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Title: Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Illumina transcription]      
keywords:
Transcriptome or Gene expression
ID:
PRJNA186445
description:
This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. Overall design: The gene transcription of 3 independent biological replicates were investigated
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA186445
authentication:
none
authorization:
none
ID:
pmid:23416946
name:
Homo sapiens
ncbiID:
ncbitax:9606
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject
  • 078219/Wellcome Trust/United Kingdom

  • 078219/Z/05/Z/Wellcome Trust/United Kingdom

  • MR/J00913X/1/Medical Research Council/United Kingdom

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