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Single cell chromatin immunocleavage sequencing (scChIC-Seq) to profile histone modification

ABSTRACT: Single cell chromatin immunocleavage sequencing (scChIC-Seq) to profile histone modification

PROVIDER: PRJNA414428 | ENA |

REPOSITORIES: ENA

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Single cell chromatin immunocleavage sequencing (scChIC-Seq) to profile histone modification

Project description:We report a single-cell chromatin immunocleavage sequencing (scChIC-seq) methodology for analyzing histone modifications, which involves targeting of the micrococcal nuclease (MNase) by tethering it to an antibody and selective PCR amplification of cleaved target sites. We show that the protocol reliably detects the H3K4me3 and H3K27me3 target sites in single human white blood cells (WBC), resulting data for successful identification of unique blood cell types based on clustering analysis.

2019-03-28 | GSE105012 | GEO

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification.

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Chromatin signature discovery via histone modification profile alignments.

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The transcriptome, histone modification and chromatin organization of kidney tubule cells

Project description:The transcriptome, histone modification and chromatin organization of kidney tubule cells

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Histone modification and nucleosome mapping in human liver cancer cells

Project description:The nucleosome is a fundamental unit of chromatin architecture, but it has been under-evaluated during the analysis of histone modification using ChIP-Seq. Thus, we developed a novel approach for defining histone modification at single nucleosome resolution by synergistic analyses of histone modification data from ChIP-Seq and high-resolution nucleosome mapping data from native MNase-Seq using a PCR-free strategy. With this approach, we have generated histone modification data at the single nucleosome resolution in human embryonic stem cells, normal hepatocytes, and liver cancer cells of both genders, and performed quantitative analysis of epigenetic regulation in stem cell differentiation into hepatocytes and neoplastic transformation of liver cancer.

2020-04-10 | GSE76344 | GEO

Functional classification of chromatin associated lncRNAs via histone modification specific PIRCh-seq analysis

Project description:Many long noncoding RNAs (lncRNAs) regulate gene transcription through binding to histone modifying complexes, therefore a comprehensive study of chromatin associated RNA in a histone modification specific manner is critical to understand their regulatory mechanisms. In this study, we developed a new method named Profiling Interacting RNAs on Chromatin followed by deep sequencing (PIRCh-seq), and profiled chromatin associated transcriptome on 3 cell types, mouse v6.5 embryonic stem cells (mESC), mouse embryonic fibroblasts (MEF) and mouse neuronal precursor cells (NPC), with antibodies attached to histone H3 and 6 active and repressive histone modifications. Compared with existing methods, PIRCh-seq identifies chromatin associated RNAs with significant lower nascent transcription, and classifies chromatin enriched lncRNAs into 6 functional groups based on the patterns of their attachment to nucleosome with specific chemical modifications. Further analysis showed that lncRNAs were also enriched with different modified chromatin in different cell types, suggesting lncRNAs’ regulation may also be cell type specific. By integrating profiles of RNA secondary structure from icSHAPE and RNA m(6)A modification, we noticed that RNA bases attached with chromatin tend to be more single stranded. These results provide a unique resource to globally study the functions of chromatin associated lncRNAs and elucidates the basic mechanisms of chromatin-RNA association.

2019-10-30 | GSE119006 | GEO

Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers

Project description:The integrated activity of cis-regulatory elements fine-tunes transcriptional programs of mammalian cells by recruiting cell type–specific as well as ubiquitous transcription factors (TFs). Despite their key role in modulating transcription, enhancers are still poorly characterized at the molecular level, and their limited DNA sequence conservation in evolution and variable distance from target genes make their unbiased identification challenging. The coexistence of high mono-methylation and low tri-methylation levels of lysine 4 of histone H3 is considered a signature of enhancers, but a comprehensive view of histone modifications associated to enhancers is still lacking. By combining chromatin immunoprecipitation (ChIP) with mass spectrometry, we investigated cis-regulatory regions in macrophages to comprehensively identify histone marks specifically associated with enhancers, and to profile their dynamics after transcriptional activation elicited by an inflammatory stimulation. The intersection of the proteomics data with ChIP-seq and RNA-seq analyses revealed the existence of novel subpopulations of enhancers, marked by specific histone modification signatures: specifically, H3K36me2/K4me1 marks transcribed enhancers, while H3K36me3/K4me1 and H3K79me2/K4me1 combinations mark distinct classes of intronic enhancers. Thus, our MS analysis of functionally distinct genomic regions revealed the combinatorial code of histone modifications, highlighting the potential of proteomics in addressing fundamental questions in epigenetics.

2017-10-09 | PXD007582 | Pride

Single-copy locus isolation identifies distinct proteomes of early- and late-firing DNA replication origin chromatin

Project description:The chromatin at origins of replication is the template for DNA replication initiation in eukaryotic genomes. However, whether the chromatin composition instructs individual origins to fire early-efficiently (EE) or late-inefficiently (LI) remains to be investigated. Here, we used site-specific recombination and a single-locus chromatin isolation approach to purify selected EE and LI replication origins from chromosome III of Saccharomyces cerevisiae. Using mass spectrometry, we define the histone modification landscape and identify the protein composition of defined ~1kb native chromatin regions surrounding the EE and LI replication start sites. We confirm expected origin interactors but also find unexpected interactions, such as the Ask1 subunit of the kinetochore-associated DASH complex. Strikingly, we show that Ask1 is a critical factor in the replication timing control of specific origins in yeast. These results highlight that our unbiased approach can specifically identify the functionally-relevant proteome at a single-copy locus of interest and provide a detailed view of histone modification and protein interaction networks on replication origin chromatin. The current dataset contains proteomic data used for the histone PTM analysis.

2023-05-10 | PXD031984 | Pride

Deduction of proportional contributions of histone-modification-related DNA from various tissues in plasma

Project description:Deduction of proportional contributions of histone-modification-related DNA from various tissues in plasma

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Expression profile (nanoCAGE-seq), chromatin accessibility (ATAC-seq) profile, and histone modification profile (ChIP-seq for H3K4me3, H3K9me3, and H3K27me3) during the course of mouse gonocyte development

Project description:Expression profile (nanoCAGE-seq), chromatin accessibility (ATAC-seq) profile, and histone modification profile (ChIP-seq for H3K4me3, H3K9me3, and H3K27me3) during the course of mouse gonocyte development

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