3D reconstruction of genomic regions from sparse interaction data

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  • dc.contributor.author Mendieta Esteban, Julen, 1992-
  • dc.contributor.author Di Stefano, Marco
  • dc.contributor.author Castillo Andreo, David
  • dc.contributor.author Farabella, Irene
  • dc.contributor.author Marti-Renom, Marc A.
  • dc.date.accessioned 2021-05-25T12:23:06Z
  • dc.date.available 2021-05-25T12:23:06Z
  • dc.date.issued 2021
  • dc.description.abstract Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. As such, pcHi-C provides sparse interaction matrices that are suitable to characterize short- and long-range enhancer-promoter interactions. Here, we introduce a new method to reconstruct the chromatin structural (3D) organization from sparse 3C-based datasets such as pcHi-C. Our method allows for data normalization, detection of significant interactions and reconstruction of the full 3D organization of the genomic region despite of the data sparseness. Specifically, it builds, with as low as the 2-3% of the data from the matrix, reliable 3D models of similar accuracy of those based on dense interaction matrices. Furthermore, the method is sensitive enough to detect cell-type-specific 3D organizational features such as the formation of different networks of active gene communities.
  • dc.description.sponsorship This study makes use of data generated by the PCHI-C Consortium available in the EGA European Genome-Phenome Archive (National Institute for Health Research of England, UK Medical Research Council (MR/L007150/1) and UK Biotechnology and Biological Research Council (BB/J004480/1)
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Mendieta-Esteban J, Di Stefano M, Castillo D, Farabella I, Marti-Renom MA. 3D reconstruction of genomic regions from sparse interaction data. NAR Genom Bioinform. 2021 Mar 22;3(1):lqab017. DOI: 10.1093/nargab/lqab017
  • dc.identifier.doi http://dx.doi.org/10.1093/nargab/lqab017
  • dc.identifier.issn 2631-9268
  • dc.identifier.uri http://hdl.handle.net/10230/47650
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.rights © Julen Mendieta-Esteban et al. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.other Genètica
  • dc.subject.other Genòmica
  • dc.title 3D reconstruction of genomic regions from sparse interaction data
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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