Automatic identification of informative regions with epigenomic changes associated to hematopoiesis
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- dc.contributor.author Carrillo-de-Santa Pau, Enrique
- dc.contributor.author Juan, David
- dc.contributor.author Pancaldi, Vera
- dc.contributor.author Were, Felipe
- dc.contributor.author Martin-Subero, José Ignacio
- dc.contributor.author Rico, Daniel
- dc.contributor.author Valencia, Alfonso
- dc.contributor.author BLUEPRINT Consortium
- dc.date.accessioned 2023-11-21T06:53:06Z
- dc.date.available 2023-11-21T06:53:06Z
- dc.date.issued 2017
- dc.description Includes supplementary material for the online appendix.
- dc.description.abstract Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet.
- dc.description.sponsorship European Union’s Seventh Framework Programme [FP7/2007–2013, 282510 (BLUEPRINT)]; Spanish Ministry of Economy, Industry and Competitiveness and European Regional Development Fund [Project Retos BFU2015–71241-R]. Funding for open access charge: Project Retos BFU2015–71241-R (to A.V.).
- dc.format.mimetype application/pdf
- dc.identifier.citation Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, et al. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Research. 2017 Sep 19;45(16):9244-59. DOI: 10.1093/nar/gkx618
- dc.identifier.doi http://dx.doi.org/10.1093/nar/gkx618
- dc.identifier.issn 0305-1048
- dc.identifier.uri http://hdl.handle.net/10230/58342
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Nucleic Acids Research. 2017 Sep 19;45(16):9244-59
- dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/282510
- dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-71241-R
- dc.rights © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.combsite].
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- dc.subject.other Hematopoesi
- dc.subject.other Sistema hematopoètic
- dc.subject.other Leucèmia
- dc.title Automatic identification of informative regions with epigenomic changes associated to hematopoiesis
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion