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Nucleosome positioning datasets

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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:

Description

Accession #

Human:

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

GSE60951

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

GSE59062

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

GSE58638

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

GSE53343

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

GSE51097

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

GSE49140

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

GSE47843

Human colo829 cell line. MNase-seq

GSE47802

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

GSE38563

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

GSE36979

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

GSE35586

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

GSE26501

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

GSE25882

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

GSE25133

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

GSE22783

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

GSE21823

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

SRA000234

Mouse:

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

GSE69098

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

GSE64910

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

GSE59062

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

GSE58101

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

GSE57170

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

GSE56938

Mouse ESCs and differentiated iMEFs. RED-seq.

GSE51821

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

GSE51766

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

GSE50706

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

GSE47802

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

GSE46716

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).

GSE44175

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

GSE40951

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

GSE26729

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

GSE58005

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

GSE47142

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

GSE62151

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

GSE66869

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

GSE55060

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

GSE56395

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

GSE38670

Drosophila melanogaster, MNase-seq:

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

GSE64507

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

GSE58957

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

GSE57166

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

GSE51599

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

GSE49526

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

GSE41686

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

GSE22119

Arabidopsis thaliana:

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

GSE50242

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

GSE38401

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

GSE21673

Caenorhabditis elegans, MNase-seq:

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

SRX000426

Chlamydomonas reinhardtii:

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

GSE62690

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).

GSE66979

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

GSE66907

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).

GSE65593

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

GSE61210

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

GSE59523

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

GSE57618

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).

GSE56994

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

GSE53718

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

GSE47073

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

GSE47023

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

GSE41494

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

GSE37465

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

GSE36792

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

GSE30900

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

GSE29292

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

GSE28839

S. cerevisiae at varying phosphate concentrations

GSE26392

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

GSE23778

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).

GSE22211

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

GSE18939

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).

GSE18530

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

http://research.fhcrc.org/tsukiyama/en/genomics-data/global_nucleosomemapping.html

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. http://atlas.bx.psu.edu

 

Saccharomyces pombe, MNase-seq:

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

GSE58012

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

GSE49572

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

GSE40451

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

http://www.acsu.buffalo.edu/~mjbuck/Fission_Yeast_chromatin.html

GSE28071

 

References

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

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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

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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

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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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