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Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data

Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensiona...

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Autores principales: Hansen, Peter, Gargano, Michael, Hecht, Jochen, Ibn-Salem, Jonas, Karlebach, Guy, Roehr, Johannes T., Robinson, Peter N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678864/
https://www.ncbi.nlm.nih.gov/pubmed/31323892
http://dx.doi.org/10.3390/genes10070548
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author Hansen, Peter
Gargano, Michael
Hecht, Jochen
Ibn-Salem, Jonas
Karlebach, Guy
Roehr, Johannes T.
Robinson, Peter N.
author_facet Hansen, Peter
Gargano, Michael
Hecht, Jochen
Ibn-Salem, Jonas
Karlebach, Guy
Roehr, Johannes T.
Robinson, Peter N.
author_sort Hansen, Peter
collection PubMed
description Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions.
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spelling pubmed-66788642019-08-19 Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data Hansen, Peter Gargano, Michael Hecht, Jochen Ibn-Salem, Jonas Karlebach, Guy Roehr, Johannes T. Robinson, Peter N. Genes (Basel) Review Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish technical artefacts from valid read pairs originating from true chromatin interactions. MDPI 2019-07-18 /pmc/articles/PMC6678864/ /pubmed/31323892 http://dx.doi.org/10.3390/genes10070548 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Hansen, Peter
Gargano, Michael
Hecht, Jochen
Ibn-Salem, Jonas
Karlebach, Guy
Roehr, Johannes T.
Robinson, Peter N.
Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
title Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
title_full Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
title_fullStr Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
title_full_unstemmed Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
title_short Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data
title_sort computational processing and quality control of hi-c, capture hi-c and capture-c data
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678864/
https://www.ncbi.nlm.nih.gov/pubmed/31323892
http://dx.doi.org/10.3390/genes10070548
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