License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2019.11
URN: urn:nbn:de:0030-drops-110418
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2019/11041/
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Cauer, Alexandra Gesine ; Yardimci, Gürkan ; Vert, Jean-Philippe ; Varoquaux, Nelle ; Noble, William Stafford

Inferring Diploid 3D Chromatin Structures from Hi-C Data

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LIPIcs-WABI-2019-11.pdf (4 MB)

Abstract

The 3D organization of the genome plays a key role in many cellular processes, such as gene regulation, differentiation, and replication. Assays like Hi-C measure DNA-DNA contacts in a high-throughput fashion, and inferring accurate 3D models of chromosomes can yield insights hidden in the raw data. For example, structural inference can account for noise in the data, disambiguate the distinct structures of homologous chromosomes, orient genomic regions relative to nuclear landmarks, and serve as a framework for integrating other data types. Although many methods exist to infer the 3D structure of haploid genomes, inferring a diploid structure from Hi-C data is still an open problem. Indeed, the diploid case is very challenging, because Hi-C data typically does not distinguish between homologous chromosomes. We propose a method to infer 3D diploid genomes from Hi-C data. We demonstrate the accuracy of the method on simulated data, and we also use the method to infer 3D structures for mouse chromosome X, confirming that the active homolog exhibits a bipartite structure, whereas the active homolog does not.

BibTeX - Entry

@InProceedings{cauer_et_al:LIPIcs:2019:11041,
  author =	{Alexandra Gesine Cauer and G{\"u}rkan Yardimci and Jean-Philippe Vert and Nelle Varoquaux and William Stafford Noble},
  title =	{{Inferring Diploid 3D Chromatin Structures from Hi-C Data}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{11:1--11:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Katharina T. Huber and Dan Gusfield},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2019/11041},
  URN =		{urn:nbn:de:0030-drops-110418},
  doi =		{10.4230/LIPIcs.WABI.2019.11},
  annote =	{Keywords: Genome 3D architecture, chromatin structure, Hi-C, 3D modeling}
}

Keywords: Genome 3D architecture, chromatin structure, Hi-C, 3D modeling
Collection: 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
Issue Date: 2019
Date of publication: 03.09.2019

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