Description
Accession Number: GSE82127
Platform:
GPL13112: Illumina HiSeq 2000 (Mus musculus)
Organism: Mus musculus
Published on 2016-11-23
Summary:
Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. Using this strategy, we uncover surprising new features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that a subset of DNA-binding proteins including insulator CTCF and pluripotency factors co-occupy DNA targets with nucleosomes. Furthermore, we provide in vivo evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA Polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Altogether, we establish an accurate method for defining the nucleosome landscape, and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.
Overall Design:
5 samples total. Chemical sample was analyzed with high throughput paired-end parallel sequencing. MNase samples were analyzed with high throughput paired-end parallel sequencing. 4 RNA samples from mouse ES cells (H4S47C Chemical vs WT) treated with 2i or Lif culture conditions.
Contact:
Name: Liqun Xi
Organization: Northwestern University
Deparment: Statistics
Address: 2006 Sheridan Road Evanston IL 60208 USA
Email: [email protected]
Organization: GEO
Address: USA
Platform:
GPL13112: Illumina HiSeq 2000 (Mus musculus)
Organism: Mus musculus
Published on 2016-11-23
Summary:
Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. Here, we develop a chemical biology approach to determine mammalian nucleosome positions genome-wide. Using this strategy, we uncover surprising new features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model, we observe that for nearly all mouse genes a class of fragile nucleosomes occupies previously designated nucleosome-depleted regions around transcription start sites and transcription termination sites. We show that a subset of DNA-binding proteins including insulator CTCF and pluripotency factors co-occupy DNA targets with nucleosomes. Furthermore, we provide in vivo evidence that promoter-proximal nucleosomes, with the +1 nucleosome in particular, contribute to the pausing of RNA Polymerase II. Lastly, we find a characteristic preference for nucleosomes at exon-intron junctions. Altogether, we establish an accurate method for defining the nucleosome landscape, and provide a valuable resource for studying nucleosome-mediated gene regulation in mammalian cells.
Overall Design:
5 samples total. Chemical sample was analyzed with high throughput paired-end parallel sequencing. MNase samples were analyzed with high throughput paired-end parallel sequencing. 4 RNA samples from mouse ES cells (H4S47C Chemical vs WT) treated with 2i or Lif culture conditions.
Contact:
Name: Liqun Xi
Organization: Northwestern University
Deparment: Statistics
Address: 2006 Sheridan Road Evanston IL 60208 USA
Email: [email protected]
Organization: GEO
Address: USA
| Date made available | Jun 1 2016 |
|---|---|
| Publisher | Gene Expression Omnibus |