Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

Sarah Rennie, Maria Dalby, Lucas van Duin, View ORCID ProfileRobin Andersson
doi: https://doi.org/10.1101/130070
Sarah Rennie
1The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Maria Dalby
1The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lucas van Duin
1The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robin Andersson
1The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Robin Andersson
  • For correspondence: robin@binf.ku.dk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

Transcriptional regulation is tightly coupled with chromosomal positioning and three-dimensional chromatin architecture. However, it is unclear what proportion of transcriptional activity is reflecting such organisation, how much can be informed by RNA expression alone, and how this impacts disease. Here, we develop a transcriptional decomposition approach separating the proportion of expression associated with genome organisation from independent effects not directly related to genomic positioning.

We show that positionally attributable expression accounts for a considerable proportion of total levels and is highly informative of topological associating domain activities and organisation, revealing boundaries and chromatin compartments. Furthermore, expression data alone accurately predicts individual enhancer-promoter interactions, drawing features from expression strength, stabilities, insulation and distance. We further characterise commonalities and differences across predictions in 76 human cell types, observing extensive sharing of domains, yet highly cell-type specific enhancer-promoter interactions and strong enrichments in relevant trait-associated variants. Our work demonstrates a close relationship between transcription and chromatin architecture, presenting a novel strategy and an unprecedented resource for investigating regulatory organisations and interpretations of disease associated genetic variants across cell types.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted July 10, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions
Sarah Rennie, Maria Dalby, Lucas van Duin, Robin Andersson
bioRxiv 130070; doi: https://doi.org/10.1101/130070
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions
Sarah Rennie, Maria Dalby, Lucas van Duin, Robin Andersson
bioRxiv 130070; doi: https://doi.org/10.1101/130070

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3479)
  • Biochemistry (7318)
  • Bioengineering (5296)
  • Bioinformatics (20197)
  • Biophysics (9976)
  • Cancer Biology (7703)
  • Cell Biology (11250)
  • Clinical Trials (138)
  • Developmental Biology (6418)
  • Ecology (9916)
  • Epidemiology (2065)
  • Evolutionary Biology (13280)
  • Genetics (9352)
  • Genomics (12554)
  • Immunology (7674)
  • Microbiology (18939)
  • Molecular Biology (7417)
  • Neuroscience (40893)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2126)
  • Physiology (3140)
  • Plant Biology (6838)
  • Scientific Communication and Education (1270)
  • Synthetic Biology (1891)
  • Systems Biology (5296)
  • Zoology (1085)