Analysis of the relationship between coexpression domains and chromatin 3D organization
| Autor: | María E. Soler-Oliva, José C. Reyes, José A. Guerrero-Martínez, Valentina Bachetti |
|---|---|
| Přispěvatelé: | Universidad de Sevilla. Departamento de Genética, Junta de Andalucía, European Commission, Ministerio de Economía y Competitividad (España), Asociación Española Contra el Cáncer, [Soler-Oliva, Maria E.] Univ Pablo de Olavide CSIC USE UPO, Univ Sevilla, CSIC, Ctr Andaluz Biol Mol & Med Regenerat CABIMER, Seville, Spain, [Guerrero-Martinez, Jose A.] Univ Pablo de Olavide CSIC USE UPO, Univ Sevilla, CSIC, Ctr Andaluz Biol Mol & Med Regenerat CABIMER, Seville, Spain, [Bachetti, Valentina] Univ Pablo de Olavide CSIC USE UPO, Univ Sevilla, CSIC, Ctr Andaluz Biol Mol & Med Regenerat CABIMER, Seville, Spain, [Reyes, Jose C.] Univ Pablo de Olavide CSIC USE UPO, Univ Sevilla, CSIC, Ctr Andaluz Biol Mol & Med Regenerat CABIMER, Seville, Spain, Spanish Ministry of Economy and Competitiveness (MINECO), Junta de Andalucia, European Union (FEDER), Asociacion Espanola Contra el Cancer (AECC), European Community |
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Gene Expression Genome Gene expression Breast Tumors Basic Cancer Research Medicine and Health Sciences Human breast-cancer Caenorhabditis-elegans Cluster Analysis Gene Regulatory Networks Breast Biology (General) Coordinate gene-regulation Genetics Ecology Chromosome Biology Chromosome Mapping Chromosomal domains Genomics Transcription factories Topological domains Eukaryotic genomes Chromatin Computational Theory and Mathematics Oncology Modeling and Simulation Neighboring genes Epigenetics Female Anatomy Normal breast Research Article QH301-705.5 Breast Neoplasms Biology Research and Analysis Methods Human Genomics 03 medical and health sciences Cellular and Molecular Neuroscience Cancer Genomics Genomic Medicine Cancer genome Breast Cancer Humans Molecular Biology Techniques Gene Molecular Biology Ecology Evolution Behavior and Systematics Housekeeping genes Human genome Gene Expression Profiling Gene Mapping Reproductive System Cancers and Neoplasms Biology and Life Sciences Computational Biology Cell Biology Chromatin Assembly and Disassembly Gene expression profiling 030104 developmental biology Gene Expression Regulation Eukaryotic chromosome fine structure Breast Tissue |
| Zdroj: | PLoS Computational Biology idUS. Depósito de Investigación de la Universidad de Sevilla instname PLoS Computational Biology, Vol 13, Iss 9, p e1005708 (2017) Digital.CSIC. Repositorio Institucional del CSIC |
| ISSN: | 1553-7358 1553-734X |
| Popis: | Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term “CODs”). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs. CODs in the normal and breast cancer genomes share similar characteristics but differ in their gene composition. COD genes have a greater tendency to be coexpressed with genes that reside in other CODs than with non-COD genes. Such inter-COD coexpression is maintained over large chromosomal distances in the normal genome but is partially lost in the cancer genome. Analyzing the relationship between CODs and chromatin 3D organization using Hi-C contact data, we find that CODs do not correspond to TADs. In fact, intra-TAD gene coexpression is the same as random for most chromosomes. However, the contact profile is similar between gene pairs that reside either in the same COD or in coexpressed CODs. These data indicate that co-regulated genes in the genome present similar patterns of contacts irrespective of the frequency of physical chromatin contacts between them. This work was funded by the Spanish Ministry of Economy and Competitiveness (MINECO) [BFU-2011-23442 and BFU2014-53543-P to JCR], Junta de Andalucía (BIO0321), and the European Union (FEDER). CABIMER is supported by Junta de Andalucía. MESO received an Asociación Española Contra el Cáncer (AECC) summer fellowship; VB received a Leonardo da Vinci fellowship from the European Community. |
| Databáze: | OpenAIRE |
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