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Mapping Novel Chromatin Regions Using Sono-Seq

ABSTRACT: We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple and broadly applicable method for mapping many open chromatin sites. Furthermore, these results give insights into reference sample types, such as Input DNA, normal IgG ChIP DNA, MNase-digested DNA, and naked DNA, that have been used in ChIP-chip and ChIP-Seq experiments. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

ORGANISM(S): Homo sapiens

PROVIDER: GSE14022 | GEO | 2008/12/18

REPOSITORIES: GEO

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Mapping Novel Chromatin Regions Using Sono-Seq

Project description:We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple and broadly applicable method for mapping many open chromatin sites. Furthermore, these results give insights into reference sample types, such as Input DNA, normal IgG ChIP DNA, MNase-digested DNA, and naked DNA, that have been used in ChIP-chip and ChIP-Seq experiments. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For this analysis, seven samples from HeLa S3 cells were included: RNA Polymerase II (GEO accession GSM320734), Sono-Seq/Input DNA (small fragments) that was size selected at 100-350 bp (GEO accession GSM320735), Sono-Seq/Input DNA (large fragments) size selected between 350-800 bp, naked DNA, normal mouse IgG, Sono-Seq/Input DNA stimulated with interferon-gamma (GEO accession GSM320737), and MNase-digested DNA. Two replicates were used for MNase-digested DNA and Sono-Seq/Input DNA (large fragments) whereas three replicates were used for all other samples. Naked DNA was used as a reference for scoring peaks.

2008-12-18 | E-GEOD-14022 | biostudies-arrayexpress

MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers

Project description:Micrococcal nuclease (MNase) is commonly used to map nucleosomes genome-wide, but nucleosome maps are affected by the degree of digestion. It has been proposed that many yeast promoters are not nucleosome-free but occupied by easily digested, unstable, “fragile” nucleosomes. We analyzed the histone content of all MNase-sensitive complexes by MNase-ChIP-seq and Sonication-ChIP-seq. We find that yeast promoters are predominantly bound by non-histone protein complexes, with little evidence for fragile nucleosomes. We do detect MNase-sensitive nucleosomes elsewhere in the genome, including transcription termination sites. However, they have high A/T-content, suggesting that MNase sensitivity does not indicate instability, but the preference of MNase for A/T-rich DNA, such that A/T-rich nucleosomes are digested faster than G/C-rich nucleosomes. We confirm our observations by analyzing ChIP-exo, chemical mapping and ATAC-seq data from other laboratories. Thus, histone ChIP-seq experiments are essential to distinguish nucleosomes from other DNA-binding proteins that protect against MNase.

2016-12-15 | GSE83123 | GEO

Genome-wide nucleosome occupancy profiling by high throughput sequencing, and microarray analysis of RNA abundance

Project description:We profiled nucleosome occupancy of different developmental stages in C. elegans. Mononucleosomal DNA was sequenced by Illumina paired-end sequencing. We used embryos, germlineless adults, germ line containing adults, and XO hermaphrodites at L3 larval stage. RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf After MNase digestion of chromatin, we purified mononucleosomal DNA and used Illumina paired-end sequencing. Mapping was done in embryo (strain N2), germlineless adults (strain JK1107), germ line containing adults (strain DH245),and XO hermaphrodites (strain TY2205) at L3 larval stage. For each experimental replicate RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase.

2010-03-02 | E-GEOD-20136 | biostudies-arrayexpress

Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq]

Project description:We utilized MNase-seq to profile nucleosome positions in wild type (Ax2) and ChdC null cells both in growing cells and a partially developed state (loose-mound) to study changes in nucleosome positioning and occupancy during development and the impact the deletion of ChdC an ATP-dependent chromatin remodeller has on nucleosome positioning and occupancy. As a control for MNase sequence bias we also digested naked DNA with MNase.

2017-02-26 | GSE70122 | GEO

High-resolution analysis of chromatin structure by Mnase-SSP

Project description:Proof-of-concept for Mnase-SSP: a variant of Mnase-seq. Mnase-SSP dramatically increases the representation of short fragments of nucleolytically-digested DNA, enabling simultaneous analysis of transcription factor binding and nucleosome occupancy using the same assay. We used MNase-SSP to demarcate chromatin architecture at murine promoters and at transcription factor binding sites in murine embryonic stem cells. Are results reveal heterogeneity in the binding mode of C2H2 zinc fingers like Ctcf and Rest, demonstrating that Mnase-SSP, and SSP in general, as a flexible platform for profiling nucleolytically digested DNA for MNase-seq, MNase-ChIP, or CUT&RUN with reduced bias.

2019-02-12 | GSE125053 | GEO

Differential features of lamina-associated domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

Project description:The nuclear lamina interacts with the genome through megabase-size lamina-associated domains (LADs). LADs have been identified in proximity labeling assays and recently by chromatin immunoprecipitation-sequencing (ChIP-seq) of A- and B-type lamins. LADs localize mainly to the nuclear periphery, they are gene-poor and largely heterochromatic. Here, we show that the mode of chromatin fragmentation for ChIP, namely either bath sonication (used to date for ChIP of nuclear lamins) or digestion with micrococcal nuclease (MNase) leads to the discovery of distinct sets of lamin-interacting domains (which we refer to as LiDs) with distinct gene content, histone composition enrichment and relationship to lamin B1-interacting domains. We find that total genome coverage by lamin A/C ('LMNA') LiDs identified in sonicated or MNase-digested chromatin is similar (~730 megabases). Over half of these domains, however, are uniquely detected in sonicated or MNase-digested chromatin. Whereas sonication-specific LMNA LiDs are gene-poor and devoid of a broad panel of histone modifications, MNase-specific LMNA LiDs are of higher gene density and are enriched in H3K9me3, H3K27me3 and in histone variant H2A.Z. Analysis of published LMNB1 LADs and of LMNB1 LiDs identified by ChIP-seq further shows that LMNA can associate with 'open' chromatin domains displaying euchromatin features which are not associated with LMNB1. The differential genetic and epigenetic properties of lamin-interacting chromatin domains indicate the existence of distinct LiD populations identifiable in different chromatin contexts, including nuclease-accessible 'open' regions presumably localized in the nuclear interior.

2015-03-24 | GSE57149 | GEO

Quantitative ChIP-MS analysis of histone modifications present on H3K4me1- and H3K4me3-enriched mono-nucleosomes purified from crosslinked IMR-90 cells

Project description:The INO80 complex is a chromatin remodeler that regulates DNA replication, repair, and transcription. Although the INO80 complex plays a crucial role in various chromatin-associated processes, the mechanism of its recruitment to specific genomic loci is not well understood. Here we used a native ChIP-MS approach to quantitatively profile modifications present on nucleosomes co-purified with INO80 from MNAse-digested HeLa chromatin.

2023-12-12 | PXD042224 | Pride

Proteomic analysis of histone modifications present on nucleosomes bound by INO80 complex

2023-12-10 | PXD042210 | Pride

Protein occupancy of Mycoplasma pneumoniae chromosome

Project description:Protein occupancy is a means of identifying all the regions in the genome that are bound to proteins. A simple protocol is used whereby cross-linked chromatin is digested with DNase to remove all non-crosslinked, naked, DNA. To distinguish the regions that are bound by RNA polymerase from the rest, a ChAPseq (chromatin affinity precipitation) with TAP-tagged alpha subunit of RNApol, was performed.

2016-04-01 | E-MTAB-3783 | biostudies-arrayexpress

FAIRE performed in human foreskin fibroblast cells

Project description:To perform FAIRE, chromatin is crosslinked with formaldehyde in vivo, sheared by sonication, and phenol-chloroform extracted. The DNA recovered in the aqueous phase is fluorescently labeled and hybridized to a DNA microarray. FAIRE performed in human cells strongly enriches DNA coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, and active promoters. Keywords: Genome wide map of active chromatin

2006-09-01 | GSE4886 | GEO

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