NucPosDB – nucleosome positioning database [old]

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  

**Also see: |  nucleosome calling/analysis software  | nucleosome positioning prediction | experimental nucleosome datasets | chromatin modifications | Protein-DNA binding: data, tools & models

DescriptionOrganismCell typeExperiment typeGEO ID
Single-molecule Regulatory Architectures Captured by Chromatin Fiber Sequencing (Stergachis et al., 2020).Homo sapiensK562Fiber-seqGSE146941
Genome information processing by the INO80 chromatin remodeler positions nucleosomes ( Oberbeckmann et al., 2020)Saccharomyces cerevisiaeHu0303MNase-seqGSE145093
Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation (Zhao et al., 2020).Arabidopsis thalianaMH-seqGSE142495
Rapid and Inexpensive Preparation of Genome-Wide Nucleosome Footprints from Model and Non-Model Organisms (McKnight et al., 2019).Schizosaccharomyces pombe, Saccharomyces cerevisiae, Neurospora crassaMNase-seqGSE141676
Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome ( Oberbeckmann et al., 2019)Saccharomyces cerevisiaeMNase-seqGSE141043
Ruler elements in chromatin remodelers set nucleosome array spacing and phasing (Oberbeckmann et al., 2020) Saccharomyces cerevisiaeMNase-seqGSE140614
MNase sensitivity of promoter chromatin in GM12878 cells during stimulation with heat-killed Salmonella typhimurium (Cole and Dennis, 2019).Homo sapiensGM12878MNase-seqGSE139224
Nucleosome profiles in strains with different number of nucleosomes at HML and HMR ( Saxton and Rine, 2019 )Saccharomyces cerevisiaeMNase-seqGSE136897
Redefining the nucleosomal architecture of active and inactive promoters in the context of cellular plasticity and cancer (Dennis et al., 2020).Homo sapiensMCF10A, MCF10A-CA1aMNase-seqGSE134297
Differential Nucleosome Spacing in Neurons and Glia (Clark et al., 2020).Mus musculusNeurons, gliaMNase-seqGSE133966
Topoisomerases modulate the timing of meiotic DNA breakage and chromosome morphogenesis in Saccharomyces cerevisiae ( Heldrich et al., 2020)Saccharomyces cerevisiaeMNase-seqGSE131994
Sir2 suppresses transcription-mediates displacement of Mcm2-7 replicative helicases at the ribosomal DNA repeats ( Foss et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE130273
Quantitative MNase-seq accurately maps nucleosome occupancy levels. (Chereji, Bryson and Henikoff, 2019). Drosophila melanogasterS2, Kc167 MNase-seqGSE128689
Distinct transcriptional roles for Histone H3-K56 acetylation during cell cycle ( Topal et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE126686
Genetic ablation of maternal SoxB1 results in the delay of gastrulation gene regulatory program in zebrafish (Gao, Veil and Onichtchouk, 2020).Danio rerioMNase-seqGSE125945
MeCP2 regulates gene expression through recognition of H3K27me3 (Lee et al., 2020)Mus musculusSH-SY5YMNase-seqGSE125585
High-resolution analysis of chromatin structure by MNase-SSP (Ramani, Qui and Shendure, 2019). Mus musculusmESCMNase-SSPGSE125053
The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions ( Seymour et al., 2016) Schizosaccharomyces pombe
Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing (Kurup, Campeanu and Kidder, 2019).Mus musculusmESCMNase-seqGSE123249
Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning ( Donovan et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE123237
NOMe-seq data obtained from mouse embryonic stem cells (Requena et al., 2019).Mus musculusmESCNOME-seqGSE122964
Transcription factor activity and nucleosome organisation in mitosis (Owens and Navarro, 2019).Mus musculusmESCMNase-seqGSE122589
Transcription factor activity and nucleosome organisation in mitosis (Owens and Navarro, 2019).Mus musculusmESCMNase-assisted H3 ChIP-seqGSE122589
The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo (Cucinotta et al., 2019).Saccharomyces cerevisiaeMNase-seqGSE121543
The nucleosome acidic patch directly interacts with subunits of the Paf1 and FACT complexes and controls chromatin architecture in vivo (Cucinotta et al., 2019).Saccharomyces cerevisiaeH3 ChIP-seqGSE121543
Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability (van Emden et al., 2019).Schizosaccharomyces pombeH3 ChIP-seqGSE121502
Crosstalk between chromatin structure, cohesin activity and transcription ( Maya-Miles et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE121067
MYCN knock-down leads to DNA-repair deficiency in human neuroblastoma (Hu et al., 2019)Homo sapiensBE(2)CMNase-seqGSE120857
The NSL complex–mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise (Lam et al., 2019).Drosophila melanogasterS2, KcMNase-seqGSE118726
The NSL complex–mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise (Lam et al., 2019).Drosophila melanogasterS2, KcMNase-ChIPGSE118726
FACT mediates cohesin function on chromatin ( Garcia-Luis et al., 2019)Saccharomyces cerevisiaeMNase-seqGSE118534
FACT activity and histone H3-K56 acetylation promote optimal establishment of chromatin architecture independent of ongoing transcription in Saccharomyces cerevisiae ( McCullough et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE118330
A role for Chromatin Remodeling in Cohesin Loading onto Chromosomes ( Muñoz et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE117881
Genome-wide nucleosome positioning maps from undifferentiated human iPS cells (hIPS) and iPS cells differentiated to neural progenitor cells (NPC) (Harwood and Harwood, 2019).Homo sapienshIPSC, NPCMNase-seqGSE117870
Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes (King et al., 2018)Mus musculusmESC
Nucleosome positioning - Transient Depletion and Recovery of the Essential RSC Chromatin Remodelin Complex ( Klein-Brill et al., 2019)Saccharomyces cerevisiaeMNase-seqGSE117598
Contrasting role of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination ( Ocampo et al., 2019)Saccharomyces cerevisiaeMNase-seqGSE117514
Nucleosome position mapping by micrococcal nuclease analysis of S. cerevisiae cells in raffinose and galactose containing media ( Donovan et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE116337
Spt6 is requires for the fidelity of promoter selectivity ( Doris et al., 2018)Saccharomyces cerevisiaeMNase-seqGSE115775
Nucleosome occupancy of C. elegans wild-type (N2) early stage embryos vs. mature sperm from him-8(e1489) males (Tabuchi, Rechtsteiner and Strome, 2018).Caenorhabditis elegansMNase-seqGSE115705
DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries (Wiehle et al., 2019).Mus musculusmESCMNase-assisted H3 ChIP-seqGSE114599
Chromatin accessibility dynamics across C. elegans development and ageing ( Jänes et al., 2018)Caenorhabditis elegansMNase-seqGSE114481
Genome-wide maps of nucleosome positioning in asynchronously growing yeast cells ( Cutler et al., 2018)Saccharomyces cerevisiaeMNase-seqGSE112427
Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (Barisic et al., 2019).Mus musculusmESCMNase-seqGSE112134
Genome-wide measurement of local nucleosome array regulatiry and spacing by nanopore sequencing (Baldi et al., 2018)Drosophila melanogasterNanopore-seq, MNase-seqGSE110807
MNase-seq for budding yeast Saccharomyces cerevisiae ( Miura et al., 2018)Saccharomyces cerevisiaeMNase-seqGSE110666
Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation (Veil et al., 2019).Danio rerioMNase-seqGSE109410
The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis (Torres and Deal, 2019). Arabidopsis thalianaMNase-seqGSE108450
CHRAC/ACF contribute to the repressive ground stated of chromatin (Scacchetti et al., 2018)Drosophila melanogasterMNase-seqGSE106731
Human exonization through differential nucleosome occupancy (Li et al., 2018)MultispeciesMNase-seqGSE106578
Histone exchange assay in loss of DOT1 ( Lee et al., 2018)Saccharomyces cerevisiaeMNase-seqGSE106450
Deciphering cis-regulatory logic with 100 million synthetic promoters ( Ocampo et al., 2019)Saccharomyces cerevisiaeMNase-seqGSE104903
Viral proteins as a potential driver of histone depletion in dinoflagellates ( Irwin et al., 2018)Saccharomyces cerevisiaeMNase-seqGSE102280
Nucleosome and H1 maps generated from AEL 3-4hr and 14-15hr D. melanogaster embryos (Hu et al., 2018). Drosophila melanogasterMNase-seqGSE101327
CBP regulates recruitment and release of promoter-proximal RNA polymerase II (Boija et al., 2017)Drosophila melanogasterS2MNase-seqGSE100614
Characterising the nuclease accessibility of DNA in human cells to map higher order structures of chromatin (Schwartz et al., 2019)Homo sapiensHeLaMNase-seqGSE100401
Enhanced chromatin accessibility of the dosage compensated Drosophila male X chromosome requires the CLAMP zinc finger protein (Urban et al., 2017)Drosophila melanogasterS2, KcMNase-seqGSE99893
Proper nucleosome positioning by the DIM-1 chromatin remodeler prevents intergenic cytosine methylation but allows DNA damage by 5-azacytidine in Neurospora crassa (Klocko et al., 2019).Neurospora crassaMNase-seqGSE98911
Proper nucleosome positioning by the DIM-1 chromatin remodeler prevents intergenic cytosine methylation but allows DNA damage by 5-azacytidine in Neurospora crassa (Klocko et al., 2019).Neurospora crassaH3 ChIP-seqGSE98911
Transcription and Remodeling produce asymmetrically unwrapped nucleosomal intermediates (Ramachandran et al., 2017)Drosophila melanogasterS2MNase-seqGSE98351
Transfer RNA Genes Affect Chromsome Architecture and Function ( Hamdadi et al., 2019 )Saccharomyces cerevisiaeMNase-seqGSE98304
DDM1 and Lsh remodelers allow methylation of DNA wrapped in nucleosomes (Lyons and Zilberman, 2017). Arabidopsis thalianaMNase-seqGSE96994
Single-cell MNase-seq (scMNase-seq) measures genome-wide nucleosome positioning and chromatin accessibility simultaneously in single cell (Lai et al., 2018).Mus musculusNIH3T3, mESC, naïve CD4 T cellsscMNase-seqGSE96688
N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena ( Wang et al., 2017)Tetrahymena thermophilaMNase-seqGSE96521
Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction (Mueller et al., 2017)Drosophila melanogasterS2MNase-seqGSE95689
Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis (Pass et al., 2017). Arabidopsis thalianaCol0MNase-seqGSE94377
Tyrosine-1 of RNAPII CTD controls global termination of gene transcription in mammals (Shah et al., 2018). Homo sapiensRaji B cellsMNase-seqGSE94330
Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning ( Gutiérrez et al., 2017)Saccharomyces cerevisiaeMNase-seqGSE94313
Histone variant H2A.L.2 guides transition protein - dependent protamine assembly in male germ cells (Barral et al., 2017). Mus musculusSpermatocyte, spermatidMNase-seqGSE93251
Mouse adenocarcinoma cells, untreated and treated with dexamethasone. Conventional and pioneer modes of glucocorticoid receptor interaction with enhancer chromatin in vivo (Johnson et al., 2018). Mus musculus3134 adenocarcinoma cellsMNase-seqGSE92505
Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells (Mylonas and Tessarz, 2018)Mus musculusmESCMNase-seq
Early-life gene expression in neurons modulates lasting epigenetic states (Stroud et al., 2017)Mus musculusNeuronMNase-seqGSE90906
A high-resolution map of transcriptional repression (Liang et al., 2017). Mus musculuspre-B cell line B3MNase-seqGSE89716
Arabidopsis Chromatin Assembly Factor 1 is required for occupancy and position of a subset of nucleosomes (Muñoz-Viana et al., 2017)Arabidopsis thalianaCol leaf, fas2 leaf, Col-0 seedling, fas2 seedlingMNase-seqGSE87421
Functional Roles of Acetylated Histone Marks at Mouse Meiotic Recombination Hot Spots (Getun et al., 2017)Mus musculusTestisMNase-seqGSE87057
A comparison of nucleosome organization in Drosophila cell lines (Martin et al., 2017)Drosophila melanogasterS2, Cme-L1, ML-DmD11, ML-DmD20, ML-DmD17MNase-seqGSE85584
ACF1 regulates nucleosome spacing in Drosophila chromatin (Baldi et al., 2018)Drosophila melanogasterBG3-c2MNase-seq, MNase-assisted H3 ChIP-seqGSE85406, GSE85407
Genomic features shaping the landscape of meiotic double-strand break hotspots in maize ( He et al., 2017)Zea mays
Using affinity purification approach to capture different stages of glial-specific information on gene expression, nucleosome occupancy and histone modifications (HMs) in Drosophila melanogaster embryo (Ye et al., 2016).Drosophila melanogasterEmbryonic glial cellsMNase-seqGSE83376
Epigenetic silencing of miR-125b is required for normal B-cell development (Li et al., 2018)Mus musculus
Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping (Voong et al., 2016)Mus musculusmESCMNase-seqGSE82127
Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. (Ye et al., 2017).Drosophila melanogasterNSC, neuronsMNase-seqGSE80457
Nucleosome fragility is associates with future transcriptional response to developmental cues and stress in C. elegans ( Jeffers and Lieb, 2017)Caenorhabditis elegansMNase-seqGSE79567
Transcriptional Regulation of the Ambient Temperature Response by H2A.Z Nucleosomes and HSF1 Transcription Factors in Arabidopsis (Cortijo et al., 2017)Arabidopsis thalianaCol0 seedlingsMNase-seqGSE79355
MNase titration with four different MNase amounts in K562 (low coverage) (Mieczkowski et al., 2016)Homo sapiensK562MNase-seqGSE78984
MNase titration reveals differences between nucleosome occupancy and chromatin accessibility (Mieczkowski et al., 2016)Mus musculusmESC, NPCMNase-seqGSE78984
Genomic analysis of N. crassa histone H1 ( Seymour et al., 2016) Neurospora crassaMNase-seqGSE78157
Nuclease footprints in sperm project past and future chromatin regulatory events (Johnson et al., 2016)Mus musculusC57BL/6MNase-seqGSE78075
MNase-seq of Tetrahymena thermophila macronucleus (MAC) and micronucleus (MIC) ( Jeffers and Lieb, 2017)Tetrahymena thermophilaMNase-seqGSE77660
Histone modification and nucleosome mapping in human liver cancer cells histone modification data at the single nucleosome resolution in human embryonic stem cells, normal hepatocytes, and liver cancer cells of both genders (Zheng et al., 2019).Homo sapiensHepG2MNase-seqGSE76344
Genome-wide maps of chromatin state during the differentiation of hESC into hNECs (Du et al., 2017)Homo sapienshESC; hESC-derived neuroectoderm cellsMNase-seqGSE76083
Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer (Gomez et al., 2016)Homo sapiensH1 ESC; Cultured Kidney CellMNase-seqGSE75172
Antisense transcription predicts a distinct chromatin environment at mammalian promoters (Lavender et al., 2016)Homo sapiensT47D/A1-2MNase-seqGSE74308
Dynamics of chromatin maturation after genome replication ( Vasseur et al., 2016)Saccharomyces cerevisiae
Targeting the SIN3A-PF1 Interaction inhibits Epithelial to Mesenchymal Transition and Maintenance of a Stem Cell Phenotype in Triple Negative Breast Cancer (Bansal et al., 2015)Homo sapiensMDA-MB-231MNase-seqGSE73869
Divergent residues within histone H3 define a unique chromatin structure in S. cerevisiae ( McBurney et al., 2016)Saccharomyces cerevisiaeMNase-seqGSE73425
Nucleosome positioning and chromatin state in GATA3-mediated mesenchymal-epithelial transition (low coverage MNase-seq) (Takaku et al., 2016)Homo sapiensMDA-MB-231MNase-seqGSE72141
Genomic nucleosome organisation recontrituted with pure proteins ( Krietenstein et al., 2016)Saccharomyces cerevisiaeMNase-seqGSE72106
Whole genome nucleosome positioning by MNase-seq on the mouse tumor line, RMA (Wight et al., 2016)Mus musculusNK-T, RMAMNase-seqGSE71863
Nucleosome Repositioning: Nicotine- and Cocaine-induced Changes (Brown et al., 2015).Homo sapiensSH-SY5YMNase-ChIPGSE71795
Intrinsic histone acetyltransferase activity of BRD4 is responsible for nucleosome eviction and transcriptional activation (Devaiah et al., 2016)Homo sapiensU2OSMNase-seqGSE71577
Histone retention loci alteration in human sperm cell genome after density selection (Yu et al., 2015)Homo sapiensSpermMNase-seqGSE71483
Rube et al. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat Commun 2016 Mar 24;7:11025 (Rube et al., 2016)Mus musculusOlfactory epitheliumMNase-seqGSE71126
GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes (Tsai et al., 2016)Drosophila melanogasterMNase-seqGSE70633
Mouse thymocytes (Teng et al., 2015)Mus musculusthymocytesMNase-seqGSE69474
The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo (Ocampo et al., 2016).Saccharomyces cerevisiaeMNase-seqGSE69400
Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster (Chereji et al., 2016).Drosophila melanogaster12h embryo and S2 cellsMNase-seqGSE69177
Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in D. melanogaster (Chereji et al., 2016).Drosophila melanogaster12h embryo and S2 cellsMNase-assisted H3 ChIP-seqGSE69177
Mouse ESCs (Ishii et al. 2015) (Ishii et al., 2015)Mus musculusmESCMNase-seq, MPE-seqGSE69098
Active N6-Methyladenine demethylation by DMAD regulates gene expression by modulating the binding dynamics of Polycomb protein in neurons (Yao et al., 2018)Drosophila melanogasterBG3-c2MNase-seqGSE67855
Rpd3 drives transcriptional quiescence ( McKnight et al., 2015)Saccharomyces cerevisiaeH3 ChIP-seqGSE67151
Rpd3 drives transcriptional quiescence ( McKnight et al., 2015)Saccharomyces cerevisiaeMNase-seqGSE67148
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
Strain W303, stationary growth phase. Wild type (WT) and with introduced DNMT3b (Morselli et al., 2015)Saccharomyces cerevisiaeStrain W303, stationary growth phaseMNase-seqGSE66907
Hypothalamus from MeCP2 knockout mice and control mice (Chen et al., 2015)Mus musculusHypothalamusMNase-seqGSE66869
Cryptic transcription is the primary driving force for nucleosome instability in Spt16 mutant cells ( Feng et al., 2016)Saccharomyces cerevisiaeMNase-seqGSE66215
The nucleosome landscape of P. falciparum reveals chromatin architecture and dynamics of regulatory sequences ( Kensche et al., 2016)Plasmodium falciparumMNase-seqGSE66185
Novel nucleosomal particles containing core histones and linker DNA but no histone H1 (Cole et al., 2016)Mus musculus, Saccharomyces cerevisiaeMNase-seqGSE65889
SF3B1 association with chromatin determines splicing outcomes (Kfir et al., 2015)Homo sapiensHeLaMNase-seqGSE65644
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 cerevisiaeMNase-seqGSE65593
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation (Sun et al., 2015)Drosophila melanogasterOrego-RMNase-seqGSE65441
MNase-seq of chromatin from control and Snail2-expressing oral keratinocytes (Lyons and Delic, 2015)Homo sapiensHN13(TVA)MNase-seqGSE65191
Mouse ESCs, wild type (WT) and Dnmt1/3a/3b triple knockout (Yearim et al., 2015)Mus musculusmESCMNase-seqGSE64910
Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells (de Dieuleveult et al., 2016)Mus musculusmESCMNase-seqGSE64825
S2 cell line. WT and stimulated by heat killed Salmonella typhimurium (Ren et al., 2015)Drosophila melanogasterS2MNase-seqGSE64507
Chlamydomonas strain CC 1609. MNase-seq (Fu et al., 2015)Chlamydomonas reinhardtiistrain: CC 1609MNase-seqGSE62690
Mouse bone marrow-derived macrophages (BMDMs) (Scruggs et al., 2015)Mus musculusBMDM, macrophageMNase-seqGSE62151
High resolution chromatin dynamics during a yeast stress response (Weiner et al., 2015).Saccharomyces cerevisiaeMNase-assisted H3 ChIP-seqGSE61888
WT and Snf2 K1493R, K1497R strains; unstressed/stressed (Dutta et al., 2014)Saccharomyces cerevisiaeK1493R, K1497R strainsMNase-seqGSE61210
HuRef lymphoblastoid line, α-satellite arrays of centromeres (Henikoff et al., 2015)Homo sapiensHuRefMNase-seqGSE60951
Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells (Huang et al., 2015)Mus musculusMEFMNase-assisted H3 ChIP-seqGSE60627
WT and modification affecting one of the following chromatin remodelers: ISW1, CHD1, FUN30, IOC3 (Ramachandran et al., 2015)Saccharomyces cerevisiaeStrain W303MNase-seqGSE59523
WCE and histone H3 ChIP-seq samples are compared to H3K27me3 ChIP-seq and RNA-seq (Flensburg et al., 2014).Mus musculusH3 ChIP-seqGSE59419
Mouse EScs, WT and remodeler BAF250a knockout (Lei et al., 2015)Mus musculusmESCMNase-seqGSE59082
Human embryonic stem cells, induced pluripotent stem cells and differentiated fibroblasts (West et al., 2014)Homo sapienshESC, hiPSC, hFibMNase-seqGSE59062
Mouse ESCs, induced pluripotent stem cells (iPSCs), somatic tail-tip fibroblasts (TTF) and liver (West et al., 2014)Mus musculusmESC, iPSC, TTFMNase-seqGSE59062
Acetylation of histone H4 at lysine 44 facilitates meiotic recombination by creating accessible chromatin ( Hu et al., 2015)Saccharomyces cerevisiaeMNase-seqGSE59004
S2 cell line. WT; treated with RNAi against Beta-galactosidase or GAGA (Fuda et al., 2015)Drosophila melanogasterS2MNase-seqGSE58957
RNAi-depleted GAF from Drosophila S2 cells and their the effects on promoter-proximal polymerase (Fuda and Lis, 2015). Drosophila melanogasterS2MNase-seqGSE58956
Chromatin modification dynamics at p53 binding sites upon treatment with DMSO or nutlin3-a (5uM) in IMR90 human lung fibroblasts using ChIP-seq and RNA-seq analyses; genomewide changes in H3, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H4K16ac, RNA polymerase II, and p53 in response to p53 activation (Sammons et al., 2015).Homo sapiensIMR90H3 ChIP-seqGSE58740
HCT116 colon cancer cells and their genetic derivatives which lack DNA methyltransferases DNMT3B and DNMT1 activity (Lay et al., 2015)Homo sapiensHCT116NOME-seqGSE58638
Mouse ESCs and sperm. Different size-selection of MNase-seq fragments (Carone et al., 2014)Mus musculusmESCMNase-seqGSE58101
Mouse liver, 3-mohth and 21-month old mice (Bochkis et al., 2014)Mus musculusLiverMNase-seqGSE58005
S. cerevisiae. Strain W303. Affected histone deacetylases Sir2 and Rpd3 (Yoshida et al., 2014)Saccharomyces cerevisiaeStrain W303MNase-seqGSE57618
Hypersensitive Nucleosomes in Chromatin Are Intrinsic to the Structure of Active, Tissue-Specific Enhancers. The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation (Iwafuchi-Doi et al., 2016)Mus musculusLiverMNase-seqGSE57558
Mouse ESCs, siRNA knockdown of EGFP, Smarca4 or MBD3 (Hainer et al., 2015)Mus musculusmESCMNase-seqGSE57170
S2 cell line. WT and Beaf32-depleted (Lhoumaud et al., 2014)Drosophila melanogasterS2MNase-seqGSE57166
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
Mouse ESCs, low MNase digestion; dinucleosome fraction (Teif et al. 2014)Mus musculusmESCMNase-seqGSE56938
Primary CD4+ CD8+ DP thymocytes and Rag2 -/- thymocytes (Zacarias-Cabeza et al. 2015)Mus musculusCD4+, CD8+, DP thymocytesMNase-seqGSE56395
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
Genome-wide maps of PARP-1-bound nucleosomes (Matveeva et al., 2016)Drosophila melanogasterS2MNase-seqGSE56120
Siklenka et al. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science 2015 Nov 6;350(6261):aab2006Mus musculusspermMNase-seqGSE55471
Cultured germline stem cells with and without Scml2 knockout (Hasegawa et al. 2015).Mus musculusCultured germline stem cellsMNase-seqGSE55060
ACF chromatin remodeling complex mediates stress-induced depressive-like behavior through nucleosome repositioning and transcriptional regulation.Mus musculusnucleus accumbensMNase-assisted H3 ChIP-seqGSE54263
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
Mouse B-cell to macrophage lineage switching, several time points. Mus musculusB-cell, macrophageMNase-seqGSE53460
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
HUVEC cells stimulated with tumour necrosis factor alpha (TNFalpha) (Diermeier et al. 2014)Homo sapiensHUVECMNase-seqGSE53343
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice (Wu, Zhang and Jiang, 2014).Oryza sativaMNase-seqGSE53027
Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cellsHomo sapiensRaji B-cell lineMNase-seqGSE52914
Mouse ESCs and differentiated iMEFs. RED-seqMus musculusmESCRED-seqGSE51821
Mouse ESCs (J1) (Zhang et al. 2014)Mus musculusmESCMNase-seq, ChIP-seqGSE51766
CTCF/CP190 and ISWI dependent regulation of nucleosome occupancy (Bohla et al., 2014)Drosophila melanogasterS2H3 ChIP-seqGSE51600
S2 cell line. WT and depletion of CTCF/P190 and ISWI (Bohla et al. 2014).Drosophila melanogasterS2MNase-seqGSE51599
MCF-7 (breast cancer cell line) with and without MBD3 knockdown (Shimbo et al. 2013)Homo sapiensMCF-7MNase-seqGSE51097
Mouse ESCs, low MNase digestion (Chen et al. 2013)Mus musculusmESCMNase-seqGSE50706
Arabidopsis, Col-0 seeds; chr11-1 chr17-1, (Li et al. 2014)Arabidopsis thalianaCol-0 seedsMNase-seqGSE50242
Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast ( DeGennaro et al., 2013) Schizosaccharomyces pombeMNase-seqGSE49572
S2 cell line, WT (Nalabothula et al. 2014).Drosophila melanogasterS2MNase-seqGSE49526
Genome-wide nucleosome maps for wild type and Rsc8-depleted Saccharomyces cerevisiae (Ganguli, Cole and Clark, 2014).Saccharomyces cerevisiaeMNase-seqGSE49512
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
Sequencing and genome-wide mapping of 146 bp mono-nucleosomal DNA from human and bovine spermHomo sapiensSpermMNase-seqGSE47843
Human colo829 cell lineHomo sapienscolo829MNase-seqGSE47802
Mouse ESCs (E14) and SMARCAD1-knock down cells.Mus musculusmESCMNase-seqGSE47802
Mouse liver, 6 time points of the 24h light:dark cycle; WT and Bmal1-/- (Menet et al. 2014).Mus musculusLiverMNase-seqGSE47142
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-seqGSE47073
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
Mouse ESCs and induced pluripotent cells (iPSC) from different layers (Tao et al. 2014)Mus musculusmESC, iPSCMNase-seqGSE46716
Nucleosome positioning changes during human embryonic stem cell differentiationHomo sapienshESC (WA09, WA09-INM, WA09-SMC)MNase-seqGSE46467
Nucleosome positioning changes during human embryonic stem cell differentiationHomo sapienshESC (WA09, WA09-INM, WA09-SMC)MNase-seqGSE46461
DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes
Homo sapiensIMR90MNase-seqGSE44985
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
Staged Drosophila embryos (Chen et al. 2013).Drosophila melanogasterS2MNase-seqGSE41686
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
Mouse ESCs, NPCs and embryonic fibroblasts (MEFs) (Teif et al. 2012). Mus musculusmESC, NPC, MEFMNase-seqGSE40951
Genome-wide nucleosome positioning during embryonic stem cell development (Teif et al., 2012).Mus musculusmESC, NPC, MEFMNase-seqGSE40910
Hrp3 controls nucleosome positioning to suppress non-coding transcription in eu- and heterochromatin ( Shim et al., 2012)Schizosaccharomyces pombeMNase-seqGSE40451
Fibroblasts from E13.5 embryos. WT, Snf5-/- and Brg1-/- (Tolstorukov et al. 2013). Mus musculusMEFMNase-seqGSE38670
CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters (Fenouil et al., 2012)Mus musculusCD4+, CD8+, DP, Raji, ESC MNase-seqGSE38577
Raji cells (lymphoblastoid-like) with and without α-amanitin (Fenouil et al. 2012)Homo sapiensRaji cellsMNase-seqGSE38563
Arabidopsis, Col-0 seeds; WT and inhibition of Pol V-produced lncRNAs. MNase-seq (Zhu et al. 2013)Arabidopsis thalianaCol-0 seedsMNase-seqGSE38401
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

7 lymphoblastoid cell lines from the HapMap project (Gaffney et al. 2012)Homo sapienslymphoblastoid cellsMNase-seqGSE36979
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
Lymphoblastoid GM12878 and K562 cell lines (Kundaje et al. 2012)Homo sapiensGM12878, K562MNase-seqGSE35586
In vivo nucleosome occupancy in yeast ( Chai et al., 2013)Saccharomyces cerevisiae
Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis (Zhang et al., 2012).Arabidopsis thalianaMNase-seqGSE34318
Poised RNA Polymerase II changes over developmental time and prepares genes for future expression ( Gaertner et al., 2012)Drosophila melanogasterMNase-seqGSE34283
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
Structural mapping of regulatory function of histone H3 and H4 residues ( Jung et al., 2015)Saccharomyces cerevisiaeMNase-seqGSE29064
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.Saccharomyces cerevisiaeS. cerevisiae, C. albicans, S. pombeMNase-seqGSE28839
Chromatin architectures at fission yeast transcriptional promoters and replication origins ( Givens et al., 2011)Schizosaccharomyces pombeMNase-seqGSE28071
Mouse liver (Li et al. 2012).Mus musculusLiverMNase-seq, ChIP-seqGSE26729
CD36+ cells with and without BRG1 knockdown (Hu et al. 2011)Homo sapiensCD36+MNase-seq, ChIP-seqGSE26501
Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes (Cole et al., 2011)

Saccharomyces cerevisiaeMNase-seqGSE26493
S. cerevisiae in varying phosphate concentrationsSaccharomyces cerevisiaeSaccharomyces cerevisiaeMNase-seqGSE26392
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-cellsMNase-seqGSE25133
MCF7EcoR cells where P53 was either activated or not (Lidor Nili et al. 2010)Homo sapiensMCF-7, MCF7EcoRMNase-seqGSE22783
Tsankov et al. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010 Jul 6;8(7):e1000414Saccharomyces cerevisiaeMNase-seqGSE22211
S2 cell line. WT, mock-treated, and NELF-depleted (Gilchrist et al. 2010).Drosophila melanogasterS2MNase-seqGSE22119
Nucleosome positioning and DNA methylation in IMR90 (Kelly et al. 2012).Homo sapiensIMR90NOME-seqGSE21823
Relationship between nucleosome positioning and methylation Chodavarapu et al., 2010).Arabidopsis thalianaMNase-seq, H3 ChIP-seqGSE21821
Col-0 seeds, shoots; MNase-seq, ChIP-seq, Bisulfite sequencing (Chodavarapu et al. 2010)Arabidopsis thalianaCol-0 seedsMNase-seqGSE21673
Comparison of nucleosome positioning in S. cerevisiae, S. paradoxus and their hybrid for wild-type and deletion mutant strains (Tirosh et al. 2010).
Saccharomyces cerevisiae, Saccharomyces 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 microarraysGSE8814
Chromatin remodelling by Isw2 (Whitehouse et al. 2007). cerevisiaeSaccharomyces cerevisiaeTiling microarraysGSE8813
Pilot ENCODE: Determination of chromatin architecture along 44 human loci selected by the ENCODE consortium as common targets for genomic analysis, totalling 30 Mbp. The patterns of core histone H3 and five histone modifications were investigated: H3ac, H4ac, H3K4me1, H3K4me2, H3K4me3 (Heintzman et al., 2007).Homo sapiensHeLaH3 ChIP-chipGSE6273
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning
(Valouev et al, 2008).
Caenorhabditis elegansMixed stage, wild-type (N2) MNase-seq
Resting and activated CD4+ T cells (Schones et al., 2008). Homo sapiensCD4+ T cellsMNase-seq
Resting and activated CD4+ T cells (Schones et al., 2008). Homo sapiensCD4+ T cellsH3 ChIP-seq
Integrative Analysis of Multi-omics Data Reveals AP-1 Is a Key Regulator in Intrahepatic Cholangiocarcinoma (He et al., 2020).Homo sapiensSSP-25, CCLP-1, TFK-1, HuCCT1, HIBEpic
Defining TP53 pioneering capabilities with competitive nucleosome binding assays (Yu and Buck, 2019).MultispeciesMiSeq
Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork (Gutiérrez, MacAlpine and MacAlpine, 2018).Saccharomyces cerevisiaeMNase-seq
The Penn State Genome Cartography Project. (Mavrich et al. 2008; Zhang and Pugh 2011; Zhang et al. 2011; Yen et al. 2013). Tiling microarrays.Saccharomyces cerevisiae, Drosophila melanogasterS. cerevisiae and D. melanogasterMNase-seq
Resolving the 3D landscape of transcription-linked mammalian chromatin folding (Hsieh et al., 2020).Mus musculusmESCMicro-CGSE130275
3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome (Xie et al., 2020).Mus musculusmESCMicro-CGSE126112
Chromatin conformation identification by Cut-C ( Shimbo et al., 2019).Homo sapiensHEK293TMicro-CGSE125988
An RNA binding region in CTCF regulates chromatin looping and CTCF nuclear organization ( Hansen et al., 2019).Mus musculusmESMicro-CGSE123636
Condensin-dependent chromatin condensation represses transcription globally during quiescence (Swygert et al., 2019).Saccharomyces cerevisiaeMicro-C XLGSE120605
Transfer RNA Genes Affect Chromosome Architecture and Function (Hamdani et al., 2019).Saccharomyces cerevisiaeMicro-CGSE98543
Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome (Hsieh et al., 2016).Schizosaccharomyces pombe, Saccharomyces cerevisiaeMicro-C XLGSE85220
Mapping nucleosome resolution chromosome folding in yeast by Micro-C (Hsieh et al., 2015).Saccharomyces cerevisiaeMicro-CGSE68016