ahmad K, Brahma S, Henikoff S. Response to ‘‘Learning from chromatin reconstitution: Pioneering factors enabling nucleosome remodelers’’ . Molecular Cell 2024 May 1. Abstract | Full text version
  • Showman S, Talbert PB, Xu Y, Adeyemi RO, Henikoff S. Expansion of human centromeric arrays in cells undergoing break-induced replication. Cell Rep. 2024 Feb 29;43(3):113851. Abstract | Full text version
  • Jaeger-Ruckstuhl CA, Lo Y, Fulton E, Waltner OG, Shabaneh TB, Simon S, Muthuraman PV, Correnti CE, Newsom OJ, Engstrom IA, Kanaan SB, Bhise SS, Peralta JMC, Ruff R, Price JP, Stull SM, Stevens AR, Bugos G, Kluesner MG, Voillet V, Muhunthan V, Morrish F, Olson JM, Gottardo R, Sarthy JF, Henikoff S, Sullivan LB, Furlan SN, Riddell SR. Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks. Immunity 2024 Feb 13;57(2):287-302.e12.  Abstract | Full text version
  • Brahma S, Henikoff S. The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes. Nature Genetics 2024 Jan;56(1):100-111.  Abstract | Full text version. News&Views: Chick BY, Hargreaves DC. RNA polymerase II promoter-proximal pausing promotes BAF chromatin binding and remodeling. Nature Genetics 2024 Jan;56(1):19-20. Abstract | Full text version
  • Ahmad K, Brahma S, Henikoff S. Epigenetic pioneering by SWI/SNF family remodelers. Molecular Cell 2024 Jan 18;84(2):194-201. Abstract | Full text version
  • Janssens DH, Greene JE, Wu SJ, Codomo CA, Minot SS, Furlan SN, Ahmad K, Henikoff S. Scalable single-cell profiling of chromatin modifications with sciCUT&Tag. Nature Protocols 2024 Jan;19(1):83-112. Abstract | Full text version

2023

  • Anderson J, Henikoff S, Ahmad K. Chromosome-specific maturation of the epigenome in the Drosophila male germline. eLife 2023 Nov 30:12:RP89373. doi: 10.7554/eLife.89373. Abstract | Full text version
  • Talbert PB, Henikoff S, Armache K-J Giant variations in giant virus genome packaging Trends in Biochemical Sciences 2023  Abstract | Full text version
  • Henikoff S, Henikoff JG, Ahmad K, Paranal RM, Janssens DH, Russell ZR, Szulzewsky F, Kugel S, Holland EC. Epigenomic analysis of Formalin-Fixed Paraffin-Embedded samples by CUT&Tag. Nature Communications 2023 14:5930  Abstract | Full text version
  • Henikoff S. The epigenetic landscape: An evolving concept. Frontiers in Epigenetics and Epigenomics 2023 1:1176449 Full text version
  • Leichter S, Henikoff S. β-catenin repositions over time. 2023 Cell Syst. Jul 19;14(7):549-550. Abstract | Full text version
  • Wooten M, Takushi B, Ahmad K, Henikoff S. Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters. Sci Adv. 2023 Jun 16;9(24):eadg3257. Abstract | Full text version
  • Jana S, Brahma S, Arora S, Wladyka CL, Hoang P, Blinka S, Hough R, Horn JL, Liu Y, Wang LJ, Depeille P, Smith E, Montgomery RB, Lee JK, Haffner MC, Vakar-Lopez F, Grivas P, Wright JL, Lam HM, Black PC, Roose JP, Ryazanov AG, Subramaniam AR, Henikoff S, Hsieh AC. Transcriptional-translational conflict is a barrier to cellular transformation and cancer progression. Cancer Cell. 2023 Apr 13:S1535-6108(23)00094-6. doi: 10.1016/j.ccell.2023.03.021. Abstract | Full text version
  • Hsieh E, Janssens DH, Paddison PJ, Browne EP, Henikoff S, OhAinle M, Emerman M. A modular CRISPR screen identifies individual and combination pathways contributing to HIV-1 latency. PLoS Pathog. 2023 Abstract | Full text version
  • Islam Z, Saravanan B, Walavalkar K, Farooq U, Singh AK, Radhakrishnan S, Thakur J, Pandit A, Henikoff S, Notani D. Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries. Genome Res. Jan;33(1):1-17, 2023  Abstract | Full text version

2022

  •  Ahmad K, Henikoff S. The Drosophila embryo as a tabula rasa for the epigenome. Faculty Reviews, Dec 23;11:40, 2022 Abstract | Full text version
  • Talbert PB, Henikoff S.Centromere drive: chromatin conflict in meiosis. Current Opinion in Genetics and Development, Dec;77:102005, 2022 Abstract | Full text version
  • Bryson TD, De Ioannes P, Valencia-Sánchez MI, Henikoff JG, Talbert PB, Lee R, La Scola B, Armache KJ, Henikoff S. A giant virus genome is densely packaged by stable nucleosomes within virions. Molecular Cell, Dec 1;82(23):4458-4470.e5, 2022 Abstract  | Full text version | Preview
  • Meers MP, Llagas G, Janssens, DH, Codomo CA, Henikoff S. Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag. Nature Biotechnology. 2022 Abstract | Full text version | Research Briefing
  • Khyzha N, Henikoff S, Ahmad K. Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation. Nature Methods, Nov;19(11):1383-1392, 2022 Abstract | Full text version  | Research Briefing
  • Henikoff S, Ahmad K. In situ tools for chromatin structural epigenomics. Protein Science Nov;31(11):e4458, 2022 Abstract | Full text
  • De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Nucleosome patterns in circulating tumor DNA reveal transcriptional regulation of advanced prostate cancer phenotypes. Cancer Discovery, Nov 18:CD-22-0692, 2022 | Abstract | Full text version
  • Talbert PB, Henikoff S. Centromeres organize (epi)genetic architecture. Cell, 185:3083-5, 2022. Abstract | Full text version  
  • Talbert PB, Armache KJ, Henikoff S. Viral histones: pickpocket's prize or primordial progenitor? Epigenetics Chromatin, May 28;15(1):21, 2022. Abstract | Full text version
  • Brahma, Henikoff S. CUT&RUN Profiling of the Budding Yeast Epigenome. In: Devaux F. (eds) Yeast Functional Genomics. Methods in Molecular Biology, vol 2477. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2257-5_9. Abstract | Full text version
  • Talbert PB, Henikoff S. The genetics and epigenetics of satellite centromeres. Genome Research, Apr;32(4):608-615, 2022 Abstract | Full text version
  • Ahmad K, Henikoff S, Ramachandran S. Managing the Steady State Chromatin Landscape by Nucleosome Dynamics. Annu Rev Biochem, Jun 21;91:183-195, 2022. Abstract | Full text version  
  • Janssens DH, Otto DJ, Meers MP, Setty M, Ahmad K, Henikoff S. CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells. Genome Biol. 2022 Mar 17;23(1):81. Abstract | Full text version
  • Thirmanne HN, Wu F, Janssens DH, Swanger J, Diab A, Feldman H, Amezquita RA, Gottardo R, Paddison PJ, Henikoff S, Clurman BE. Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations. Elife. 2022 Feb 28;11:e74338. Abstract | Full text version

2021

  • Bartlett DA, Dileep V, Handa T, Ohkawa Y, Kimura H, Henikoff S, Gilbert DM. High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq). J Cell Biol. 2021 Dec 6;220(12):e202103078. Abstract | Full text version
  • Janssens DH, Meers MP, Wu SJ, Babaeva E, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S. Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia Nat Genet. 2021. Abstract | Full text version
  • Ahmad K and Henikoff S. The H3.3K27M oncohistone antagonizes reprogramming in Drosophila. PLoS Genetics 17:e1009225. Abstract | Full text version
  • Henikoff S, Henikoff JG, Ahmad K, Simplified Epigenome Profiling Using Antibody-tethered Tagmentation. bio-protocol 11(11), June 05, 2021 Abstract | Full text version
  • Valencia-Sánchez MI, Abini-Agbomson S, Wang M, Lee R, Vasilyev N, Zhang J, De Ioannes P, La Scola B, Talbert P, Henikoff S, Nudler E, Erives A, Armache KJ. The structure of a virus-encoded nucleosome. Nat Struct Mol Biol. 2021 Apr 29. doi: 10.1038/s41594-021-00585-7. Abstract | Full text version
  • Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci. 2021 Apr 21;22(9):4309. Abstract | Full text version
  • Wu SJ, Furlan SN, Mihalas AB, Kaya-Okur HS, Feroze AH, Emerson SN, Zheng Y, Carson K, Cimino PJ, Keene CD, Sarthy JF, Gottardo R, Ahmad K, Henikoff S, Patel AP. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat Biotechnol. 2021 Apr 12. doi: 10.1038/s41587-021-00865-z. Abstract | Full text version
  • Talbert PB, Henikoff S. Remodeler-variant tag team slams transposons. Nat Cell Biol. 2021 Apr;23(4):297-298. Abstract | Full text version
  • Talbert PB, Henikoff S. The yin and yang of histone marks in transcription. Ann Rev Genomics Hum Genet. 2021 Mar 29. doi: 10.1146/annurev-genom-120220-085159. Abstract | Full text version
  • Talbert PB, Henikoff S. Histone variants at a glance. J Cell Sci. Mar 26;134(6):jcs244749. doi: 10.1242/jcs.244749. Abstract | Full text version
  • Zentner GE, Policastro RA and Henikoff S. ChEC-seq produces robust and specific maps of transcriptional regulators. bioRxiv 2021.02.11.430831 Full text version
  • Chew GL, Bleakley M, Bradley RK, Malik HS, Henikoff S, Molaro A, Sarthy J Short H2A histone variants are expressed in cancer Nat Commun 12:490 https://doi.org/10.1038/s41467-020-20707-x Abstract | Full text version

2020

  • Molaro A, Wood AJ, Janssens D, Kindelay SM, Eickbush MT, Wu S, Singh P, Muller CH, Henikoff S, Malik HS, PLoS Biol. 2020 Dec 23;18(12):e3001001  Abstract | Full text version
  • Henikoff S, Henikoff JG, Kaya-Okur HS, Ahmad K, Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation. eLife 2020 Nov 16 9:e63274 Abstract | Full text version
  • Fang H, Bonora G, Lewandowski JP, Thakur J, Filippova GN, Henikoff S, Shendure J, Duan, Z  Rinn JL, Deng X, Noble WS, Disteche CM. Trans- and cis-acting effects of the lncRNA Firre on epigenetic and structural features of the inactive X chromosome. Nat Commun. 2020 Nov 27;11(1):6053. Abstract | Full text version
  • Kaya-Okur HS, Janssens DH, Henikoff JG, Ahmad K, Henikoff S, Efficient low-cost chromatin profiling with CUT&Tag. Nat Protoc. 2020 Sep 10. doi: 10.1038/s41596-020-0373-x Abstract | Full-text version
  • Sarthy JF, Meers MP, Janssens DH, Henikoff JG, Feldman H, Paddison PJ, Lockwood CM, Vitanza NA, Olson JM, Ahmad K, Henikoff S, Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones. Elife. 2020 Sep 9;9:e61090. doi: 10.7554/eLife.61090. Abstract | Full-text version
  • Thakur J, Henikoff S, Architectural RNA in chromatin organization. Biochem Soc Trans. 2020 Sep 8:BST20191226. doi: 10.1042/BST20191226. Abstract | Full-text version
  • Henikoff S, Ahmad K, Evolution: Heterochromatin diversity in early-branching land plants. Curr Biol. 2020 Feb 24: 30(4); R161-R163. Abstract | Full-text version
  • Zeineldin M, Federico S, Chen X, Fan Y, Xu B, Stewart E, Zhou X, Jeon J, Griffiths L, Nguyen R, Norrie J, Easton J, Mulder H, Yergeau D, Liu Y, Wu J, Van Ryn C, Naranjo A, Hogarty MD, Kamiński MM, Valentine M, Pruett-Miller SM, Pappo A, Zhang J, Clay MR, Bahrami A, Vogel P, Lee S, Shelat A, Sarthy JF, Meers MP, George RE, Mardis ER, Wilson RK, Henikoff S, Downing JR, Dyer MA, MYCN amplification and ATRX mutations are incompatible in neuroblastoma.  Nat Commun. 2020 Feb 14; 11(1): 913.  Abstract | Full-text version
  • Talbert PB, Henikoff S, What makes a centromere? Exp Cell Res 2020 Apr 15; 389(2): 111895. Abstract | Full-text version
  • Brahma S, Henikoff S. Epigenome Regulation by Dynamic Nucleosome Unwrapping. Trends Biochem Sci. 2020 Jan; 45(1):13-26 Abstract | Full-text version

2019

  • Thakur J, Fang H, Llagas T, Disteche CM, Henikoff S. Architectural RNA is required for heterochromatin organization. bioRxiv doi.org/10.1101/784835 Full-text version.
  • Resnick R, Wong CJ, Hamm DC, Bennett SR, Skene PJ, Hake SB, Henikoff S, van der Maarel S, Tapscott SJ. DUX4-Induced Histone Variants H3.X and H3.Y Mark DUX4 Target Genes for Expression. Cell Reports 29(7):1812–1820. Abstract | Full-text version
  • Sarthy JF, Henikoff S. Bringing oncohistones into the fold. Cancer Discovery 9(10):1346-1348. Abstract | Full-text version
  • Drinnenberg IA, Berger F, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. EvoChromo: towards a synthesis of chromatin biology and evolution. Development. 2019 Sep 26;146(19) Abstract | Full-text version
  • Chereji RV, Bryson TD, Henikoff S. Quantitative MNase-seq accurately maps nucleosome occupancy levels. Genome biology 20 (1), 1-18. Abstract | PDF
  • Henikoff S, Ahmad K. Nucleosomes remember where they were. Proceedings of the National Academy of Sciences, 201914581. Full-text version
  • H Mathsyaraja, B Freie, PF Cheng, E Babaeva, JT Catchpole, D Janssens, Henikoff S, Eisenman RN. Max deletion destabilizes MYC protein and abrogates Eµ-Myc lymphomagenesis. Genes & Development 33 (17-18), 1252-1264. Abstract | Full-text version
  • Meers MP, Tenenbaum D, Henikoff S. Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling. Epigenetics & chromatin 12 (1), 42 Abstract | Full-text version
  • Meers MP, Janssens DJ, Henikoff S. Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded. Mol Cell. 75(3):562-575.e5. Abstract | Full-text version
  • Meers MP, Bryson T, Henikoff JG, Henikoff S. Improved tools for CUT&RUN chromatin profiling. eLife 8:e46314 Abstract | Full-text version
  • Kaya-Okur HS, Wu SJ, Codomo CA, Pledger ES, Bryson TD, Henikoff JG, Ahmad K, Henikoff S.  CUT&Tag for efficient epigenomic profilling of small samples and single cells.  Nat Commun. Apr 29 10: (1) :1930 Abstract | PDF
  • Brahma S, Henikoff S. RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast. Mol Cell. 17;73(2):238-249.e3. Abstract | Full-text version
  • Sarthy JF, Henikoff S, Ahmad K. Chromatin bottlenecks in cancer.  Trends Cancer. Mar;5(3):183-194. Abstract | PDF
  • Talbert PB, Meers MP, Henikoff S. Old cogs, new tricks: the evolution of gene expression in a chromatin context. Nat Rev Genet doi: 10.1038/s41576-019-0105-7 Abstract | PDF

2018

  • Janssens DH, Wu SJ, Sarthy JF, Meers MP, Myers CH, Olson JM, Ahmad K, Henikoff S. Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs. Epigenetics Chromatin. 2018 Dec 21;11(1):74. PMID:30577869 Abstract | Full-text version
  • Ahmad K, Henikoff S. No strand left behind. Science. 2018 Sep 28;361(6409):1311-1312. doi: 10.1126/science.aav0871. Link
  • Ramachandran S, Henikoff S. MINCE-Seq: Mapping In Vivo Nascent Chromatin with EdU and Sequencing.  Methods Mol Biol. 2018;1832:159-168. doi: 10.1007/978-1-4939-8663-7_8. PMID: 30073526 Full-text version
  • Henikoff S, Ramachandran S. Pioneers Invade the Nucleosomal Landscape. Mol Cell. 2018 Jul 19;71(2):193-194. doi: 10.1016/j.molcel.2018.07.004 PMID 30028998 Full-text version
  • Henikoff S Darwin meets Waddington. Current Biol. 2018 12:R682-4 Full-text version
  • Talbert PB and Henikoff S. Transcribing centromeres: Nocoding RNAs and kinetochore assembly. Trends Genet. 2018 doi: 10.1016/j.tig.2018.05.001. Abstract | Full-text version
  • Henikoff S and Church GM. Simultaneous discovery of cell-free DNA and the nucleosome ladder. Genetics 2018 209:27-29. Full-text version
  • Skene PJ, Henikoff JG and Henikoff S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protocols 2018 13:1006-1019. Abstract | Full-text version
  • Chereji RV, Ramachandran S, Bryson TD, Henikoff S. Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biol. 2018 Feb 9;19(1):19. Abstract | Full-text version
  • Thakur J and Henikoff S. Unexpected conformational variations of the human centromeric chromatin complex. Genes Dev 2018 doi: 10.1101/gad.307736.117. Abstract | Full-text version
  • Kasinathan S and Henikoff S. Non-B-form DNA structures mark centromeres. Mol Biol Evol. 2018 Jan 22. doi: 10.1093/molbev/msy010. Abstract | Full-text version
  • Talbert PB, Kasinathan S and Henikoff S. Simple and Complex Centromeric Satellites in Drosophila Sibling Species. Genetics 2018 doi: 10.1534/genetics.117.300620. Abstract | Full-text version

2017

  • Ramachandran S, Ahmad K and Henikoff S. Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell 2017 https://doi.org/10.1016/j.molcel.2017.11.015. PDF (20.7M)
  • Henikoff S, Thakur J, Kasinathan S and Talbert PB. Remarkable evolutionary plasticity of centromeric chromatin. Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXXI 2017 doi: 10.1101/sqb.2017.82.033605. Abstract | PDF (856k)
  • Henikoff S. Structural biology: Probing the origin of chromatin. Current Biology 27:R1118-1120. Abstract | PDF (706k)
  • Skene PJ and Henikoff S. CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers. biorxiv 2017 https://doi.org/10.1101/193219. Abstract | PDF (6.3M)
  • Kasinathan S, Zentner GE, Kasinathan S, Xin B, Rohs R and Henikoff S. Correspondence: Reply to 'DNA shape is insufficient to explain binding. Nat Commun. 2017 Jun 5;8:15644. Full-text version
  • Ramachandran S, Ahmad K and Henikoff S. Capitalizing on disaster: Establishing chromatin specificity behind the replication fork. Bioessays 2017 doi: 10.1002/bies.201600150.
    Abstract | PDF (922k)
  • Skene PJ and Henikoff S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 2017: 6:e21856 doi: 10.7554/eLife.21856.
    Abstract | PDF (28M)

2016

  • Talbert PB and Henikoff S Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 2016 18: 115-126 doi: 10.1038/nrm.2016.148. Abstract | PDF (640k)
  • Gruenberg S, Henikoff S, Hahn S & Zentner GE. Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters EMBO J. 22016 Nov 15;35(22):2435-2446. Abstract | PDF (1.6M)
  • Henikoff S. Mechanisms of nucleosome dynamics in vivo. Cold Spring Harb Perspect Med 2016 doi: 10.1101/cshperspect.a026666. Abstract | Full-text version
  • Henikoff S and Greally JM. Epigenetics, cellular memory and gene regulation. Current Biol 2016 26:R641-666. Abstract | PDF (618k)
  • Thakur J and Henikoff S CENPT bridges adjacent CENPA nucleosomes on young human α-satellite dimers. Genome Res. 2016 Jul 6. pii: gr.204784.116. Abstract | Full-text version
  • Ramachandran S and Henikoff S Transcriptional regulators compete with nucleosomes post-replication. Cell 2016 165(3):180-192. Abstract | PDF (5M)
  • Ramachandran S and Henikoff S Nucleosome dynamics during chromatin remodeling in vivo. Nucleus 2016 7:1,20-26. Abstract | Full-text version
  • Drinnenberg IA, Henikoff S and Malik HS Evolutionary turnover of kinetochore proteins: A Ship of Theseus? Trends Cell Biol 2016 doi: 10.1016/j.tcb.2016.01.005. Abstract | PDF (2M)

2015

  • Zentner GE, Kasinathan S, Xin B, Rohs R and Henikoff S ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nature Communications 2015 6:8733. Abstract | Full-text version
  • Thakur J, Talbert PB and Henikoff S Inner kinetochore protein interactions with regional centromeres of fission yeast. Genetics 2015 201:543-601. Abstract | Full-text version
  • Ramachandran S and Henikoff S Replicating nucleosomes. Science Advances 2015 1:e1500187. Abstract | Full-text version
  • Henikoff S The genetic map enters its second century. Genetics 2015 200:671-674. Abstract | Full-text version
  • Skene PJ and Henikoff S A simple method for generating high-resolution maps of genome wide protein binding. eLife 2015 Jun 16:e09225. Abstract | Full-text version
  • Henikoff S Epigenomic landscapes reflect neuronal diversity. Neuron 2015 86:1319-1321. Abstract | PDF (655k)
  • Zentner GE and Henikoff S Epigenomic editing made easy. Nature Biotech 2015 33:606-607. PDF (358k)
  • Steiner F and Henikoff S Diversity in the organization of centromeric chromatin. Curr Opin Genet Dev 2015 31:28-35. Abstract | PDF (772k)
  • Williams BP, Pignatta D, Henikoff S and Gehring M Methylation-sensitive expression of a DNA demethylase gene serves as an epigenetic rheostat. Plos Genetics 2015 11(3):e1005142. Abstract | Full-text version
  • Orsi GA, Kasinathan S, Zentner GE, Henikoff S and Ahmad K Mapping regulatory factors by immunoprecipitation from native chromatin. Curr Protoc Mol Biol 2015 110:21.31.1-21.31.25. Abstract | PDF (971k)
  • Henikoff JG, Thakur J, Kasinathan S and Henikoff S A unique chromatin complex occupies young α-satellite arrays of human centromeres. Science Advances 2015 1:e1400234. Abstract | Full-text version
  • Yang F, Kemp CJ and Henikoff S Anthracyclines induce double-strand breaks at active gene promoters. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 2015 773:9-15. Abstract | PDF (3.7M)
  • Henikoff S and Smith MM Histone variants and epigenetics. Cold Spring Harb Perspect Biol 2015:7:a019364. Abstract | Publisher PDF | Additional PDF (2M)
  • Ramachandran S, Zentner G and Henikoff S Asymmetric nucleosomes flank promoters in the budding yeast genome. Genome Res 2015 doi: 10.1101/gr.182618.114. Abstract | Full-text version
  • Steiner FA and Henikoff S Cell type-specific affinity purification of nuclei for chromatin profiling in whole animals. Methods Mol Biol. 2015 1228:3-14. Abstract | PDF (357k)

2014

  • Teves SS, Weber, CM and Henikoff S Transcribing through the nucleosome. Trends Bio Sci 2014 39:577-86. Abstract | PDF (363k)
  • Kasinathan S and Henikoff S 5-Aza-CdR delivers a gene body blow. Cancer Cell 2014 26:449-51. Abstract | PDF (363k)
  • Zentner GE and Henikoff S High-resolution digital profiling of the epigenome. Nat Rev Genet 2014 doi: 10.1038/nrg3798. Abstract | PDF (1M)
  • Drinnenberg IA, deYoung D, Henikoff S, Malik HS Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. eLife 2014 3:03676. Abstract | Full-text version
  • Talbert PB and Henikoff S Environmental responses mediated by histone variants. Trends Cell Biol. 2014 doi: 10.1016/j.tcb.2014.07.006. Abstract | PDF (605k)
  • Skene PJ and Henikoff S Histones push the envelope.  Nat. Struct. Mol. Biol. 2014 21:651-2. Abstract | PDF (358k)
  • Teves S and Henikoff S DNA torsion as a feedback mediator of transcription and chromatin dynamics. Nucleus 2014 5 epub. Abstract | Full-text version
  • Skene PJ, Hernandez AE, Groudine M and Henikoff S The nucleosomal barrier to promoter escape by RNA Polymerase II is overcome by the chromatin remodeler Chd. eLife 2014 3:e02042. Abstract | Full-text version
  • Steiner FA and Henikoff S Holocentromeres are dispersed point centromeres localized at transcription factor hotspots. eLife 2014 3:e02025. Abstract | Full-text version
  • Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang J-P and Henikoff JG The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. eLife 2014 3:e01861. Abstract | Full-text version
  • Weber CM and Henikoff S Histone variants: dynamic punctuation in transcription. Genes Dev. 28:672-82. Abstract | Full-text version
  • Orsi GA, Kasinathan S, Hughes KT, Saminadin-Peter S, Henikoff S and Ahmad K High-resolution mapping defines the cooperative architecture of Polycomb response elements. Genome Res. 24:809-820. Abstract | PDF (2.4M)
  • Weber CM, Ramachandran S and Henikoff S Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Molecular Cell 2014, 53:819-830. Abstract | PDF (2.8M)
  • Krassovsky K and Henikoff S Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster. BMC Genomics 2014 15:105. Abstract | Full-text version
  • Codomo CA, Furuyama T and Henikoff S CENP-A octamers do not confer a reduction in nucleosome height by AFM. Nat. Struct. Mol. Biol. 2014 21:4-5. Abstract | PDF (442k)
  • Yang F, Teves SS, Kemp CJ and Henikoff S Doxorubicin, DNA torsion and chromatin dynamics. BBA Reviews Cancer Dec 19, 2013 1845:84-9. Abstract | PDF (576k)
  • Kasinathan S, Orsi GA, Zentner GE, Ahmad K and Henikoff S High-resolution mapping of transcription factor binding sites on native chromatin. Nature Methods 2014 11:203-209. Abstract | PDF (1.1M)
  • Teves SS and Henikoff S Transcription-generated torsional stress destabilizes nucleosomes. Nat. Struct. Mol. Biol. 2014 21:88-94. Abstract | PDF (2.1M)

2013

  • Zhang T., Talbert PB, Zhang W, Wua Y, Yang Z, Henikoff JG, Henikoff S and Jiang J. The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proc Natl Acad Sci USA 2013 110E4875-83. Abstract | Full-text version
  • Zentner GE and Henikoff S. Mot1 redistributes TBP from TATA-containing to TATA-less promoters. Mol Cell Biol. 2013 33:4996-5004. Abstract | PDF (1008k)
  • Talbert PB and Henikoff S. Phylogeny as the basis for naming histones. Trends Genet. 2013 29:499-500. PDF (115k)
  • Skene P and Henikoff S. Histone variants in pleuripotency and disease. Development. 2013 Jun;140(12):2513-2524. Abstract | PDF (475k)
  • Furuyama T, Codomo, CA and Henikoff S. Reconstitution of hemisomes on budding yeast centromeric DNA. Nucl. Acids Res. (2013) doi: 10.1093/nar/gkt314. Abstract | Full-text version
  • Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. Sixty years of genome biology. Genome Biol. 2013 Apr 25;14(4):113. Abstract | Full-text version
  • Yang F, Kemp CJ and Henikoff S. Doxorubicin enhances nucleosome turnover around promoters. Curr Biol. 2013 May 6;23(9):782-7. Abstract | PDF (632k)
  • Zentner GE, Tsukiyama T and Henikoff S. ISWI and CHD Chromatin remodelers bind promoters but act in gene bodies. PLoS Genet. 2013 Feb;9(2):e1003317. Abstract | Full-text version
  • Zentner GE and Henikoff S. Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol. 2013 Mar;20(3):259-66. Abstract | PDF (1.4M)
  • Henikoff S and Grosveld F. Epigenetics and chromatin: Interactions and processes. Epigenetics Chromatin. 2013 Feb 27;6(1):2. Abstract | Full-text version
  • Teves SS and Henikoff S. The heat shock response: A case study of chromatin dynamics in gene regulation. Biochem Cell Biol. 2013 Feb;91(1):42-8. Abstract | PDF (1.2M)
  • Cooper JL, Henikoff S, Comai L, Till BJ. TILLING and Ecotilling in rice. Methods Mol Biol. 2013 956:39-56. Abstract | PDF (382k)

2012

  • Talbert PB and Henikoff S. Chromatin: Packaging without nucleosomes. Curr Biol. 2012 Dec 18;22(24):R1040-3. Abstract | Full-text version
  • Skene P and Henikoff S. Chromatin roadblocks to reprogramming 50 years on. BMC Biol. 10:83, 2012. Abstract | Full-text version
  • Zentner G and Henikoff S. Surveying the epigenomic landscape, one base at a time. Genome Biol. 13:250, 2012. Abstract | PDF (2.4M)
  • Teves SS, Deal RB and Henikoff S. Measuring genome-wide nucleosome turnover using CATCH-IT. Methods Enzymol. 513:169-84, 2012. Abstract | PDF (1.1M)
  • 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 (2012) A unified phylogeny-based nomenclature for histone variants. Epigenetics Chromatin 5(1):7. Abstract | Full-text version
  • Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC. SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res. 2012 Jun 11. Abstract | Full-Text version
  • Henikoff S and Furuyama T. The unconventional structure of centromeric nucleosomes. Chromosoma (DOI) 10.1007/s00412-012-0372-y, 2012. Abstract | Full-text version
  • Henikoff S and Henikoff JG. "Point" centromeres of Saccharomyces harbor single centromere-specific nucleosomes. Genetics 190(4):1575-7, 2012. Abstract | Full-text version
  • Henikoff S. Chromatin process, epigenetic inheritance, centromere structure and function and evolution. Current Biology 2012 22(4):R106-7. PDF (70k)
  • Steiner FA, Talbert PB, Kasinathan S, Deal RB, Henikoff S. Cell type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res. 22:766-77, 2012. Abstract | Full-text version
  • Teves SS and Henikoff S. Salt fractionation of nucleosomes for genome-wide profiling. Methods Mol Biol. 2012 833:421-32. Abstract | PDF (425k)
  • Krassovsky K, Henikoff JG and Henikoff S. Tripartite organization of centromeric chromatin in budding yeast. Proc Natl Acad Sci U S A. 2012 109(1):243-8. Abstract | Full-text version

2011

  • Teves SS and Henikoff S. Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. Genes Dev. 2011 Nov 15;25(22):2387-2397. Abstract | Full-text version
  • Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM and Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18318-23. Abstract | Full-text version
  • Gehring M, Missirian V and Henikoff S. Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds. PLoS One 2011 6(8): e23687. Abstract | Full-text version
  • Henikoff S and Shilatifard A. Histone modifications: Cause or cog? Trends Genet. 2011 27:389-96. Abstract | PDF (127k)
  • Henikoff S. Summary: The nucleus - A close-knit community of dynamic structures. Cold Spring Harbor Symp Quant Biol. 2011 75:607-615. Abstract | PDF (127k)
  • Deal RB and Henikoff S. Histone variants and modifications in plant gene regulation. Curr Opin Plant Biol. 2011 14:116-22. Abstract | PDF (209k)
  • Deal RB and Henikoff S. The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana. Nature Protocols 2011 6:56-68. Abstract | PDF (610k)

2010

  • Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, Maccoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. Science 2010 330:1775-1787. Abstract | Full-text version
  • The modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, Macalpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, Macalpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010 330:1787-97. Abstract | Full-text version
  • Weber CM, Henikoff JG and Henikoff S. H2A.Z nucleosomes enriched over active genes are homotypic. Nature Struct Mol Biol 2010 Dec;17(12):1500-7. Abstract | PDF (688k)
  • Henikoff S and Furuyama T. Epigenetic inheritance of centromeres. Cold Spring Harbor Symp Quant Biol. 2010 75:978-1-936113-07-1. Abstract | PDF (4.8M)
  • Deal RB and Henikoff S. Chromatin dynamics and the regulation of genome function. Genome Biol. 2010 11:218. Abstract | Full-text version
  • Conerly ML, Teves SS, Diolaiti D, Ulrich M, Eisenman RN and Henikoff S. Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis. Genome Res. 2010 Oct;20(10):1383-90. Abstract | Full-text version
  • Deal RB and Henikoff S. Catching a glimpse of nucleosome dynamics. Cell Cycle 2010 9(17):3389-90. Full-text version
  • Deal RB and Henikoff S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 2010 18:1030-40. Video abstract | PDF (1.9M)
  • Deal RB, Henikoff JG and Henikoff S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 2010 238:1161-1164. Abstract | PDF (1.9M)
  • Bryson TD, Weber CM and Henikoff S. Baculovirus-encoded protein expression for epigenomic profiling in Drosophila cells. Fly 2010 DOI: 10.4161/fly.4.3.12177. Abstract | PDF (651k)
  • Talbert PB and Henikoff S. Histone variants - ancient wrap artists of the genome. Nat Rev Mol Cell Biol 2010 11:256-75. Abstract | PDF (738k)
  • Talbert PB and Henikoff S. Centromeres convert but don't cross. PLoS Biol 2010 8(3):e1000326. Full-Text version
  • Deal RB and Henikoff S. A chromatin thermostat. Nature 2010 463:887-88. PDF (1100k)
  • Nègre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, Henikoff JG, Feng X, Ahmad K, Russell S, White RA, Stein L, Henikoff S, Kellis M, White KP. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 2010 Jan 15;6(1):e1000814. Abstract | Full-Text version
  • Ooi SL, Henikoff JG and Henikoff S. A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans. Nucleic Acids Res. 2010 38:e26. Abstract | Full-Text version

2009

  • Malik HS and Henikoff S. Major evolutionary transitions in centromere complexity. Cell 2009 138:1067-1082. Abstract | PDF (1900k)
  • Furuyama T and Henikoff S. Centromeric nucleosomes induce positive DNA supercoils. Cell 2009 138:104-113; Lavelle et al. Letter to the Editor, Furuyama and Henikoff Response. Cell 2009 139:1216-18. Abstract | PDF (1200k)
  • Henikoff S and Grosveld F. Epigenetics & Chromatin celebrates its first anniversary.  Epigenetics Chromatin 2009 2:13. Full-Text version
  • Henikoff S. Labile H3.3+H2A.Z nucleosomes mark 'nucleosome-free regions'. Nat Genet. 2009 41:855-56. Abstract | PDF (273k)
  • Kumar P., Henikoff S. and Ng, PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009 4:1073-81. Abstract | PDF (1000k)
  • De Bustos C, Ramos E, Young JM, Tran RK, Menzel U, Langford CF, Eichler EE, Hsu L, Henikoff S, Dumanski JP, Trask BJ. Tissue-specific variation in DNA methylation levels along human chromosome 1. Epigenetics Chromatin. 2009 Jun 8;2(1):7. Full-Text version
  • Gehring M, Bubb K and Henikoff S. Extensive demethylation of repetitive elements during seed development  underlies gene imprinting. Science 2009 324:1447-51. Abstract | PDF (860k)
  • Talbert PB and Henikoff S. Chromatin-based transcriptional punctuation. Genes Dev. 2009 23:1037-41. Full-Text version
  • Gehring M, Reik W, Henikoff S. DNA methylation by DNA repair. Trends Genet. 2009 25:82-90. Abstract | PDF (712k)
  • Henikoff S, Henikoff JG, Sakai A, Loeb GB and Ahmad K. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res. 2009 Mar;19(3):460-9. Abstract | Full-Text version
  • Henikoff, S. (2009) Epigenetic profiling of histone variants, in "Epigenomics" Eds. Ferguson-Smith A, Greally JM and Martienssen RA, Springer pp. 101-118.
  • Talbert PB, Bayes J and Henikoff, S. (2009) Evolution of centromeres and kinetochores: A two-part fugue. in "The Kinetochore" Eds. DeWulf P and Earnshaw WC., Springer, pp. 193-230. PDF (784k)
  • Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH; modENCODE Consortium. Unlocking the secrets of the genome. Nature. 2009 Jun 18;459(7249):927-30. Abstract | Full-Text version

2008

  • Wang H, Dalal Y, Henikoff S and Lindsay S. Single-epitope recognition imaging of native chromatin. Epigenetics Chromatin 2008 1:10. Full-Text version
  • Cooper JL, Till BJ and Henikoff S. Fly-TILL: Reverse genetics using a living point mutation resource. Fly 2008 2:6; 1-3. Full-Text version
  • Yan H, Talbert PB, Lee, H-R, Jett, J, Henikoff S, Chen F and Jiang J. Intergenic locations of rice centromeric chromatin. PLoS Biol. 2008 6:e286. Full-Text version
  • Henikoff S and Grosveld F. Welcome to Epigenetics & Chromatin. Epigenetics Chromatin 2008 1:1. Full-Text version
  • Henikoff S, Strahl BD and Warburton PE. Epigenomics: Roadmap to chromatin. Science 2008  322:853. PDF (110k)
  • Zilberman D, Coleman-Derr, D, Ballinger, T and Henikoff S. Histone H2A.Z and DNA methylation are mutually exclusive chromatin marks. Nature 2008 456:125-129. Abstract | PDF (980k)
  • Cooper JL, Greene EA, Till BJ, Codomo CA, Wakimoto BT and Henikoff S. Retention of induced mutations in a Drosophila reverse-genetic resource. Genetics 2008 180:661-667. Abstract | PDF (166k)
  • Gehring M and Henikoff S. DNA methylation and demethylation in Arabidopsis. The Arabidopsis Book 2008 DOI:10.1199/tab.0102. Full-Text version
  • Cooper JL, Till BJ, Laport RG, Darlow MC, Kleffner JM, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, Bilyeu KD, Meksem K, Comai L and Henikoff S. TILLING to detect induced mutations in soybean. BMC Plant Biol. 2008 Jan 24;8(1):9. Abstract | Full-Text version
  • Henikoff S. Nucleosome destabilization in the epigenetic regulation of gene expression. Nature Reviews Genetics 2008 Jan;9(1):15-26. Abstract | PDF (1200k)

2007

  • Henikoff S. Nucleosomes at active promoters: unforgettable loss. Cancer Cell 2007 12(5):407-09. Abstract | PDF (257k)
  • Zilberman D and Henikoff S. Genome-wide analysis of DNA methylation patterns. Development 134:3959-65. Abstract | PDF (324k)
  • Dalal Y, Furuyama T, Vermaak D and Henikoff S. Structure, dynamics and evolution of centromeric nucleosomes. Proc. Natl. Acad. Sci. USA 2007  2007 104(41):15974-81. Abstract | Full-Text version
  • Dalal Y, Wang H, Lindsay S and Henikoff S. Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol. 2007 Aug;5(8):e218. Abstract | Full-Text version
  • Henikoff S. ENCODE and our very busy genome. Nat Genet. 2007 Jul;39(7):817-8. Abstract | PDF (198k)
  • Ooi SL Henikoff S. Germline histone dynamics and epigenetics. Curr Opin Cell Biol. 2007 Jun;19(3):257-65. Abstract | PDF (592k)
  • Till BJ, Cooper J, Tai TH, Colowit P, Greene EA, Henikoff S and Comai L. Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol. 2007 Apr 11;7(1):19. Abstract | Full-Text version
  • Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S and Fischer RL. DNA demethylation in the Arabidopsis genome. Proc. Natl. Acad. Sci. USA 2007 104(16):6752-7. Abstract | PDF (1600k)
  • Mito Y, Henikoff JG and Henikoff S. Histone replacement marks the boundaries of cis-regulatory domains. Science 2007 315:1408-1411. Abstract | PDF (335k)
  • Gehring M and Henikoff S. DNA methylation dynamics in plant genomes. Biochim. Biophys. Acta 2007 epub. Abstract | PDF (488k)

2006

  • Till BJ, Zerr T, Comai, L and Henikoff S. A protocol for TILLING and Ecotilling in plants and animals. Nature Protocols 2006 1:2465-2477. Abstract | PDF (484k)
  • Zilberman D, Gehring M, Tran RK, Ballinger T and Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet. 2007 Jan;39(1):61-9. Abstract | PDF (1400k)
  • Dawe RK and Henikoff S. Centromeres put epigenetics in the driver's seat. Trends Bio Sci 2006 Dec;31(12):662-9. Abstract | PDF (628k) | Cover art (3200k)
  • Talbert PB and Henikoff S. Spreading of silent chromatin: inaction at a distance. Nat Rev Genet. 2006 Oct;7(10):793-803. Abstract | PDF (730k)
  • Till, BJ, Zerr, T, Bowers, E, Greene, EA, Comai, L and Henikoff S. High-throughput discovery of rarae human nucleotide polymorphisms by Ecotilling. Nucl. Acids Res. 2006 34(13):e99. Abstract | Full-text version
  • Ng, PC, Henikoff S. Predicting the Effects of Amino Acid Substitutions on Protein Function. Annu. Rev. Genomics. Hum. Genet. 2006 7:61-80. Abstract | PDF (276k) | Supplement (79k)
  • Till, BJ, Colbert T, Codomo C, Enns L, Johnson J, Reynolds SH, Henikoff JG, Greene EA, Steine MN, Comai L, Henikoff S. High-throughput TILLING for Arabidopsis. Methods Mol Biol. 2006 323:127-35. Abstract | PDF (2876k)
  • Ooi, SL, Priess, JR and Henikoff S. Histone H3.3 variant dynamics in the germline of Caenorhabditis elegans. PLoS Genet. 2006 2(6):e97. Abstract | Full-text version
  • Furuyama T and Henikoff S. Biotin-tag affinity purification of a centromeric nucleosome assembly complex. Cell Cycle 2006 5(12). Abstract | Full-text version
  • Lieb JD, Beck, S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T and Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenet. Genome Res. 2006 114(1):1-15. Abstract | PDF (384k)
  • Furuyama T, Dalal Y and Henikoff S. Chaperone-mediated assembly of centromeric chromatin in vitro. Proc. Natl. Acad. Sci. USA 2006 103:doi/10.1073. Abstract | Full-text version
  • Comai L and Henikoff S. TILLING: Practical single-nucleotide mutation discovery. Plant J. 2006 45:684-94. Abstract | Full-text version
  • Feinberg AP, Ohlsson R and Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet. 2006 Jan;7(1):21-33. Abstract | PDF (405k)

2005

  • Yan H, Jin W, Nagaki K, Tian S, Ouyang S, Buell CR, Talbert PB, Henikoff S, Jiang J. Transcription and histone modifications in the recombination-free region spanning a rice centromere. Plant Cell. 2005 Dec;17(12):3227-38. Abstract | PDF (336k)
  • Henikoff S. Rapid changes in plant genomes. Plant Cell 2005 17:2852-55. Full-text version
  • Malik HS and Henikoff S. Positive Selection of Iris, a Retroviral Envelope-Derived Host Gene in Drosophila melanogaster. PLoS Genet. 2005 Oct 21;1(4):e44. Abstract | Full-text version
  • Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J., Boyle T, Kwong S, Bryson TD, Jacobsen SE and Henikoff S. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol. 2005 6:R90. Abstract | Full-text version
  • Mito Y, Henikoff JG and Henikoff S. Genome-scale profiling of histone H3.3 replacement patterns. Nat Genet. 2005, Oct;37(10):1090-7. Abstract | PDF (668k) | News & Views
  • Vermaak, D, Henikoff, S and Malik, HS. Positive selection drives the evolution of rhino, a member of the Heterochromatin Protein 1 family in Drosophila. PLoS Genet. 2005 July;1(1)e9. Abstract | Full-text version
  • Henikoff, S, McKittrick E and Ahmad K. Epigenetics, histone H3 variants, and the inheritance of chromatin states. Cold Spring Harb Symp Quant Biol. 2004;69:235-43. PDF (1700k)
  • Zilberman D and Henikoff S. Epigenetic inheritance in Arabidopsis: selective silence. Curr Opin Genet Dev. 2005 Oct;15(5):557-62. Abstract | PDF (138k)
  • Henikoff S and Ahmad K. Assembly of variant histones into chromatin. Ann. Rev. Cell Dev. Biol. 2005 Nov 10;21:133-153. Abstract | PDF (327k)
  • Zerr T and Henikoff S. Automated band mapping in electrophoretic gel images using background information. Nucleic Acids Res. 2005;33(9):2806-2812. Full-text version | GelBuddy website
  • Henikoff S. Histone modifications: combinatorial complexity or cumulative simplicity? Proc. Natl. Acad. Sci. USA. 2005 Apr 12;102(15):5308-09. Abstract | PDF (102k)
  • Henikoff S and Dalal, Y. Centromeric chromatin: what makes it unique? Curr Opin Genet Dev. 2005 Apr;15(2):177-84. Abstract | PDF (183k)
  • Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE and Henikoff S. DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes. Curr Biol. 2005 Jan 26;15(2):154-9. Abstract | PDF (399k)

2004

  • Zilberman D. and Henikoff S. Silencing transposons in plant genomes. Kick them when they're down Genome Biol. 2004 5:249. Abstract | Full text version | PDF (91k)
  • Haig D. and Henikoff S. Genomes and Evolution. Defining the genomic palimpsest. Curr. Opin. Genet. Dev. 2004 Dec;14:599-602. PDF (81k)
  • Talbert PB, Bryson TD and Henikoff S. Adaptive evolution of centromere proteins in plants and animals. J. Biol. 2004 Aug 31; 3:18. Abstract | Full text version | Research news | Minireview
  • Till BJ, Reynolds SH, Weil C, Springer N, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, Greene EA, Comai L and Henikoff S. Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol. 2004 Jul 28; 4:12. Abstract | Full text version | Maize TILLING website
  • Cooper JL and Henikoff S. Adaptive evolution of the histone fold domain in centromeric histones. Mol Biol Evol. 2004 Sep;21(9):1712-8. Abstract | PDF (247k)
  • Henikoff S, Furuyama T and Ahmad K. Histone variants, nucleosome assembly and epigenetic inheritance. Trends Genet. 2004 Jul; 20(7):320-326. Abstract | PDF (985k)
  • Henikoff S, Till BJ and Comai L. TILLING. Traditional Mutagenesis Meets Functional Genomics. Plant Physiol. 2004 Jun; 135(2):630-6. Abstract | PDF (126k) | Seattle TILLING Project website
  • Till BJ, Burtner C, Comai L and Henikoff S. Mismatch cleavage by single-strand specific nucleases. Nucleic Acids Res. 2004;32(8):2632-2641. Abstract | Full text version
  • Henikoff S Visualizing gene expression; an unfolding story. Cell. 2004 Mar 5;116(5):633-4. Abstract | PDF (92k)
  • Jin W, Melo JR, Nagaki K, Talbert PB, Henikoff S, Dawe RK, Jiang J. Maize centromeres: organization and functional adaptation in the genetic background of oat. Plant Cell. 2004 Mar;16(3):571-81. Abstract | PDF (322k)
  • Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff S. Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J. 2004 Mar;37(5):778-86. Abstract | PDF (266k)
  • McKittrick E, Gafken PR, Ahmad K, Henikoff S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc. Natl. Acad. Sci. USA 2004 101(6):1525-30. Abstract | PDF (426k) | Commentary
  • Nagaki K, Cheng Z, Ouyang S, Talbert P, Kim M, Jones KM, Henikoff S, Buell CR and Jiang J. Sequencing of a rice centromere uncovers active genes. Nat. Genet. 2004 Feb: 36(2):138-45. Abstract | PDF (880k) | Minireview

2003

  • Greil F, Van Der Kraan I, Delrow J, Smothers JF, De Wit E, Bussemaker HJ, Van Driel R, Henikoff S, Van Steensel B. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev. 2003 Nov 15;17(22):2825-38. Abstract | PDF (644k)
  • Malik, H.S., Henikoff S. Phylogenomics of the nucleosome. Nature Struct. Biol. 2003 Nov; 10(11):882-91. Abstract | PDF (1379k)
  • van Steensel B., Henikoff S. Epigenomic profiling using microarrays. Biotechniques. 2003 Aug; 35:346-57. Abstract
  • Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003 Jul 1; 31(13):3812-4. Abstract | PDF (301k) | SIFT website
  • Rose, TM, Henikoff JG, Henikoff S. CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res. 2003 Jul 1; 31(13):3763-6. Abstract | PDF (235k) | CODEHOP website
  • Henikoff S. Gene regulation: Versatile assembler. Nature 2003 Jun 19;423:814-817. PDF (185k)
  • Greene EA, Codomo, CA, Taylor, NE, Henikoff, JG, Till BJ, Reynolds, SH, Enns, LC, Burtner, C, Johnson, JE, Odden, AR, Comai, L, Henikoff S. Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics 2003 Jun;164:731-740. Abstract | PDF (162k)
  • Vermaak D, Ahmad K, Henikoff S. Maintenance of chromatin states: An open-and-shut case. Curr. Opin. Cell Biol. 2003 15:266-274. Abstract | PDF (338k)
  • Henikoff S, Comai L. Single-nucleotide mutations for plant functional genomics. Ann. Rev. Plant Biol. 2003 54:375-401. Abstract | PDF (771k)
  • Nagaki K, Talbert PB, Zhong CX, Dawe RK, Henikoff S, Jiang J. Chromatin Immunoprecipitation Reveals That the 180-bp Satellite Repeat Is the Key Functional DNA Element of Arabidopsis thaliana Centromeres. Genetics. 2003 Mar;163(3):1221-5. Abstract | PDF (121k)
  • Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, Henikoff JG, Comai L, Henikoff S. Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res. 2003 Mar;13(3):524-530. Abstract | PDF (526k)
  • Rutherford S, Henikoff S. Quantitative Epigenetics. Nat. Genet. 2003 Jan 1;33(1):6-8. PDF (104k)

2002

  • Ahmad K, Henikoff S. Epigenetic consequences of nucleosome dynamics. Cell 2002 Nov 1;111(3):281-284. Abstract | PDF (77k)
  • Smothers, JF, Henikoff S, Carter, P. Affinity selection from biological libraries. Science 2002 (Oct 18) 298;621-622. Abstract | PDF (564k)
  • Malik, HS, Henikoff S. Conflict begets complexity: the evolution of centromeres. Curr. Opin. Genet. Dev. 2002 November 12;711-718. Abstract | PDF (132k)
  • Vermaak D, Hayden, HS, Henikoff S. Centromere targeting element within the histone fold domain of Cid. Mol. Cell Biol. 2002 November 22;7553-7561. Abstract | PDF (1188k)
  • Ahmad K, Henikoff S. Histone H3 variants specify modes of nucleosome assembly. Proceedings of the National Academy of Sciences of the United States of America. 2002 December 10;99 Suppl 4:16477-84. Abstract | PDF (248k)
  • Talbert P, Masuelli R, Tyagi, AP, Comai, L, Henikoff S. Centromeric localization and adaptive evolution of an Arabidopsis Histone H3 variant. Plant Cell. 2002 May 14;1053-1066. Abstract | PDF (412k)
  • Ahmad K, Henikoff S. The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol. Cell 2002 June;9(6):1191-1200. Abstract | PDF (1200k)
  • Henikoff S, Malik HS. Centromeres: selfish drivers. Nature. 2002 May 16;417:227. PDF (68k)
  • Henikoff S. Near the edge of a chromosome's 'black hole'. Trends Genet. 2002 Apr;18(4):165-67. Abstract | PDF (276k)
  • Ng PC, Henikoff S. Accounting for human polymorphisms predicted to affect protein function. Genome Research 12(3): 436-46, 2002. Abstract | PDF (164k)
  • Henikoff S. Beyond the central dogma. Bioinformatics. 2002 Feb;18(2):233-35.
  • Malik HS, Vermaak D, Henikoff, S. Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone Proc. Natl. Acad. Sci. USA. 2002 Feb;99(3): 1449-54. Abstract | PDF (675k)
  • Tompa R, McCallum CM, Delrow J, Henikoff, JG, van Steensel, B Henikoff, S. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3 Curr Biol. 2002 Jan 8;12(1):65-8. Abstract | PDF (128k)
  • Borodin PM; Henikoff S, Ahmad K, Malik HS. Speciation and centromere evolution; Response. Science. 294(5551): 2479-80, 2001. PDF (34k)

2001

  • Henikoff S. Chromosomes on the move. Trends Genet. 2001 Dec;17(12):689-90. Abstract | PDF (121k)
  • Smothers JF, Henikoff S. Predicting in vivo protein peptide interactions with random phage display. Comb Chem High Throughput Screen. 2001 Nov;4(7):585-91. Abstract | Full Text Article
  • Ahmad K, Henikoff S. Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila. Cell. 104(6): 839-47, 2001. Abstract | PDF (1031k) | Bioessay | Research News
  • Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science. 292(5524): 2077-80, 2001. Abstract | PDF (742k)
  • Henikoff S, Ahmad K, Malik HS. The centromere paradox: stable inheritance with rapidly evolving DNA. Science. 293(5532): 1098-102, 2001. Abstract | PDF (240k) | Cover
  • Ahmad K, Henikoff S. Centromeres are specialized replication domains in heterochromatin. Journal of Cell Biology. 153(1): 101-10, 2001. Abstract | PDF (474k)
  • Colbert T, Till BJ, Tompa R, Reynolds S, Steine MN, Yeung AT, McCallum CM, Comai L, Henikoff S. High-throughput screening for induced point mutations. Plant Physiology. 126(2): 480-4, Jun 2001. Abstract | PDF (846k)
  • Ng PC, Henikoff S. Predicting deleterious amino acid substitutions. Genome Research. 11(5): 863-74, May 2001. Abstract | PDF (742k)
  • Henikoff S, Henikoff JG. Protein family databases. Encyclopedia of Life Sciences
  • Smothers JF, Henikoff S. The hinge and chromo shadow domain impart distinct targeting of HP1-like proteins. Molecular and Cellular Biology. 21(7): 2555-69, Apr 2001. Abstract | PDF (5540k)
  • Malik HS, Henikoff S. Adaptive evolution of Cid, a centromere-specific histone in Drosophila. Genetics. 157(3): 1293-8, Mar 2001. Abstract | PDF (254k)
  • van Steensel B, Delrow J, Henikoff S. Chromatin profiling using targeted DNA adenine methyltransferase. Nature Genetics. 27(3): 304-8, Mar 2001. Abstract | PDF (174k)

2000

  • Henikoff S, Vermaak D. Bugs on drugs go GAGAA. Cell. 103(5): 695-8, 2000. Abstract | PDF (264k)
  • Malik HS, Henikoff S, Eickbush TH. Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Research. 10(9): 1307-18, Sep 2000. Abstract | PDF (2418k) | Cover
  • Ng PC, Henikoff JG, Henikoff S. PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics. 16(9): 760-6, Sep 2000. Abstract
  • Malik HS, Henikoff S. Dual recognition-incision enzymes might be involved in mismatch repair and meiosis. Trends in Biochemical Sciences. 25(9): 414-8, Sep 2000. Abstract | PDF (242k)
  • Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S. Blocks-based methods for detecting protein homology. Electrophoresis. 21(9): 1700-6, May 2000. Abstract | Blocks website
  • McCallum CM, Comai L, Greene EA, Henikoff S. Targeted screening for induced mutations. Nature Biotechnology. 18(4): 455-7, Apr 2000. Abstract | PDF (207k) | Perspective
  • McCallum CM, Comai L, Greene EA, Henikoff S. Targeting Induced Local Lesions in Genomes (TILLING) for plant functional genomics. Plant Phys. 123(2): 439-442, Jun 2000. Abstract | PDF (154k)
  • Henikoff JG, Henikoff S. Drosophila genomic sequence annotation using the BLOCKS database. Genome Research. 10(4): 543-6, Apr 2000. Abstract | PDF (234k)
  • van Steensel B, Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nature Biotechnology. 18(4): 424-8, Apr 2000. Abstract | PDF (225k) | News and Views
  • Rubin GM et al.. Comparative genomics of the eukaryotes. Science. 287(5461): 2204-2215, 24 Mar 2000. Abstract | PDF (1373k)
  • Henikoff S. Heterochromatin function in complex genomes. Biochimica Et Biophysica Acta. 1470(1): O1-8, Feb 2000
  • Talbert PB, Henikoff S. A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster. Genetics. 154(1): 259-72, Jan 2000. Abstract | PDF (300k)
  • Henikoff JG, Greene EA, Pietrokovski S, Henikoff S. Increased coverage of protein families with the blocks database servers. Nucleic Acids Research. 28(1): 228-30, Jan 2000. Abstract | PDF (232k)
  • Henikoff S, Ahmad K, Platero JS, van Steensel B. Heterochromatic deposition of centromeric histone H3-like proteins. Proceedings of the National Academy of Sciences of the United States of America. 97(2): 716-21, Jan 2000. Abstract | PDF (691k)
  • Smothers JF, Henikoff S. The HP1 chromo shadow domain binds a consensus peptide pentamer. Current Biology. 10(1): 27-30, Jan 2000. Abstract | PDF (98k)
  • Henikoff S, Henikoff JG. Amino acid substitution matrices. Advances in Protein Chemistry. 54: 73-97, 2000
  • Henikoff S, Eissenberg JC, Hilliker AJ, Schmidt ER, Wallrath LL. Reaching for new heitz. Genetica. 109(1-2): 7-8, 2000
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