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Nucleosome profiles for mammalian tissues [RNA-Seq]

ABSTRACT: Nucleosome profiles for mammalian tissues [RNA-Seq]

PROVIDER: PRJNA417274 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6261040_1.fastq.gz	Fastqsanger.gz
	SRR6261040_2.fastq.gz	Fastqsanger.gz
	SRR6261050_1.fastq.gz	Fastqsanger.gz
	SRR6261050_2.fastq.gz	Fastqsanger.gz
	SRR6261041_1.fastq.gz	Fastqsanger.gz

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Nucleosome profiles for mammalian tissues

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Nucleosome profiles for mammalian tissues [RNA-Seq]

Project description:Chromatin structure affects gene splicing and nucleosome as the basic packaged unit is associated with exon recognition. But little is known about the function of nucleosome occupancy in the process of exon origination. Here we performed MNase-seq to obtain genome-wide nucleosome profiles for several tissues of human, rhesus monkey, treeshrew, mouse and pig. At the first time we found conserved nucleosome profile for different tissues. By combining RNA-seq data of each species, we traced the nucleosome occupancy changes of human new exons. Surprisingly, we found nucleosomes were higher occupied before exon formation. And this pre-occupancy contributed to the formation of exon-intron GC difference and maintain splice site strength. Thus we proposed a preadaption model for the function of nucleosome occupancy in human exons origination.

2018-08-07 | GSE106577 | GEO

Nucleosome profiles for mammalian tissues [Mnase-Seq]

Project description:Chromatin structure affects gene splicing and nucleosome as the basic packaged unit is associated with exon recognition. But little is known about the function of nucleosome occupancy in the process of exon origination. Here we performed MNase-seq to obtain genome-wide nucleosome profiles for several tissues of human, rhesus monkey, tree shrew, mouse and pig. At the first time we found conserved nucleosome profile for different tissues. By combining RNA-seq data of each species, we traced the nucleosome occupancy changes of human new exons. Surprisingly, we found nucleosomes were higher occupied before exon formation. And this pre-occupancy contributed to the formation of exon-intron GC difference and maintain splice site strength. Thus we proposed a preadaption model for the function of nucleosome occupancy in human exons origination.

2018-08-07 | GSE106578 | GEO

nucleosome profiles 972 EMM

Project description:nucleosome profiles 972 EMM

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Nucleosome profiles for mammalian tissues

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-08-06 | GSE106580 | GEO

CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq)

Project description:One clear hallmark of mammalian promoters is the presence of CpG islands (CGIs) at more than two thirds of genes whereas TATA boxes are only present at a minority of promoters. Using genome-wide approaches, we show that GC content and CGIs are major promoter elements in mammalian cells, able to govern open chromatin conformation and support paused transcription. First, we define three classes of promoters with distinct transcriptional directionality and pausing properties which correlate with their GC content. We further analyze the direct influence of GC content on nucleosome positioning and depletion, and show that CGIs correlate with nucleosome depletion both in vivo and in vitro. We also show that transcription is not essential for nucleosome exclusion but influences both a weak +1 and a well-positioned nucleosome at CGI borders. Altogether our data support the idea that CGIs have become an essential feature of promoter structure defining novel regulatory properties in mammals. Nucleosome density and positioning were studied by high-throughput sequencing of DNA previously treated with Mnase. In parallel, chIPseq for PolII and H3K27ac were performed in mouse and human with different conditions to assess a potential effect of transcription on nucleosomes properties. To investigate transcription at promoters, we analyzed together with genome-wide Pol II accumulation by ChIP-Seq, paused bidirectional transcripts associated with transcription start sites (TSS RNAs).

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CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters

Project description:This SuperSeries is composed of the following subset Series: GSE38560: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (RNA-seq) GSE38561: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (ChIP-seq) GSE38562: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (genomic SEQ) GSE38563: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (MNase-seq) GSE38564: CpG islands and GC content dictate nucleosome depletion in a transcription independent manner at mammalian promoters (5) Refer to individual Series

2012-06-11 | E-GEOD-38577 | biostudies-arrayexpress

The Nucleosome Map of the Mammalian Liver

Project description:Mammalian genomes contain billions of basepairs of DNA that must be highly compacted as chromatin to fit into the nano-scale of the nucleus, but yet be accessible to allow for transcription to occur. Binding to nucleosomal DNA is critical for ÔpioneerÕ transcription factors such as Foxa1 and Foxa2 to regulate chromatin structure and gene activation. Here we report the genome-wide map of nucleosome positions in the mouse liver, with emphasis on transcriptional start sites, CpG islands, Foxa2 binding sites, and their correlation with gene expression. Despite the heterogeneity of liver tissue, we could clearly discern the nucleosome pattern of the predominant liver cell, the hepatocyte. By analyzing nucleosome occupancy and the distributions of heterochromatin protein 1 (Hp1), CBP, and p300 in Foxa1/2-deficient livers we find, surprisingly, that the maintenance of nucleosome position and chromatin structure surrounding Foxa2 binding sites is independent of Foxa1/2. Original data matrix is in the archive: E-MTAB-514.additional.zip

2011-05-05 | E-MTAB-514 | biostudies-arrayexpress

Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (Mnase-Seq)

Project description:Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (Mnase-Seq)

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