NucPosDB – nucleosome positioning database

NucPosDB is a manually curated collection of experimental nucleosome positioning datasets and computational tools related to nucleosome positioning. it  is being constantly updated, comments are very welcome. NucPosDB includes separate sections on theoretical algorithms to predict nucleosome positioning and computational tools to analyse nucleosome positionig data. For protein-DNA interaction of non-histone proteins and TFs, see the section on TF-DNA binding. Also, have a look at the epigenetic modifications section of the site.

*How to cite: Teif V.B. (2016). Nucleosome positioning: resources and tools online.  Briefings in Bioinformatics 17, 745-757. Open Access article  

DescriptionOrganismCell typeExperiment typeGEO accession numberComments
HuRef lymphoblastoid line, α-satellite arrays of centromeres (Henikoff et al. 2015).Homo sapiensHuRef ChIP-seqGSE60951
Human embryonic stem cells, induced pluripotent stem cells and differentiated fibroblastsHomo sapienshESC, hiPSC, hFibMNase-seqGSE59062
HCT116 colon cancer cells and their genetic derivatives which lack DNA methyltransferases DNMT3B and DNMT1 activity (Lay et al. 2015)Homo sapiensHCT116NOME-seqGSE58638
HUVEC cells stimulated with tumour necrosis factor alpha (TNFalpha) (Diermeier et al. 2014)Homo sapiensHUVECMNase-seqGSE53343
MCF-7 (breast cancer cell line) with and without MBD3 knockdown (Shimbo et al. 2013)Homo sapiensMCF-7MNase-seqGSE51097
Human embryonic stem cells (H1 and H9 hESCs)Homo sapiensH1, H9 hESCMNase-seqGSE49140
Human sperm (Samans et al. 2014). Limited regions retain nucleosomes in sperm.Homo sapiensSpermMNase-seqGSE47843
Human colo829 cell lineHomo sapienscolo829MNase-seqGSE47802
Raji cells (lymphoblastoid-like) with and without α-amanitin (Fenouil et al. 2012)Homo sapiensRaji cellsMNase-seqGSE38563
7 lymphoblastoid cell lines from the HapMap project (Gaffney et al. 2012)Homo sapiensPrimary lymphoblastoid cellsMNase-seqGSE36979
Lymphoblastoid GM12878 and K562 cell lines (Kundaje et al. 2012)Homo sapiensGM12878, K562MNase-seqGSE35586
CD36+ cells with and without BRG1 knockdown (Hu et al. 2011)Homo sapiensCD36+MNase-seq, ChIP-seqGSE26501
Human embryonic carcinoma (NCCIT) cell line (Jung et al. 2012)Homo sapiensNCCITMNase-seq, ChIP-seqGSE25882
Primary CD4+ T-cells, CD8+ T-cells and granulocytes (Valouev et al. 2011)Homo sapiensCD4+, CD8+ T-cells MNase-seqGSE25133
MCF7EcoR cells where P53 was either activated or not (Lidor Nili et al. 2010)Homo sapiensMCF-7, MCF7EcoRMNase-seqGSE22783
Nucleosome positioning and DNA methylation in IMR90 (Kelly et al. 2012). Homo sapiensIMR90NOME-seqGSE21823
Resting and activated CD4+ T cells (Schones et al. 2008)Homo sapiensCD4+ T cellsMNase-seq; H3, H2A.Z ChIP-seqSRA000234
DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes
Homo sapiensIMR90MNase-seqGSE44985
Nucleosome positioning changes during human embryonic stem cell differentiationHomo sapienshESC (WA09, WA09-INM, WA09-SMC)MNase-seqGSE46461
Nucleosome positioning changes during human embryonic stem cell differentiationHomo sapienshESC (WA09, WA09-INM, WA09-SMC)MNase-seqGSE46467
Sequencing and genome-wide mapping of 146 bp mono-nucleosomal DNA from human and bovine spermHomo sapiensSpermMNase-seqGSE47843
Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cellsHomo sapiensRaji B-cell lineMNase-seqGSE52914
MNase-seq of chromatin from control and Snail2-expressing oral keratinocytesHomo sapiensHN13(TVA)MNase-seqGSE65191
Histone retention loci alteration in human sperm cell genome after density selectionHomo sapiensSpermMNase-seqGSE71483
Nucleosome positioning and chromatin state in GATA3-mediated mesenchymal-epithelial transition (low coverage MNase-seq)Homo sapiensMDA-MB-231MNase-seqGSE72141
Targeting the SIN3A-PF1 Interaction inhibits Epithelial to Mesenchymal Transition and Maintenance of a Stem Cell Phenotype in Triple Negative Breast CancerHomo sapiensMDA-MB-231MNase-seqGSE73869
Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human CancerHomo sapiensH1 ESC; Cultured Kidney CellMNase-seqGSE75172
Genome-wide maps of chromatin state during the differentiation of hESC into hNECsHomo sapienshESC; hESC-derived neuroectoderm cellsMNase-seqGSE76083
MNase titration with four different MNase amounts in K562 (low coverage)Homo sapiensK562MNase-seqGSE78984
Tyrosine-1 of RNAPII CTD controls global termination of gene transcription in mammalsHomo sapiensRaji B cellsMNase-seqGSE94330
Mouse ESCs (Ishii et al. 2015). Mus musculusmESCMNase-seq, MPE-seqGSE69098
Mouse ESCs, wild type (WT) and Dnmt1/3a/3b triple knockout (Yearim et al. 2015). Mus musculusmESCMNase-seqGSE64910
Mouse EScs, WT and remodeler BAF250a knockout (Lei et al. 2015)Mus musculusmESCMNase-seqGSE59082
Mouse ESCs, induced pluripotent stem cells (iPSCs), somatic tail-tip fibroblasts (TTF) and liver (West et al. 2014)Mus musculusmESC, iPSC, TTF MNase-seqGSE59062
Mouse ESCs and sperm (Carone et al. 2014). Different size-selection of MNase-seq fragments.Mus musculusmESCMNase-seqGSE58101
Mouse ESCs, siRNA knockdown of EGFP, Smarca4 or MBD3 (Hainer et al. 2015)Mus musculusmESC MNase-seqGSE57170
Mouse ESCs, low MNase digestion; dinucleosome fraction (Teif et al. 2014)Mus musculusmESC MNase-seqGSE56938
Mouse ESCs and differentiated iMEFs. RED-seqMus musculusmESCRED-sesqGSE51821
Mouse ESCs (J1) (Zhang et al. 2014)Mus musculusmESCMNase-seq, ChIP-seqGSE51766
Mouse ESCs, low MNase digestion (Chen et al. 2013)Mus musculusmESCMNase-seqGSE50706
Mouse ESCs (E14) and SMARCAD1-knock down cells.Mus musculusmESCMNase-seqGSE47802
Mouse ESCs and induced pluripotent cells (iPSC) from different layers (Tao et al. 2014)Mus musculusmESC, iPSCMNase-seqGSE46716
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). Mus musculusmESC, NPCMNase-seqGSE44175
Mouse ESCs, NPCs and embryonic fibroblasts (MEFs) (Teif et al. 2012). Mus musculusmESC, NPC, MEFMNase-seqGSE40951
Mouse thymocytesMus musculusthymocytesMNase-seqGSE69474
Mouse B-cell to macrophage lineage switching, several time points. Mus musculusB-cell, macrophageMNase-seqGSE53460
Mouse liver, 3-mohth and 21-month old mice (Bochkis et al. 2014).Mus musculusLiver MNase-seqGSE58005
Mouse liver, 6 time points of the 24h light:dark cycle; WT and Bmal1-/- (Menet et al. 2014).Mus musculusLiverMNase-eqGSE47142
Mouse liver (Li et al. 2012).Mus musculusLiverMNase-seq, ChIP-seqGSE26729
Mouse bone marrow-derived macrophages (BMDMs) (Scruggs et al. 2015)Mus musculusBMDM, macrophageMNase-seqGSE62151
Hypothalamus from MeCP2 knockout mice and control mice (Chen et al. 2015)Mus musculusHypothalamus MNase-seqGSE66869
Cultured germline stem cells with and without Scml2 knockout (Hasegawa et al. 2015).Mus musculusCultured germline stem cellsMNase-seqGSE55060
Primary CD4+ CD8+ DP thymocytes and Rag2 -/- thymocytes (Zacarias-Cabeza et al. 2015)Mus musculusCD4+, CD8+, DP thymocytesMNase-seqGSE56395
Fibroblasts from E13.5 embryos. WT, Snf5-/- and Brg1-/- (Tolstorukov et al. 2013). Mus musculusMEFMNase-seqGSE38670
Mouse adenocarcinoma cells, untreated and treated with dexamethasone. Johnson et al., Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo. Nucleic Acids Res 2018 Jan 9;46(1):203-214.Mus musculus3134 adenocarcinoma cellsMNase-seqGSE92505
Getun et al. Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hot Spots. Mol Cell Biol 2017 Feb 1;37(3)Mus musculusTestisMNase-seqGSE87057
Liang et al. A high-resolution map of transcriptional repression. Elife 2017 Mar 20;6Mus musculuspre-B cell line B3MNase-seqGSE89716
Histone variant H2A.L.2 guides transition protein - dependent protamine assembly in male germ cells. Barral et al. Histone Variant H2A.L.2 Guides Transition Protein-Dependent Protamine Assembly in Male Germ Cells. Mol Cell 2017 Apr 6;66(1):89-101.e8Mus musculusSpermatocyte, round spermatid, condensing spermatidMNase-seqGSE93251
Transcriptional landscape of Rag2 -/- thymocytes. Cauchy et al. Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation. Nucleic Acids Res 2016 May 5;44(8):3567-85Mus musculusRag2 -/- thymocytes, primary CD4+ CD8+ DP thymocytesMNase-seqGSE56360
Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers. Iwafuchi-Doi et al. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Mol Cell 2016 Apr 7;62(1):79-91Mus musculusLiverMNase-seqGSE57558
Rube et al. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat Commun 2016 Mar 24;7:11025Mus musculusOlfactory epitheliumMNase-seqGSE71126
de Dieuleveult et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature 2016 Feb 4;530(7588):113-6.Mus musculusmESCMNase-seqGSE64825
Mieczkowski et al. MNase titration reveals differences between nucleosome occupancy and chromatin accessibility. Nat Commun 2016 May 6;7:11485.Mus musculusmESC, NPCMNase-seqGSE78984
Voong et al. Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell 2016 Dec 1;167(6):1555-1570.e15Mus musculusmESCMNase-seq; chemical mappingGSE82127
Nucleosome density map during B-cell to Macrophage lineage switching. van Oevelen et al. C/EBPα Activates Pre-existing and De Novo Macrophage Enhancers during Induced Pre-B Cell Transdifferentiation and Myelopoiesis. Stem Cell Reports 2015 Aug 11;5(2):232-47Mus musculusHAFTL (pre-B cells)MNase-seqGSE53460
ACF chromatin remodeling complex mediates stress-induced depressive-like behavior through nucleosome repositioning and transcriptional regulation.Mus musculusnucleus accumbensH3 MNase-ChIP-seqGSE54263
Siklenka et al. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science 2015 Nov 6;350(6261):aab2006Mus musculusspermMNase-seqGSE55471
Huang et al. Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells. Sci Rep 2015 Dec 7;5:17691Mus musculusMEFH3 MNase-ChIP-seqGSE60627
S2 cell line. WT and stimulated by heat killed Salmonella typhimurium.Drosophila melanogasterS2MNase-seqGSE64507
S2 cell line. WT; treated with RNAi against Beta-galactosidase or GAGA (Fuda et al. 2015).Drosophila melanogasterS2MNase-seqGSE58957
S2 cell line. WT and Beaf32-depleted (Lhoumaud et al. 2014).Drosophila melanogasterS2MNase-seqGSE57166
S2 cell line. WT and depletion of CTCF/P190 and ISWI (Bohla et al. 2014).Drosophila melanogasterS2MNase-seqGSE51599
S2 cell line, WT (Nalabothula et al. 2014).Drosophila melanogasterS2MNase-seqGSE49526
Staged Drosophila embryos (Chen et al. 2013).Drosophila melanogasterS2MNase-seqGSE41686
S2 cell line. WT, mock-treated, and NELF-depleted (Gilchrist et al. 2010).Drosophila melanogasterS2MNase-seqGSE22119
Nucleosome and H1 maps generated from AEL 3-4hr and 14-15hr D. melanogaster embryosDrosophila melanogasterembryoMNase-seqGSE101327
Arabidopsis, Col-0 seeds; chr11-1 chr17-1, (Li et al. 2014)Arabidopsis thalianaCol-0 seedsMNase-seqGSE50242
Arabidopsis, Col-0 seeds; WT and inhibition of Pol V-produced lncRNAs. MNase-seq (Zhu et al. 2013)Arabidopsis thalianaCol-0 seedsMNase-seqGSE38401
Col-0 seeds, shoots; MNase-seq, ChIP-seq, Bisulfite sequencing (Chodavarapu et al. 2010)Arabidopsis thalianaCol-0 seedsMNase-seqGSE21673
The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in ArabidopsisArabidopsis thaliana4-5 leaf developmentally-staged shoot tissueMNase-seqGSE108450
Lyons DB, Zilberman D. DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes. Elife 2017 Nov 15;6Arabidopsis thaliana1-month-old leafMNase-seqGSE96994
Muñoz-Viana et al. Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes. Plant J 2017 Nov;92(3):363-374Arabidopsis thalianaCol leaf, fas2 leaf, Col-0 seedling, fas2 seedlingMNase-seqGSE87421
Cortijo et al. Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis. Mol Plant 2017 Oct 9;10(10):1258-1273Arabidopsis thalianaCol0 seedlingsMNase-seqGSE79355
Pass et al. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet 2017 Sep;13(9):e1006988Arabidopsis thalianaCol0MNase-seqGSE94377
Mixed stage, wild-type (N2) C. elegans. SOLiD paired-end sequencing (Valouev et al. 2008)Caenorhabditis elegansMixed stage, wild-type (N2) MNase-seqSRX000426
Chlamydomonas strain CC 1609. MNase-seq (Fu et al. 2015)Chlamydomonas reinhardtiistrain: CC 1609MNase-seqGSE62690
S. cerevisiae hho1, ioc3isw1, and chd1 deletion mutants complemented with the corresponding copies from K. lactis (Hughes and Rando 2015)Saccharomyces cerevisiaeS. cerevisiae hho1, ioc3isw1, and chd1 deletion mutants; K. lactis MNase-seqGSE66979
S. cerevisiae. Strain W303, stationary growth phase. Wild type (WT) and with introduced DNMT3b (Morselli et al. 2015). Saccharomyces cerevisiaeStrain W303, stationary growth phaseMNase-seqGSE66907
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).Saccharomyces cerevisiaeStrains carrying the Sth1 degron allele and either pGal-UBR1 (YBC3386) or ubr1 null (YBC3387) represent RSC null and RSC wild type correspondinglyMNase-seqGSE65593
WT and Snf2 K1493R, K1497R strains; unstressed/stressed (Dutta et al. 2014)Saccharomyces cerevisiaeK1493R, K1497R strainsMNase-seqGSE61210
S. cerevisiae. Strain W303. WT and modification affecting one of the following chromatin remodelers: ISW1, CHD1, FUN30, IOC3 (Ramachandran et al. 2015).Saccharomyces cerevisiaeStrain W303MNase-seqGSE59523
S. cerevisiae. Strain W303. Affected histone deacetylases Sir2 and Rpd3 (Yoshida et al. 2014).Saccharomyces cerevisiaeStrain W303MNase-seqGSE57618
S. cerevisiae. Strain YK699, WT and changes addressing the following: Scc2-4; Sth1-3; a2/MCM1; TATAC; TATA∆. Replicates at 25C and 37C (Lopez-Serra et al. 2014).Saccharomyces cerevisiaeStrain YK699MNase-seqGSE56994
Dang et al. Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response. Cell Metab 2014 Jun 3;19(6):952-66Saccharomyces cerevisiaeCalorie restricted and non-restricted WT, ISW2DEL and ISW2K215R strainsMNase-seqGSE53718
Woo S, Zhang X, Sauteraud R, Robert F et al. PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data. Bioinformatics 2013 Aug 15;29(16):2049-50 Saccharomyces cerevisiaeStrain W303 (yFR212) MNase-seq and H2A.Z ChIP-seqGSE47073
“Young yeast”, “old yeast”, and “old yeast with histone over expression”. Hu et al. Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging. Genes Dev 2014 Feb 15;28(4):396-408Saccharomyces cerevisiaeStrain S288c (BY4741).MNase-seqGSE47023
Exposed/not exposed to osmostress. Nadal-Ribelles et al. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol 2012 Nov 18;13(11):R106Saccharomyces cerevisiaeStrain BY4741, WT and Hog1 mutant.MNase-seqGSE41494
Chen et al. Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8-Tup1 corepressor. Genome Res 2013 Feb;23(2):312-22Saccharomyces cerevisiaeStrain BY4742, WT, Ssn6 KO and Tup1 KO

Van de Vosse et al. A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell 2013 Feb 28;152(5):969-83Saccharomyces cerevisiaeStrain S288C. WT, Nup170∆ and Sth1p depletion MNase-seqGSE36792
Huebert DJ, Kuan PF, Keleş S, Gasch AP. Dynamic changes in nucleosome occupancy are not predictive of gene expression dynamics but are linked to transcription and chromatin regulators. Mol Cell Biol 2012 May;32(9):1645-53Saccharomyces cerevisiaeStrain BY4741MNase-seqGSE30900
Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 2012;8(6):e1002771Saccharomyces cerevisiaeStrain YEF473AMNase-seqGSE29292
Tsankov et al. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res 2011 Nov;21(11):1851-62.S. cerevisiae, C. albicans, S. pombeS. cerevisiae, C. albicans, S. pombeMNase-seqGSE28839
S. cerevisiae in varying phosphate concentrationsSaccharomyces cerevisiaeSaccharomyces cerevisiaeMNase-seqGSE26392
Tsankov et al. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010 Jul 6;8(7):e1000414Saccharomyces mikatae, Saccharomyces bayanus, Saccharomyces castellii, Saccharomyces cerevisiae, Kluyveromyces waltii, Saccharomyces paradoxus, Candida glabrata, Candida albicans, Debaryomyces hansenii, Kluyveromyces lactis, Saccharomyces kluyveryii, Yarrowia lipolytica
Saccharomyces mikatae, Saccharomyces bayanus, Saccharomyces castellii, Saccharomyces cerevisiae, Kluyveromyces waltii, Saccharomyces paradoxus, Candida glabrata, Candida albicans, Debaryomyces hansenii, Kluyveromyces lactis, Saccharomyces kluyveryii, Yarrowia lipolyticaMNase-seqGSE22211
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, S. paradoxusS. cerevisiae, S. paradoxusMNase-seqGSE18939
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).Saccharomyces cerevisiaeStrains BY4741 and RPO21. MNase-seqGSE18530
Chromatin remodelling by Isw2 (Whitehouse et al. 2007). cerevisiaeSaccharomyces cerevisiaeTiling microarraysGSE8813
Chromatin remodelling by Isw2 (Whitehouse et al. 2007). cerevisiaeSaccharomyces cerevisiaeTiling microarraysGSE8814
The Penn State Genome Cartography Project. (Mavrich et al. 2008; Zhang and Pugh 2011; Zhang et al. 2011; Yen et al. 2013). Tiling microarrays. S. cerevisiae and D. melanogaster S. cerevisiae and D. melanogaster MNase-seq
Snyder et al. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell 2016 Jan 14;164(1-2):57-68Homo Sapienscell-free DNA from blood plasma of healthy individualscfDNAGSE71378