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Nucleosome positioning datasets

Gene Regulation Info

Quantitative descriptions of gene regulation






Below is a manually curated collection of experimental nucleosome positioning datasets. This list is being constantly updated, comments are very welcome. Related lists: MNase-seq analysis software | nucleosome positioning prediction | experimental protocols | TF-DNA binding | epigenetic modifications |

*How to cite: Teif V.B. (2016). Nucleosome positioning: resources and tools online. Briefings in Bioinformatics 17, 745-757.  | Published version | Author's PDF


Nucleosome positioning datasets sorted by cell type, newest first:


Accession #


HuRef lymphoblastoid line, α-satellite arrays of centromeres (Henikoff et al., 2015). ChIP-seq.


H1-OGN embryonic stem cells, H1-OGN induced pluripotent stem cells, and fibroblasts differentiated from H1-OGN ESCs (West et al., 2014). MNase-seq.


HCT116 colon cancer cells and their genetic derivatives which lack DNA methyltransferases DNMT3B and DNMT1 activity (Lay et al., 2015). NOME-seq.


Primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFalpha) (Diermeier et al., 2014). MNase-seq.


MCF-7 (breast cancer) with and without MBD3 knockdown (Shimbo et al., 2013). MNase-seq.


Human embryonic stem cells (H1 and H9 hESCs). MNase-seq


Human sperm (Samans et al., 2014); Limited regions retain nucleosomes in sperm. MNase-seq.


Human colo829 cell line. MNase-seq


Raji cells (lymphoblastoid-like) with and without α-amanitin (Fenouil et al., 2012). MNase-seq.


7 lymphoblastoid cell lines from the HapMap project (Gaffney et al., 2012). MNase-seq.


Lymphoblastoid GM12878 and K562 cell lines (Kundaje et al., 2012). MNase-seq.


CD36+ cells with and without BRG1 knockdown (Hu et al., 2011). MNase-seq, ChIP-seq.


Human embryonic carcinoma (NCCIT) cell line (Jung et al., 2012). MNase-seq, ChIP-seq.


Primary CD4+ T-cells, CD8+ T-cells and granulocytes (Valouev et al., 2011). MNase-seq.


MCF7EcoR cells where P53 was either activated or not (Lidor Nili et al., 2010). MNase-seq.


Nucleosome positioning and DNA methylation in IMR90 (Kelly et al., 2012). NOME-seq.


Resting and activated CD4+ T cells (Schones et al., 2008). MNase-seq; H3, H2A.Z ChIP-seq.



Mouse ESCs (Ishii et al., 2015). MNase-seq, MPE-seq, MPE-ChIP-seq


Mouse ESCs, wild type and Dnmt1/3a/3b triple knockout (Yearim et al., 2015). MNase-seq


Mouse ESCs, induced pluripotent stem cells (iPCs), somatic tail-tip fibroblasts (TTF) and liver (West et al., 2014). MNase-seq.


Mouse ESCs and sperm (Carone et al., 2014). Different size-selection of MNase-seq fragments.


Mouse ESCs, siRNA knockdown of EGFP, Smarca4 or MBD3 (Hainer et al., 2015). MNase-seq


Mouse ESCs, low MNase digestion; dinucleosome fraction (Teif et al., 2014). MNase-seq.


Mouse ESCs and differentiated iMEFs. RED-seq.


Mouse ESCs (J1) (Zhang et al., 2014). MNase-seq, ChIP-seq


Mouse ESCs, low MNase digestion (Chen et al., 2013c). MNase-seq.


Mouse ESCs (E14) and Smarcad1-knock down cells. MNase-seq.


Mouse ESCs and induced pluripotent cells (iPSC) from different layers (Tao et al., 2014)


Mouse ESCs, neural progenitor cells (NPCs) and neurons with and without HMGN1 knockout. MNase-seq using high and low MNase digestion levels
(Deng et al., 2013).


Mouse ESCs, NPCs and embryonic fibroblasts (MEFs) (Teif et al., 2012). MNase-seq.


Mouse liver (Li et al., 2012). MNase-seq and ChIP-seq.


Mouse liver, 3-mohth and 21-month old mice (Bochkis et al., 2014). MNase-seq.


Mouse liver, 6 time points of the 24h light:dark cycle; WT and Bmal1-/- (Menet et al., 2014).


Mouse bone marrow-derived macrophages (BMDMs) (Scruggs et al., 2015). MNase-seq.


Hypothalamus from MeCP2 knockout mice and control mice (Chen et al., 2015). MNase-seq.


Cultured germline stem cells with and without Scml2 knockout (Hasegawa et al., 2015). MNase-seq.


Primary CD4+ CD8+ DP thymocytes and Rag2 -/- thymocytes (Zacarias-Cabeza et al., 2015). MNase-seq.


Fibroblasts from E13.5 embryos. WT, Snf5-/- and Brg1-/- (Tolstorukov et al., 2013). MNase-seq.


Drosophila melanogaster, MNase-seq:

S2 cell line. WT and stimulated by heat killed Salmonella typhimurium.


S2 cell line. WT; treated with RNAi against Beta-galactosidase or GAGA (Fuda et al., 2015).


S2 cell line. WT and Beaf32-depleted (Lhoumaud et al., 2014).


S2 cell line. WT and depletion of CTCF/P190 and ISWI (Bohla et al., 2014).


Wild-type (WT) S2 cell line (Nalabothula et al., 2014).


Staged Drosophila embryos (Chen et al., 2013a).


S2 cell line. WT, mock-treated, and NELF-depleted (Gilchrist et al., 2010).


Arabidopsis thaliana:

Col-0 seeds; chr11-1 chr17-1, MNase-seq(Li et al., 2014)


Col-0 seeds; WT and inhibition of Pol V-produced lncRNAs. MNase-seq(Zhu et al., 2013)


Col-0 seeds, shoots; MNase-seq, ChIP-seq, Bisulfite sequencing (Chodavarapu et al., 2010)


Caenorhabditis elegans, MNase-seq:

Mixed stage, wild-type (N2) C. elegans. SOLiD paired-end sequencing (Valouev et al., 2008)


Chlamydomonas reinhardtii:

Chlamydomonas strain CC 1609. MNase-seq(Fu et al., 2015)


Saccharomyces cerevisiae and related species, MNase-seq:

S. cerevisiae hho1, ioc3isw1, and chd1 deletion mutants complemented with the corresponding copies from K. lactis (Hughes and Rando, 2015).


S. cerevisiae. Strain W303, stationary growth phase. Wild type (WT) and with introduced DNMT3b (Morselli et al., 2015).


S. cerevisiae. Strains carrying the Sth1 degron allele and either pGal-UBR1 (YBC3386) or ubr1 null (YBC3387) represent RSC null and RSC wild type correspondingly (Parnell et al., 2015).


S. cerevisiae. WT and Snf2 K1493R, K1497R strains; unstressed/stressed (Dutta et al., 2014)


S. cerevisiae. Strain W303. WT and modification affecting one of the following chromatin remodelers: ISW1, CHD1, FUN30, IOC3 (Ramachandran et al., 2015).


S. cerevisiae. Strain W303. Affected histone deacetylases Sir2 and Rpd3 (Yoshida et al., 2014).


S. cerevisiae. Strain YK699, WT and changes addressing the following: Scc2-4; Sth1-3; a2/MCM1;  TATAC; TATA∆. Replicates at 25°C and 37°C (Lopez-Serra et al., 2014).


S. cerevisiae. Calorie restricted and non-restricted WT, ISW2DEL and ISW2K215R strains (Dang et al., 2014)


S. cerevisiae. Strain W303 (yFR212) (Woo et al., 2013). MNase-seq and H2A.Z ChIP-seq


S. cerevisiae. Strain S288c (BY4741). “Young yeast”, “old yeast”, and “old yeast with histone over expression” (Hu et al., 2014).


S. cerevisiae. Strain BY4741, WT and Hog1 mutant. Exposed/not exposed to osmostress (Nadal-Ribelles et al., 2012).


S. cerevisiae. Strain BY4742, WT, ssn6 KO and tup1 KO (Chen et al., 2013b).


S. cerevisiae. Strain S288C. WT, nup170∆  and sth1p depletion (Van de Vosse et al., 2013).


S. cerevisiae. Strain BY4741. Study of response to H2O2 over time in the S288c derivative (Huebert et al., 2012).


S. cerevisiae. Strain YEF473A. WT and mutant with H3 shutoff to study histone H3 depletion (Gossett and Lieb, 2012).


WT and mutant strains in S. cerevisiae, C. albicans, and S. pombe (Tsankov et al., 2011).


S. cerevisiae at varying phosphate concentrations


S. cerevisiae. Strain XF218. H3 Chip-seq (Fan et al., 2010)


12 Ascomycete species: Saccharomyces mikatae, Saccharomyces bayanus, Saccharomyces castellii, Saccharomyces cerevisiae, Kluyveromyces waltii, Saccharomyces paradoxus, Candida glabrata, Candida albicans, Debaryomyces hansenii, Kluyveromyces lactis, Saccharomyces kluyveryii, Yarrowia lipolytica (Tsankov et al., 2010).


Comparison of nucleosome positioning in S. cerevisiae, S. paradoxus and their hybrid for wild-type and deletion mutant strains (Tirosh et al., 2010).


S. cerevisiae. Strains BY4741 and RPO21. MNase titration series from three different titration levels –  underdigested, typical digestion, and overdigested BY4741 cells. Time dependence series: MNase-seq at 0, 20, and 120 minutes after shifting RPO21 cells from 25 C to 37 C (Weiner et al., 2010).


S. cerevisiae. Chromatin remodelling by Isw2 (Whitehouse et al., 2007). Tiling microarrays.

GSE8813, GSE8814, GSE8815

The Penn State Genome Cartography Project. S. cerevisiae and D. melanogaster (Yen et al., 2013; Zhang et al., 2011; Zhang and Pugh, 2011; Mavrich et al., 2008). Tiling microarrays.


Saccharomyces pombe, MNase-seq:

Strain Hu1867. WT and without Fun30 chromatin remodeler Fft3 (Steglich et al., 2015).


Strain FWP172. WT and spt6-1 at two different MNase concentrations (DeGennaro et al., 2013). Spt6 is a histone chaperone.


Wild type (ade6-M210 leu1-32 ura4-D18) and without CHD remodeler Hrp3 (Shim et al., 2012).


Strain D18, log phase and stationary Phase (Givens et al., 2012).




Bochkis I M, Przybylski D, Chen J and Regev A 2014 Changes in nucleosome occupancy associated with metabolic alterations in aged Mammalian liver Cell reports 9 996-1006

Bohla D, Herold M, Panzer I, Buxa M K, Ali T, Demmers J, Kruger M, Scharfe M, Jarek M, Bartkuhn M and Renkawitz R 2014 A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking PLoS ONE 9 e107765

Carone B R, Hung J H, Hainer S J, Chou M T, Carone D M, Weng Z, Fazzio T G and Rando O J 2014 High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm Dev Cell 30 11-22

Chen K, Johnston J, Shao W, Meier S, Staber C and Zeitlinger J 2013a A global change in RNA polymerase II pausing during the Drosophila midblastula transition Elife 2 e00861

Chen K, Wilson M A, Hirsch C, Watson A, Liang S, Lu Y, Li W and Dent S Y 2013b Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor Genome Res 23 312-22

Chen L, Chen K, Lavery L A, Baker S A, Shaw C A, Li W and Zoghbi H Y 2015 MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome Proc Natl Acad Sci U S A 112 5509-14

Chen P, Zhao J, Wang Y, Wang M, Long H, Liang D, Huang L, Wen Z, Li W, Li X, Feng H, Zhao H, Zhu P, Li M, Wang Q F and Li G 2013c H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin Genes Dev 27 2109-24

Chodavarapu R K, Feng S, Bernatavichute Y V, Chen P Y, Stroud H, Yu Y, Hetzel J A, Kuo F, Kim J, Cokus S J, Casero D, Bernal M, Huijser P, Clark A T, Kramer U, Merchant S S, Zhang X, Jacobsen S E and Pellegrini M 2010 Relationship between nucleosome positioning and DNA methylation Nature 466 388-92

Dang W, Sutphin G L, Dorsey J A, Otte G L, Cao K, Perry R M, Wanat J J, Saviolaki D, Murakami C J, Tsuchiyama S, Robison B, Gregory B D, Vermeulen M, Shiekhattar R, Johnson F B, Kennedy B K, Kaeberlein M and Berger S L 2014 Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response Cell Metab 19 952-66.

Deng T, Zhu ZI, Zhang S et al. HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells, Mol Cell Biol 2013;33:3377-3389.

DeGennaro C M, Alver B H, Marguerat S, Stepanova E, Davis C P, Bahler J, Park P J and Winston F 2013 Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast Mol Cell Biol 33 4779-92

Diermeier S, Kolovos P, Heizinger L, Schwartz U, Georgomanolis T, Zirkel A, Wedemann G, Grosveld F, Knoch T A, Merkl R, Cook P R, Langst G and Papantonis A 2014 TNFalpha signalling primes chromatin for NF-kappaB binding and induces rapid and widespread nucleosome repositioning Genome Biol 15 536

Dutta A, Gogol M, Kim J H, Smolle M, Venkatesh S, Gilmore J, Florens L, Washburn M P and Workman J L 2014 Swi/Snf dynamics on stress-responsive genes is governed by competitive bromodomain interactions Genes Dev 28 2314-30

Fan X, Moqtaderi Z, Jin Y, Zhang Y, Liu X S and Struhl K 2010 Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation Proc Natl Acad Sci U S A 107 17945-50

Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza J Z, Innocenti C, Ferrier P, Spicuglia S, Gut M, Gut I and Andrau J C 2012 CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters Genome Res 22 2399-408

Fu Y, Luo G Z, Chen K, Deng X, Yu M, Han D, Hao Z, Liu J, Lu X, Dore L C, Weng X, Ji Q, Mets L and He C 2015 N6-methyldeoxyadenosine marks active transcription start sites in chlamydomonas Cell 161 879-92

Fuda N J, Guertin M J, Sharma S, Danko C G, Martins A L, Siepel A and Lis J T 2015 GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters PLoS Genet 11 e1005108

Gaffney D J, McVicker G, Pai A A, Fondufe-Mittendorf Y N, Lewellen N, Michelini K, Widom J, Gilad Y and Pritchard J K 2012 Controls of nucleosome positioning in the human genome PLoS Genet 8 e1003036

Gilchrist D A, Dos Santos G, Fargo D C, Xie B, Gao Y, Li L and Adelman K 2010 Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation Cell 143 540-51

Givens R M, Lai W K, Rizzo J M, Bard J E, Mieczkowski P A, Leatherwood J, Huberman J A and Buck M J 2012 Chromatin architectures at fission yeast transcriptional promoters and replication origins Nucleic Acids Res 40 7176-89

Gossett A J and Lieb J D 2012 In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae PLoS Genet 8 e1002771

Hainer S J, Gu W, Carone B R, Landry B D, Rando O J, Mello C C and Fazzio T G 2015 Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF Genes Dev 29 362-78

Hasegawa K, Sin H S, Maezawa S, Broering T J, Kartashov A V, Alavattam K G, Ichijima Y, Zhang F, Bacon W C, Greis K D, Andreassen P R, Barski A and Namekawa S H 2015 SCML2 establishes the male germline epigenome through regulation of histone H2A ubiquitination Dev Cell 32 574-88

Henikoff J G, Thakur J, Kasinathan S and Henikoff S 2015 A unique chromatin complex occupies young alpha-satellite arrays of human centromeres Sci Adv 1

Hu G, Schones D E, Cui K, Ybarra R, Northrup D, Tang Q, Gattinoni L, Restifo N P, Huang S and Zhao K 2011 Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1 Genome Res 21 1650-8

Hu Z, Chen K, Xia Z, Chavez M, Pal S, Seol J H, Chen C C, Li W and Tyler J K 2014 Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging Genes Dev 28 396-408

Huebert D J, Kuan P F, Keles S and Gasch A P 2012 Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators Mol Cell Biol 32 1645-53

Hughes A L and Rando O J 2015 Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo G3 (Bethesda)

Ishii H, Kadonaga J T and Ren B 2015 MPE-seq, a new method for the genome-wide analysis of chromatin structure Proc Natl Acad Sci U S A

Jung I, Kim S K, Kim M, Han Y M, Kim Y S, Kim D and Lee D 2012 H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells Genome Res 22 1026-35

Kelly T K, Liu Y, Lay F D, Liang G, Berman B P and Jones P A 2012 Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules Genome Res 22 2497-506

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith C L, Raha D, Winters E E, Johnson S M, Snyder M, Batzoglou S and Sidow A 2012 Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements Genome Res 22 1735-47

Lay F D, Liu Y, Kelly T K, Witt H, Farnham P J, Jones P A and Berman B P 2015 The role of DNA methylation in directing the functional organization of the cancer epigenome Genome Res 25 467-77

Lhoumaud P, Hennion M, Gamot A, Cuddapah S, Queille S, Liang J, Micas G, Morillon P, Urbach S, Bouchez O, Severac D, Emberly E, Zhao K and Cuvier O 2014 Insulators recruit histone methyltransferase dMes4 to regulate chromatin of flanking genes EMBO J 33 1599-613

Li G, Liu S, Wang J, He J, Huang H, Zhang Y and Xu L 2014 ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis The Plant journal : for cell and molecular biology 78 706-14

Li Z, Gadue P, Chen K, Jiao Y, Tuteja G, Schug J, Li W and Kaestner K H 2012 Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation Cell 151 1608-16

Lidor Nili E, Field Y, Lubling Y, Widom J, Oren M and Segal E 2010 p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy Genome Res 20 1361-8

Lopez-Serra L, Kelly G, Patel H, Stewart A and Uhlmann F 2014 The Scc2-Scc4 complex acts in sister chromatid cohesion and transcriptional regulation by maintaining nucleosome-free regions Nat Genet 46 1147-51

Mavrich T N, Jiang C, Ioshikhes I P, Li X, Venters B J, Zanton S J, Tomsho L P, Qi J, Glaser R L, Schuster S C, Gilmour D S, Albert I and Pugh B F 2008 Nucleosome organization in the Drosophila genome Nature 453 358-62

Menet J S, Pescatore S and Rosbash M 2014 CLOCK:BMAL1 is a pioneer-like transcription factor Genes Dev 28 8-13

Morselli M, Pastor W A, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark A T, Ottonello S, Jacobsen S E and Pellegrini M 2015 In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse Elife 4 e06205

Nadal-Ribelles M, Conde N, Flores O, Gonzalez-Vallinas J, Eyras E, Orozco M, de Nadal E and Posas F 2012 Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling Genome Biol 13 R106

Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard J K and Fondufe-Mittendorf Y N 2014 The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation BMC Genomics 15 92

Parnell T J, Schlichter A, Wilson B G and Cairns B R 2015 The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism Elife 4 e06073

Ramachandran S, Zentner G E and Henikoff S 2015 Asymmetric nucleosomes flank promoters in the budding yeast genome Genome Res 25 381-90

Samans B, Yang Y, Krebs S, Sarode G V, Blum H, Reichenbach M, Wolf E, Steger K, Dansranjavin T and Schagdarsurengin U 2014 Uniformity of nucleosome preservation pattern in Mammalian sperm and its connection to repetitive DNA elements Dev Cell 30 23-35

Schones D E, Cui K, Cuddapah S, Roh T Y, Barski A, Wang Z, Wei G and Zhao K 2008 Dynamic regulation of nucleosome positioning in the human genome Cell 132 887-98

Scruggs B S, Gilchrist D A, Nechaev S, Muse G W, Burkholder A, Fargo D C and Adelman K 2015 Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin Mol Cell 58 1101-12

Shim Y S, Choi Y, Kang K, Cho K, Oh S, Lee J, Grewal S I and Lee D 2012 Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin EMBO J 31 4375-87

Shimbo T, Du Y, Grimm S A, Dhasarathy A, Mav D, Shah R R, Shi H and Wade P A 2013 MBD3 localizes at promoters, gene bodies and enhancers of active genes PLoS Genet 9 e1004028

Steglich B, Stralfors A, Khorosjutina O, Persson J, Smialowska A, Javerzat J P and Ekwall K 2015 The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast PLoS Genet 11 e1005101

Tao Y, Zheng W, Jiang Y, Ding G, Hou X, Tang Y, Li Y, Gao S, Chang G, Zhang X, Liu W, Kou X, Wang H and Jiang C 2014 Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers BMC Biol 12 109

Teif V B, Beshnova D A, Vainshtein Y, Marth C, Mallm J P, Höfer T and Rippe K 2014 Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development Genome Research 24 1285-95

Teif V B, Vainstein E, Marth K, Mallm J-P, Caudron-Herger M, Höfer T and Rippe K 2012 Genome-wide nucleosome positioning during embryonic stem cell development Nat Struct Mol Biol 19 1185-92

Tirosh I, Sigal N and Barkai N 2010 Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences Mol Syst Biol 6 365

Tolstorukov M Y, Sansam C G, Lu P, Koellhoffer E C, Helming K C, Alver B H, Tillman E J, Evans J A, Wilson B G, Park P J and Roberts C W 2013 Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters Proc Natl Acad Sci U S A 110 10165-70

Tsankov A, Yanagisawa Y, Rhind N, Regev A and Rando O J 2011 Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization Genome Res 21 1851-62

Tsankov A M, Thompson D A, Socha A, Regev A and Rando O J 2010 The role of nucleosome positioning in the evolution of gene regulation PLoS Biol 8 e1000414

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek J A, Costa G, McKernan K, Sidow A, Fire A and Johnson S M 2008 A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning Genome Res 18 1051-63

Valouev A, Johnson S M, Boyd S D, Smith C L, Fire A Z and Sidow A 2011 Determinants of nucleosome organization in primary human cells Nature 474 516-20

Van de Vosse D W, Wan Y, Lapetina D L, Chen W M, Chiang J H, Aitchison J D and Wozniak R W 2013 A role for the nucleoporin Nup170p in chromatin structure and gene silencing Cell 152 969-83

Weiner A, Hughes A, Yassour M, Rando O J and Friedman N 2010 High-resolution nucleosome mapping reveals transcription-dependent promoter packaging Genome Res 20 90-100

West J A, Cook A, Alver B H, Stadtfeld M, Deaton A M, Hochedlinger K, Park P J, Tolstorukov M Y and Kingston R E 2014 Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming Nature communications 5 4719

Whitehouse I, Rando O J, Delrow J and Tsukiyama T 2007 Chromatin remodelling at promoters suppresses antisense transcription Nature 450 1031-5

Woo S, Zhang X, Sauteraud R, Robert F and Gottardo R 2013 PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data Bioinformatics 29 2049-50

Yearim A, Gelfman S, Shayevitch R, Melcer S, Glaich O, Mallm J P, Nissim-Rafinia M, Cohen A H, Rippe K, Meshorer E and Ast G 2015 HP1 is involved in regulating the global impact of DNA methylation on alternative splicing Cell reports 10 1122-34

Yen K, Vinayachandran V and Pugh B F 2013 SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes Cell 154 1246-56

Yoshida K, Bacal J, Desmarais D, Padioleau I, Tsaponina O, Chabes A, Pantesco V, Dubois E, Parrinello H, Skrzypczak M, Ginalski K, Lengronne A and Pasero P 2014 The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast Mol Cell 54 691-7

Zacarias-Cabeza J, Belhocine M, Vanhille L, Cauchy P, Koch F, Pekowska A, Fenouil R, Bergon A, Gut M, Gut I, Eick D, Imbert J, Ferrier P, Andrau J C and Spicuglia S 2015 Transcription-dependent generation of a specialized chromatin structure at the TCRbeta locus J Immunol 194 3432-43

Zhang Y, Vastenhouw N L, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier A F and Liu X S 2014 Canonical nucleosome organization at promoters forms during genome activation Genome Res 24 260-6

Zhang Z and Pugh B F 2011 High-resolution genome-wide mapping of the primary structure of chromatin Cell 144 175-86

Zhang Z, Wippo C J, Wal M, Ward E, Korber P and Pugh B F 2011 A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome Science 332 977-80

Zhu Y, Rowley M J, Bohmdorfer G and Wierzbicki A T 2013 A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing Mol Cell 49 298-309



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