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

TSA-Seq Mapping of Nuclear Genome Organization

Yu Chen, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva K. Brinkman, Stephen A. Adam, Robert Goldman, Bas van Steensel, Jian Ma, Andrew S. Belmont
doi: https://doi.org/10.1101/307892
Yu Chen
1Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yang Zhang
2Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
3Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yuchuan Wang
3Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Liguo Zhang
1Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eva K. Brinkman
4Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stephen A. Adam
5Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert Goldman
5Department of Cell and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Bas van Steensel
4Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1016 HM Amsterdam, the Netherlands.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jian Ma
3Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew S. Belmont
1Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
6Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.
7Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: asbel@illinois.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Summary

While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. Here we describe TSA-Seq, a new mapping method able to estimate mean chromosomal distances from nuclear speckles genome-wide and predict several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple, spatially separated nuclear domains, including two types of transcription “hot-zones”. Transcription hot-zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, house-keeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for nuclear spatial organization of transcription.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted April 25, 2018.
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.
TSA-Seq Mapping of Nuclear Genome Organization
(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
TSA-Seq Mapping of Nuclear Genome Organization
Yu Chen, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva K. Brinkman, Stephen A. Adam, Robert Goldman, Bas van Steensel, Jian Ma, Andrew S. Belmont
bioRxiv 307892; doi: https://doi.org/10.1101/307892
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
TSA-Seq Mapping of Nuclear Genome Organization
Yu Chen, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva K. Brinkman, Stephen A. Adam, Robert Goldman, Bas van Steensel, Jian Ma, Andrew S. Belmont
bioRxiv 307892; doi: https://doi.org/10.1101/307892

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 (2516)
  • Biochemistry (4964)
  • Bioengineering (3466)
  • Bioinformatics (15166)
  • Biophysics (6885)
  • Cancer Biology (5379)
  • Cell Biology (7709)
  • Clinical Trials (138)
  • Developmental Biology (4518)
  • Ecology (7128)
  • Epidemiology (2059)
  • Evolutionary Biology (10206)
  • Genetics (7497)
  • Genomics (9763)
  • Immunology (4821)
  • Microbiology (13174)
  • Molecular Biology (5128)
  • Neuroscience (29354)
  • Paleontology (203)
  • Pathology (835)
  • Pharmacology and Toxicology (1460)
  • Physiology (2127)
  • Plant Biology (4728)
  • Scientific Communication and Education (1008)
  • Synthetic Biology (1337)
  • Systems Biology (4001)
  • Zoology (768)