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Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

ABSTRACT: Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

PROVIDER: PRJNA865739 | ENA |

REPOSITORIES: ENA

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Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

Project description:We report a comprehensive analysis of nucleosomal and subnucleosomal organization at cis-regulatory elements (CREs) in mouse embryonic stem (ES) cells. We used chromatin fragmented by a moderate dose of micrococcal nuclease (MNase) as input for ChIP-seq with antibodies against histones and transcription factors and high-coverage deep-sequencing. Centrifugation of chromatin through sucrose gradients, followed by ChIP-seq, allowed the characterization of different subclasses of subnucleosomal particles having distribution patterns specific to enhancers, gene promoters and CTCF binding sites. We also provide datasets showing that this particular chromatin organization of CREs is conserved in the human melanoma 501Mel cell line.

2023-06-13 | GSE210780 | GEO

Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

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Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

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Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells (chip-seq gradient)

Project description:We report an in-depth analysis of nucleosomal and subnucleosomal organization at cis-regulatory elements (CREs) in mouse embryonic stem (ES) cells. We used chromatin fragmented by a moderate dose of micrococcal nuclease (MNase) as input for ChIP-seq with antibodies against histones and transcription factors, and high-coverage deep-sequencing. Centrifugation of chromatin through sucrose gradients, followed by ChIP-seq, allowed the characterization of different subclasses of subnucleosomal particles having distribution patterns specific to enhancers, gene promoters and CTCF binding sites. We also provide datasets showing that this particular chromatin organization of CREs is conserved in the human melanoma 501Mel cell line.

2024-06-03 | GSE255089 | GEO

Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

Project description:Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

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Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

Project description:Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

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Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells (chip-seq gradient)

Project description:Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells (chip-seq gradient)

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Mus musculus

Project description:Nucleosomal and subnucleosomal organization of transcription cis-regulatory elements in mouse embryonic stem cells

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Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome

Project description:In the yeast genome, a large proportion of nucleosomes occupy well-defined positions. While the contribution of chromatin remodelers and DNA binding proteins to maintain this organization is well established, the relevance of the DNA sequence to nucleosome positioning in the genomic context remains controversial. Through genome-wide, quantitative analysis of nucleosome positioning and high-resolution mutagenenesis of mononucleosomal DNA, we show that sequence changes distort the nucleosomal pattern at the level of individual nucleosomes. This effect is equally detected in transcribed and non-transcribed regions, suggesting the existence of sequence elements contributing to positioning. To identify such elements, we incorporated information from nucleosomal signatures into artificial synthetic DNA molecules and found that they generated regular nucleosomal arrays indistinguishable from those of endogenous sequences. Strikingly, this information is species-specific and can be combined with coding information through the use of synonymous codons such that genes from one species can be engineered to adopt the nucleosomal organization of another. These findings open up the possibility of designing coding and non-coding DNA molecules capable of directing their own nucleosomal organization.

2016-09-20 | GSE84910 | GEO

Characterization of GJB2 cis-regulatory elements in the DFNB1 locus

Project description:Although most disease-causing variants are within coding region of genes, it is now well established that cis-acting regulatory sequences, depending on 3D-chromatin organization, are required for temporal and spatial control of gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic disease. Hence, recurrent monoallelic cases of the most common hereditary type of nonsyndromic hearing loss (i.e. DFNB1) carrying out only one identified pathogenic allele, led to strongly suggest the presence of uncharacterized distal cis-acting elements in the missing allele. Herewith, we study the spatial organization of a large DFNB1 locus encompassing the gap junction protein beta 2 (GJB2) gene, the most frequently mutated gene in this inherited hearing loss, with the chromosome conformation capture carbon copy technology (5C). By combining this approach with functional activity reporter assays and mapping of CCCTC-binding factor (CTCF) along the DFNB1 locus by quantitative real-time PCR chromatin immunoprecipitation, we identify a novel set of cooperating GJB2 cis-acting elements and propose a DFNB1 three-dimensional looping regulation model. A loop chromatin forming, allows bringing closer enhancers to the GJB2 promoter, but also avoids GJB2 silencing with an enhancer-blocking insulator activity.

2020-03-26 | GSE128881 | GEO

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