HENIKOFF LAB -- Publications

Henikoff Lab Publications

2017

  • Kasinathan S, Zentner GE, Zin B, Rohs R and Henikoff S.  Correspondence: Reply to "DNA shape is insufficient to explain binding'.  Nat Commun 2017 8: 15644 doi: 10.1038/ncomms15644
  • Ramachandran S, Ahmad K, and Henikoff S Capitalizing on disaster: Establishing chromatin specificity behind the replicaiton fork.  Bioessays 2017 39 doi: 10.1002/bies.201600150
  • Skene, P & Henikoff S.  An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 2017 doi: https://doi.org/10.1101/097188

2016

  • Talbert PB and Henikoff S Histone variants on the move: substrates for chromatin dynamics. Nat Rev Mol Cell Biol 2016 doi: 10.1038/nrm.2016.148.
  • 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 . 2016 e201695020 DOI:10.15252/embj.201695020.
  • Henikoff S. Mechanisms of nucleosome dynamics in vivo. Cold Spring Harb Perspect Med 2016 doi: 10.1101/cshperspect.a026666.
  • Henikoff S and Greally JM. Epigenetics, cellular memory and gene regulation. Current Biol 2016 26:R641-666
  • 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.
  • Ramachandran S and Henikoff S. Transcriptional regulators compete with nucleosomes post-replication. Cell 2016 v.165 doi: 10.1016/j.cell.2016.02.062.
  • Ramachandran S and Henikoff S.  Nucleosome dynamics during chromatin remodeling in vivo. Nucleus 2016 7:1,20-26.
  • 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.

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 Comm. Oct 22. doi: 10.1038/ncomms9733, 2015
  • Thakur J, Talbert P and Henikoff S.  Inner kinetochore protein interactions with regional centromeres of fission yeast.  Genetics 201: 543-561, 2015
  • Ramachandran S and Henikoff S.  Replicating nucleosomes.  Sci. Adv. 1, e1500587, 2015.
  • Henikoff S The genetic map enters its second century. Genetics 200:671-674 2015.
  • Skene PJ and Henikoff S A simple method for generating high-resolution maps of genome wide protein binding. eLife Jun 16;4. doi: 10.7554/eLife.09225 2015.
  • Henikoff S Epigenomic landscapes reflect neuronal diversity. Neuron 86:1319-1321 2015
  • Zentner GE and Henikoff S Epigenomic editing made easy Nature Biotech 33:606-607 2015
  • Steiner F and Henikoff S Diversity in the organization of centromeric chromatin. Curr Opin Genet Dev 31:28-35 2015
  • 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.
  • 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.
  • 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
  • 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.
  • Henikoff S and Smith M.  Histone variants and epigenetics. Cold Spring Harb Perspect Biol 2015,:7:a019364.
  • Ramachandran S, Zentner G, and Henikoff S.  Asymmetric nucleosomes flank promoters in the budding yeast genome. Genome Res. 2015, 25: 381-90 dio: 10.1101/gr.182618.114
  • 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.

2014

  • Teves SS, Weber, CM and Henikoff S. Transcribing through the nucleosome. Trends Bio Sci 2014, 39:577-86.
  • Kasinathan S and Henikoff S..  5-Aza-CdR delivers a gene body blow. Cancer Cell  2014, 26:449-51
  • Zentner GE and Henikoff S. High-resolution digital profiling of the epigenome. Nat Rev Genet  2014, doi: 10.1038/nrg3798.
  • Drinnenberg IA, deYoung D, Henikoff S, and Malik HS.  Recurrent loss of CenH3 is associated with independent transitions to holocentricity in insects. eLife 2014, 3:03676.
  • Talbert PB and Henikoff S..  Environmental responses mediated by histone variants. Trends Cell Biol. 2014, doi: 10.1016/j.tcb.2014.07.006
  • Skene PJ and Henikoff S Histones push the envelope. Nat. Struct. Mol. Biol. 2014, 21:651-2.
  • Teves S and Henikoff S..  DNA torsion as a feedback mediator of transcription and chromatin dynamics. Nucleus. 2014, 5: 211-8
  • Weber CM and Henikoff S Histone variants: dynamic punctuation in transcription. Genes Dev. 2014,  28:672-82.
  • 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. 2014, 24:809-20.
  • 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, in press
  • Steiner FA and Henikoff S Holocentromeres are dispersed point centromeres localized at transcription factor hotspots. eLife 2014, in press.
  • Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang J-P and Henikoff JG (2014) The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. eLife 2014, in press.
  • Weber CM, Ramachandran S and Henikoff S Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Molecular Cell 2014, 53:819-830.
  • Krassovsky K and Henikoff S Distinct chromatin features characterize different classes of repeat sequences in Drosophila melanogaster. BMC Genomics 2014 15:105.
  • 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.
  • Yang F, Teves SS, Kemp CJ and Henikoff S Doxorubicin, DNA torsion and chromatin dynamics. BBA Reviews Cancer Dec 19, 2013 1845:84-9.
  • 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.
  • Teves SS and Henikoff S Transcription-generated torsional stress destabilizes nucleosomes. Nat. Struct. Mol. Biol. 2014 21:88-94.

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.
  • Zentner GE and Henikoff S. Mot1 redistributes TBP from TATA-containing to TATA-less promoters. Mol Cell Biol. 2013 33:4996-5004.
  • Talbert PB and Henikoff S. Phylogeny as the basis for naming histones. Trends Genet. 2013 Jul; http://dx.doi.org/10.1016/j.tig.2013.06.009.
  • Skene P and Henikoff S. Histone variants in pleuripotency and disease. Development. 2013 Jun;140(12):2513-2524.
  • Furuyama T, Codomo, CA and Henikoff S. Reconstitution of hemisomes on budding yeast centromeric DNA. Nucl. Acids Res. (2013) doi: 10.1093/nar/gkt314.
  • 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.
  • Yang F, Kemp CJ and Henikoff S. Doxorubicin enhances nucleosome turnover around promoters. Curr Biol. 2013 May 6;23(9):782-7.
  • 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.
  • Zentner GE and Henikoff S. Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol. 2013 Mar;20(3):259-66.
  • Henikoff S and Grosveld F. Epigenetics and chromatin: Interactions and processes. Epigenetics Chromatin. 2013 Feb 27;6(1):2.
  • 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.

2012

  • Talbert PB and Henikoff S. Chromatin: Packaging without nucleosomes. Curr Biol. 2012 Dec 18;22(24):R1040-3.
  • Cooper JL, Henikoff S, Comai L, Till BJ. TILLING and Ecotilling in rice. Methods Mol Biol. 2013;956:39-56.
  • Skene P and Henikoff S. Chromatin roadblocks to reprogramming 50 years on. BMC Biol. 10:83, 2012.
  • Zentner G and Henikoff S. Surveying the epigenomic landscape, one base at a time. Genome Biol. 13:250, 2012.
  • Teves SS, Deal RB and Henikoff S. Measuring genome-wide nucleosome turnover using CATCH-IT. Methods Enzymol. 513:169-84, 2012.
  • 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.
  • 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.
  • Henikoff S and Furuyama T. The unconventional structure of centromeric nucleosomes. Chromosoma (DOI) 10.1007/s00412-012-0372-y, 2012.
  • Henikoff S and Henikoff JG. "Point" centromeres of Saccharomyces harbor single centromere-specific nucleosomes. Genetics 190(4):1575-7, 2012.
  • Henikoff S. Steven Henikoff. Current Biology 2012 22(4):R106-7.
  • 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.
  • Teves SS and Henikoff S. Salt fractionation of nucleosomes for genome-wide profiling. Methods Mol Biol. 2012 833:421-32.
    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


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.
  • 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.

  • 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.
  • Henikoff S and Shilatifard A. Histone modifications: Cause or cog? Trends Genet. 2011 27:389-96.
  • Henikoff S. Summary: The nucleus - A close-knit community of dynamic structures. Cold Spring Harbor Symp Quant Biol. 2011 75:607-615.
  • Deal RB and Henikoff S. Histone variants and modifications in plant gene regulation. Curr Opin Plant Biol. 2011 14:116-22.
  • Deal RB and Henikoff S. (2011) The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana. Nature Protocols 6:56-68

2010

  • Deal RB and Henikoff S. (2010) Histone variants and modifications in plant gene regulation. Curr Opin Plant Biol. 2010 14 DOI 10.1016/j.pbi.2010.11.005.
  • 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.
  • 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.
  • Weber CM, Henikoff JG and Henikoff S.(Dec 2010) H2A.Z nucleosomes enriched over active genes are homotypic Nature Struct Mol Biol; 17(12):1500-7.
  • Henikoff S and Furuyama T. (2010) Epigenetic inheritance of centromeres. Cold Spring Harbor Symp Quant Biol. 75:978-1-936113-07-1.
  • Deal RB and Henikoff S. (2010) Chromatin dynamics and the regulation of genome function. Genome Biol. 11:218.
  • Conerly ML, Teves SS, Diolaiti D, Ulrich M, Eisenman RN and Henikoff S. (Oct 2010) Changes in H2A.Z occupancy and DNA methylation during B-cell lymphomagenesis. Genome Res. 20(10):1383-90.
  • Deal RB and Henikoff S. (2010) Catching a glimpse of nucleosome dynamics. Cell Cycle 9(17):3389-90.
  • Bryson TD, Weber CM, Henikoff S (Jul 2010) Baculovirus-encoded protein expression for epigenomic profiling in Drosophila cells., Fly, 4 (3)
  • Deal RB, Henikoff S (Jun 2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue., Developmental cell, 18 (6), 1030-40
  • Deal RB, Henikoff JG, Henikoff S (May 2010) Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones., Science (New York, N.Y.), 328 (5982), 1161-4
  • Talbert PB, Henikoff S (Apr 2010) Histone variants--ancient wrap artists of the epigenome., Nature reviews. Molecular cell biology, 11 (4), 264-75  
  • Ooi SL, Henikoff JG, Henikoff S (Mar 2010) A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans., Nucleic acids research, 38 (4), e26
  • Deal RB, Henikoff S (Feb 2010) Gene regulation: A chromatin thermostat., Nature, 463 (7283), 887-8
  • Talbert PB, Henikoff S (2010) Centromeres convert but don't cross., PLoS biology, 8 (3), e1000326
  • 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 (2010) A comprehensive map of insulator elements for the Drosophila genome., PLoS genetics, 6 (1), e1000814

2009

  • Malik HS, Henikoff S (Sep 2009) Major evolutionary transitions in centromere complexity., Cell, 138 (6), 1067-82
  • Henikoff S (Aug 2009) Labile H3.3+H2A.Z nucleosomes mark 'nucleosome-free regions'., Nature genetics, 41 (8), 865-6
  • Furuyama T, Henikoff S (Jul 2009) Centromeric nucleosomes induce positive DNA supercoils., Cell, 138 (1), 104-13
  • 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 (Jun 2009) Unlocking the secrets of the genome.,Nature, 459 (7249), 927-30
  • Gehring M, Bubb KL, Henikoff S (Jun 2009) Extensive demethylation of repetitive elements during seed development underlies gene imprinting., Science (New York, N.Y.), 324 (5933), 1447-51
  • Talbert PB, Henikoff S (May 2009) Chromatin-based transcriptional punctuation., Genes & development, 23 (9), 1037-41
  • Gehring M, Reik W, Henikoff S (Feb 2009) DNA demethylation by DNA repair., Trends in genetics : TIG, 25 (2), 82-90
  • Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm., Nature protocols, 4 (7), 1073-81
  • De Bustos C, Ramos E, Young JM, Tran RK, Menzel U, Langford CF, Eichler EE, Hsu L, Henikoff S, Dumanski JP, Trask BJ (2009) Tissue-specific variation in DNA methylation levels along human chromosome 1., Epigenetics & chromatin, 2 (1), 7

2008

  • Wang H, Dalal Y, Henikoff S, Lindsay S (Dec 2008) Single-epitope recognition imaging of native chromatin., Epigenetics & chromatin, 1 (1), 10
  • Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K (Dec 2008) Genome-wide profiling of salt fractions maps physical properties of chromatin., Genome research
  • Cooper JL, Till BJ, Henikoff S (Nov 2008) Fly-TILL: Reverse genetics using a living point mutation resource., Fly, 2 (6)
  • Henikoff S, Strahl BD, Warburton PE (Nov 2008) Epigenomics: a roadmap to chromatin., Science (New York, N.Y.), 322 (5903), 853
  • Yan H, Talbert PB, Lee HR, Jett J, Henikoff S, Chen F, Jiang J (Nov 2008) Intergenic locations of rice centromeric chromatin., PLoS biology, 6 (11), e286
  • Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S (Nov 2008) Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks., Nature, 456 (7218), 125-9
  • Cooper JL, Greene EA, Till BJ, Codomo CA, Wakimoto BT, Henikoff S (Sep 2008) Retention of induced mutations in a Drosophila reverse-genetic resource., Genetics, 180 (1), 661-7
  • Henikoff S, Grosveld F (2008) Welcome to Epigenetics & Chromatin., Epigenetics & chromatin, 1 (1), 1
  • 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, Henikoff S (2008) TILLING to detect induced mutations in soybean., BMC plant biology, 8, 9
  • Henikoff S (Jan 2008) Nucleosome destabilization in the epigenetic regulation of gene expression., Nature reviews. Genetics, 9 (1), 15-26

2007

  • Zilberman D, Henikoff S (Nov 2007) Genome-wide analysis of DNA methylation patterns., Development (Cambridge, England), 134 (22), 3959-65
  • Henikoff S (Nov 2007) Nucleosomes at active promoters: unforgettable loss., Cancer cell, 12 (5), 407-9
  • Dalal Y, Furuyama T, Vermaak D, Henikoff S (Oct 2007) Structure, dynamics, and evolution of centromeric nucleosomes., Proceedings of the National Academy of Sciences of the United States of America, 104 (41), 15974-81
  • Dalal Y, Wang H, Lindsay S, Henikoff S (Aug 2007) Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells., PLoS biology, 5 (8), e218
  • Henikoff S (Jul 2007) ENCODE and our very busy genome., Nature genetics, 39 (7), 817-8
  • Ooi SL, Henikoff S (Jun 2007) Germline histone dynamics and epigenetics., Current opinion in cell biology, 19 (3), 257-65
  • Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL (Apr 2007) DNA demethylation in the Arabidopsis genome., Proceedings of the National Academy of Sciences of the United States of America, 104 (16), 6752-7
  • Mito Y, Henikoff JG, Henikoff S (Mar 2007) Histone replacement marks the boundaries of cis-regulatory domains.,Science (New York, N.Y.), 315 (5817), 1408-11
  • Gehring M, Henikoff S (2007) DNA methylation dynamics in plant genomes., Biochimica et biophysica acta, 1769 (5-6), 276-86
  • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (Jan 2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription., Nature genetics, 39 (1), 61-9
  • Till BJ, Cooper J, Tai TH, Colowit P, Greene EA, Henikoff S, Comai L (2007) Discovery of chemically induced mutations in rice by TILLING., BMC plant biology, 7, 19

2006

  • Dawe RK, Henikoff S (Dec 2006) Centromeres put epigenetics in the driver's seat., Trends in biochemical sciences, 31 (12), 662-9
  • Talbert PB, Henikoff S (Oct 2006) Spreading of silent chromatin: inaction at a distance., Nature reviews. Genetics, 7 (10), 793-803
  • Furuyama T, Henikoff S (2006) Biotin-tag affinity purification of a centromeric nucleosome assembly complex, Cell Cycle, 5 (12), 1269-74
  • Till BJ, Zerr T, Comai L, Henikoff S (2006) A protocol for TILLING and Ecotilling in plants and animals., Nature protocols, 1 (5), 2465-77
  • Feinberg AP, Ohlsson R, Henikoff S (2006) The epigenetic progenitor origin of human cancer, Nat Rev Genet, 7 (1), 21-33
  • Comai L, Henikoff S (2006) Practical single-nucleotide mutation discovery, Plant J, 45, 684-94
  • Furuyama T, Dalal Y, Henikoff S (2006) Chaperone-mediated assembly of centromeric chromatin in vitro, Proc. Natl. Acad. Sci. USA, 103 (16), 172-7
  • Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM (2006) Applying whole-genome studies of epigenetic regulation to study human disease, Cytogenet. Genome Res., 114 (1), 1-15
  • Ooi SL, Priess JR, Henikoff S (2006) Histone H3.3 variant dynamics in the germline of Caenorhabditis elegans, PLoS Genet, 2 (6), e97
  • Till BJ, Colbert T, Codomo C, Enns L, Johnson J, Reynolds SH, Henikoff JG, Greene EA, Steine MN, Comai L, Henikoff S (2006) High-throughput TILLING for Arabidopsis, Methods Mol Biol, 323, 127-35 
  • Ng PC, Henikoff S (2006) Predicting the Effects of Amino Acid Substitutions on Protein Function, Annu. Rev. Genomics. Hum. Genet, 7, 61-80 
  • Till BJ, Zerr T, Bowers E, Greene EA, Comai L, Henikoff S (2006) High-throughput discovery of rarae human nucleotide polymorphisms by Ecotilling, Nucl. Acids Res, 34 (13), e99 
  • Till BJ, Zerr T, Comai L, Henikoff S (2006) A protocol for TILLING and Ecotilling in plants and animals., Nature Protocols, 1, 2465-77 
  • Yan H, Jin W, Nagaki K, Tian S, Ouyang S, Buell CR, Talbert PB, Henikoff S, Jiang J (2005) Transcription and histone modifications in the recombination-free region spanning a rice centromere, Plant Cell, 17 (12), 3227-38 

2005

  • Malik HS, Henikoff S (2005) Positive Selection of Iris, a Retroviral Envelope-Derived Host Gene in Drosophila melanogaster, PLoS Genet, 1 (4), e44 
  • Mito Y, Henikoff JG, Henikoff S (2005) Genome-scale profiling of histone H3.3 replacement patterns, Nat Genet, 37 (10), 1090-7 
  • Mito Y, Henikoff JG, Henikoff S (Oct 2005) Genome-scale profiling of histone H3.3 replacement patterns., Nature Genetics, 37 (10), 1090-7  
  • Vermaak D, Henikoff S, Malik HS (2005) Positive selection drives the evolution of rhino, a member of the Heterochromatin Protein 1 family in Drosophila, PLoS Genet, 1 (1), e9 
  • Henikoff S, Histone Modifications: Combinatorial Complexity Or Cumulative Simplicity?, Proceedings of the National Academy of Sciences of the United States of America., 102(15), 5308-9, Apr 2005 
  • Henikoff S, Dalal Y (Apr 2005) Centromeric chromatin: what makes it unique?, Current Opinion in Genetics & Development, 15 (2), 177-84  
  • Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S, DNA Methylation Profiling Identifies CG Methylation Clusters In Arabidopsis Genes., Current Biology : Cb, 15(2), 154-9, Jan 2005  
  • 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 (2005) Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis, Genome Biol, 6, R90 
  • Henikoff S (2005) Rapid changes in plant genomes, Plant Cell, 17, 2852-55 

2004

  • Cooper JL, Henikoff S, Adaptive evolution of the histone fold domain in centromeric histones, Molecular Biology and Evolution, 21(9), 1712-8, September 2004  
  • Henikoff S, Furuyama T, Ahmad K, Histone variants, nucleosome assembly and epigenetic inheritance, Trends in Genetics : Tig, 20(7), 320-6, July 2004  
  • Henikoff S, Till BJ, Comai L, TILLING. Traditional mutagenesis meets functional genomics, Plant Physiology, 135(2), 630-6, June 2004  
  • Henikoff S, Visualizing gene expression: an unfolding story, Cell, 116(5), 633-4, 2004  
  • 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, The Plant Cell, 16(3), 571-81, 2004  
  • 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, The Plant Journal : for Cell and Molecular Biology, 37(5), 778-86, 2004  
  • McKittrick E, Gafken PR, Ahmad K, Henikoff S, Histone H3.3 is enriched in covalent modifications associated with active chromatin, Proceedings of the National Academy of Sciences of the United States of America., 101(6), 1525-30, 2004  
  • Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J, Sequencing of a rice centromere uncovers active genes, Nature Genetics, 36(2), 138-45, 2004  
  • Till BJ, Burtner C, Comai L, Henikoff S, Mismatch cleavage by single-strand specific nucleases, Nucleic Acids Research, 32(8), 2632-41, 2004  
  • Zilberman D, Henikoff S, Silencing of Transposons in Plant Genomes: Kick Them When They're Down., Genome Biology, 5(12), 249, 2004  
  • Henikoff S, McKittrick E, Ahmad K (2004) Epigenetics, histone H3 variants, and the inheritance of chromatin states.,Cold Spring Harbor Symposia On Quantitative Biology, 69, 235-43  
  • Talbert PB, Bryson TD, Henikoff S (2004) Adaptive evolution of centromere proteins in plants and animals., Journal of Biology (online), 3 (4), 18  

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 and Development, 17(22), 2825-38, November 2003  
  • Malik HS, Henikoff S, Phylogenomics of the nucleosome, Nature Structural Biology, 10(11), 882-91, November 2003  
  • van Steensel B, Henikoff S, Epigenomic profiling using microarrays, Biotechniques, 35(2), 346-50, 352-4, 356-7, August 2003  
  • Ng PC, Henikoff S, SIFT: Predicting amino acid changes that affect protein function, Nucleic Acids Research, 31(13), 3812-4, July 2003  
  • Rose TM, Henikoff JG, Henikoff S, CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design, Nucleic Acids Research, 31(13), 3763-6, July 2003  
  • Henikoff S, Versatile assembler, Nature, 423(6942), 814-5, 817, June 2003  
  • Vermaak D, Ahmad K, Henikoff S, Maintenance of chromatin states: an open-and-shut case, Current Opinion in Cell Biology, 15(3), 266-74, June 2003  
  • 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, 164(2), 731-40, June 2003 
  • 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 Research, 13(3), 524-30, March 2003  
  • 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, 163(3), 1221-5, March 2003 
  • Rutherford SL, Henikoff S, Quantitative epigenetics, Nature Genetics, 33(1), 6-8, January 2003  
  • Till BJ, Colbert T, Tompa R, Enns LC, Codomo CA, Johnson JE, Reynolds SH, Henikoff JG, Greene EA, Steine MN, Comai L, Henikoff S, High-Throughput TILLING for Functional Genomics, Methods in Molecular Biology (clifton, N.j.), 236, 205-20, 2003  
  • Henikoff S, Comai L, Single-nucleotide mutations for plant functional genomics, Annual Review of Plant Biology, 54, 375-401, 2003  

2002

  • Malik HS, Henikoff S, Conflict begets complexity: the evolution of centromeres, Current Opinion in Genetics & Development, 12(6), 711-8, December 2002  
  • Ahmad K, Henikoff S, Histone H3 variants specify modes of chromatin assembly, Proceedings of the National Academy of Sciences (USA), 99 Suppl 4, 16477-84, December 2002  
  • Ahmad K, Henikoff S, Epigenetic consequences of nucleosome dynamics, Cell, 111(3), 281-4, November 2002 
  • Vermaak D, Hayden HS, Henikoff S, Centromere Targeting Element within the Histone Fold Domain of Cid, Molecular and Cellular Biology, 22(21), 7553-61, November 2002  
  • Smothers JF, Henikoff S, Carter P, Tech.Sight. Phage display. Affinity selection from biological libraries, Science, 298(5593), 621-2, October 2002  
  • Ahmad K, Henikoff S, The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly, Molecular Cell, 9(6), 1191-200, June 2002  
  • Henikoff S, Malik HS, Centromeres: selfish drivers, Nature, 417(6886), 227, May 2002  
  • Talbert PB, Masuelli R, Tyagi AP, Comai L, Henikoff S, Centromeric localization and adaptive evolution of an Arabidopsis histone h3 variant, The Plant Cell, 14(5), 1053-66, May 2002  
  • Henikoff S, Near the edge of a chromosome's 'black hole', 18(4), 165-7, April 2002  
  • Ng PC, Henikoff S, Accounting for human polymorphisms predicted to affect protein function, Genome Research, 12(3), 436-46, March 2002  
  • Henikoff S, Beyond the central dogma, 18(2), 223-5, February 2002  
  • Malik HS, Vermaak D, Henikoff S, Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone, Proceedings of the National Academy of Sciences (USA), 99(3), 1449-54, February 2002  
  • Tompa R, McCallum CM, Delrow J, Henikoff JG, van Steensel B, Henikoff S, Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3, Current Biology : Cb, 12(1), 65-8, January 2002 

2001

  • Henikoff S, Chromosomes on the move, Trends in Genetics : Tig, 17(12), 689-90, December 2001  
  • Smothers JF, Henikoff S, Predicting in vivo protein peptide interactions with random phage display, Combinatorial Chemistry & High Throughput Screening, 4(7), 585-91, November 2001  
  • Henikoff S, Ahmad K, Malik HS, The centromere paradox: stable inheritance with rapidly evolving DNA, Science, 293(5532), 1098-102, 2001  
  • 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  
  • 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, June 2001  
  • Ng PC, Henikoff S, Predicting deleterious amino acid substitutions, Genome Research, 11(5), 863-74, May 2001 
  • Ahmad K, Henikoff S, Centromeres are specialized replication domains in heterochromatin, Journal of Cell Biology, 153(1), 101-10, 2001  
  • 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, April 2001  
  • Ahmad K, Henikoff S, Modulation of a transcription factor counteracts heterochromatic gene silencing in Drosophila, Cell, 104(6), 839-47, 2001  
  • Malik HS, Henikoff S, Adaptive evolution of Cid, a centromere-specific histone in Drosophila, Genetics, 157(3), 1293-8, March 2001  
  • van Steensel B, Delrow J, Henikoff S, Chromatin profiling using targeted DNA adenine methyltransferase, Nature Genetics, 27(3), 304-8, March 2001  

2000

  • Henikoff S, Vermaak D, Bugs on drugs go GAGAA, Cell, 103(5), 695-8, 2000  
  • Malik HS, Henikoff S, Eickbush TH, Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses, Genome Research, 10(9), 1307-18, September 2000  
  • Ng PC, Henikoff JG, Henikoff S, PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane, Bioinformatics, 16(9), 760-6, September 2000
  • Malik HS, Henikoff S, Dual recognition-incision enzymes might be involved in mismatch repair and meiosis, Trends in Biochemical Sciences, 25(9), 414-8, September 2000
  • Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S, Blocks-based methods for detecting protein homology, Electrophoresis, 21(9), 1700-6, May 2000
  • McCallum CM, Comai L, Greene EA, Henikoff S, Targeted screening for induced mutations, Nature Biotechnology, 18(4), 455-7, April 2000
  • Henikoff JG, Henikoff S, Drosophila genomic sequence annotation using the BLOCKS database, Genome Research, 10(4), 543-6, April 2000
  • van Steensel B, Henikoff S, Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase, Nature Biotechnology, 18(4), 424-8, April 2000
  • Rubin GM et al., Comparative genomics of the eukaryotes, Science, 287(5461), 2204-2215, 24 Mar 2000
  • Henikoff S, Heterochromatin function in complex genomes, Biochimica Et Biophysica Acta, 1470(1), O1-8, February 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
  • 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
  • Henikoff S, Ahmad K, Platero JS, van Steensel B, Heterochromatic deposition of centromeric histone H3-like proteins, Proceedings of the National Academy of Sciences (USA), 97(2), 716-21, Jan 2000
  • Smothers JF, Henikoff S, The HP1 chromo shadow domain binds a consensus peptide pentamer, Current Biology, 10(1), 27-30, Jan 2000
  • 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

1999

  • Platero JS, Ahmad K, Henikoff S, A distal heterochromatic block displays centromeric activity when detached from a natural centromere, Molecular Cell, 4(6), 995-1004, December 1999
  • Buchwitz BJ, Ahmad K, Moore LL, Roth MB, Henikoff S, A histone-H3-like protein in C. elegans, Nature, 401(6753), 547-8, October 1999
  • Henikoff S, Henikoff JG, Pietrokovski S, Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations., Bioinformatics, 15(6), 471-9, June 1999
  • Sass GL, Henikoff S, Pairing-dependent mislocalization of a Drosophila brown gene reporter to a heterochromatic environment, Genetics, 152(2), 595-604, June 1999
  • Martienssen R, Henikoff S, The House, Nature Genetics, 22(1), 6-7, May 1999
  • Henikoff JG, Henikoff S, Pietrokovski S, New features of the Blocks Database servers, Nucleic Acids Research, 27(1), 226-8, Jan 1999

1998

  • Fanti L, Dorer DR, Berloco M, Henikoff S, Pimpinelli S, Heterochromatin protein 1 binds transgene arrays, Chromosoma, 107(5), 286-92, November 1998
  • Csink AK, Henikoff S, Large-scale chromosomal movements during interphase progression in Drosophila, Journal of Cell Biology, 143(1), 13-22, October 1998
  • Henikoff S, Conspiracy of silence among repeated transgenes, Bioessays, 20(7), 532-5, July 1998
  • Henikoff S, Comai L, A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis, Genetics, 149(1), 307-18, May 1998
  • Csink AK, Henikoff S, Something from nothing: the evolution and utility of satellite repeats, Trends in Genetics, 14(5), 200-4, May 1998
  • Henikoff S, Comai L, Trans-sensing effects: the ups and downs of being together, Cell, 93(3), 329-32, May 1998
  • Clark DV, Sabl JF, Henikoff S, Repetitive arrays containing a housekeeping gene have altered polytene chromosome morphology in Drosophila, Chromosoma, 107(2), 96-104, May 1998
  • Rose TM, Schultz ER, Henikoff JG, Pietrokovski S, McCallum CM, Henikoff S, Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences., Nucleic Acids Research, 26(7), 1628-35, 1 1998
  • Pietrokovski S, Henikoff JG, Henikoff S, Exploring protein homology with the Blocks server., Trends In Genetics, 14(4), 162-3, 1998
  • Platero JS, Csink AK, Quintanilla A, Henikoff S, Changes in chromosomal localization of heterochromatin-binding proteins during the cell cycle in Drosophila, Journal of Cell Biology, 140(6), 1297-306, March 1998
  • Sass GL, Henikoff S, Comparative analysis of position-effect variegation mutations in Drosophila melanogaster delineates the targets of modifiers, Genetics, 148(2), 733-41, February 1998
  • Henikoff S, Pietrokovski S, Henikoff JG, Superior performance in protein homology detection with the Blocks Database servers, Nucleic Acids Research, 26(1), 309-12, Jan 1998  

1997

  • Henikoff S, Greene EA, Pietrokovski S, Bork P, Attwood TK, Hood L, Gene families: the taxonomy of protein paralogs and chimeras, Science, 278(5338), 609-14, October 1997  
  • Greene EA, Pietrokovski S, Henikoff S, Bork P, Attwood T, Hood L, Bairoch A, Genome maps 8. Building gene families. Wall chart, Science, 278(5338), 615-30, October 1997
  • Henikoff S, Nuclear organization and gene expression: homologous pairing and long-range interactions., Curr Opin Cell Biol, 9(3), 388-95, 1997
  • Henikoff S, Henikoff JG, Embedding strategies for effective use of information from multiple sequence alignments., Protein Science, 6(3), 698-705, 1997
  • Henikoff JG, Pietrokovski S, Henikoff S, Recent enhancements to the Blocks Database servers., Nucleic Acids Research, 25(1), 222-5, 1 1997