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Large-scale 3D chromatin reconstruction from chromosomal contacts
BACKGROUND: Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C tec...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456969/ https://www.ncbi.nlm.nih.gov/pubmed/30967119 http://dx.doi.org/10.1186/s12864-019-5470-2 |
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author | Zhang, Yanlin Liu, Weiwei Lin, Yu Ng, Yen Kaow Li, Shuaicheng |
author_facet | Zhang, Yanlin Liu, Weiwei Lin, Yu Ng, Yen Kaow Li, Shuaicheng |
author_sort | Zhang, Yanlin |
collection | PubMed |
description | BACKGROUND: Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C technology, which detects long-range chromosomal interactions. Distance geometry-based algorithms, such as ChromSDE and ShRec3D, have been able to utilize Hi-C data to infer 3D chromosomal structures. However, these algorithms, being matrix-based, are space- and time-consuming on very large datasets. A human genome of 100 kilobase resolution would involve ∼30,000 loci, requiring gigabytes just in storing the matrices. RESULTS: We propose a succinct representation of the distance matrices which tremendously reduces the space requirement. We give a complete solution, called SuperRec, for the inference of chromosomal structures from Hi-C data, through iterative solving the large-scale weighted multidimensional scaling problem. CONCLUSIONS: SuperRec runs faster than earlier systems without compromising on result accuracy. The SuperRec package can be obtained from http://www.cs.cityu.edu.hk/~shuaicli/SuperRec. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5470-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6456969 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-64569692019-04-19 Large-scale 3D chromatin reconstruction from chromosomal contacts Zhang, Yanlin Liu, Weiwei Lin, Yu Ng, Yen Kaow Li, Shuaicheng BMC Genomics Research BACKGROUND: Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C technology, which detects long-range chromosomal interactions. Distance geometry-based algorithms, such as ChromSDE and ShRec3D, have been able to utilize Hi-C data to infer 3D chromosomal structures. However, these algorithms, being matrix-based, are space- and time-consuming on very large datasets. A human genome of 100 kilobase resolution would involve ∼30,000 loci, requiring gigabytes just in storing the matrices. RESULTS: We propose a succinct representation of the distance matrices which tremendously reduces the space requirement. We give a complete solution, called SuperRec, for the inference of chromosomal structures from Hi-C data, through iterative solving the large-scale weighted multidimensional scaling problem. CONCLUSIONS: SuperRec runs faster than earlier systems without compromising on result accuracy. The SuperRec package can be obtained from http://www.cs.cityu.edu.hk/~shuaicli/SuperRec. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5470-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-04 /pmc/articles/PMC6456969/ /pubmed/30967119 http://dx.doi.org/10.1186/s12864-019-5470-2 Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Zhang, Yanlin Liu, Weiwei Lin, Yu Ng, Yen Kaow Li, Shuaicheng Large-scale 3D chromatin reconstruction from chromosomal contacts |
title | Large-scale 3D chromatin reconstruction from chromosomal contacts |
title_full | Large-scale 3D chromatin reconstruction from chromosomal contacts |
title_fullStr | Large-scale 3D chromatin reconstruction from chromosomal contacts |
title_full_unstemmed | Large-scale 3D chromatin reconstruction from chromosomal contacts |
title_short | Large-scale 3D chromatin reconstruction from chromosomal contacts |
title_sort | large-scale 3d chromatin reconstruction from chromosomal contacts |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456969/ https://www.ncbi.nlm.nih.gov/pubmed/30967119 http://dx.doi.org/10.1186/s12864-019-5470-2 |
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