Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers
| Autor: | Daniele Tavernari, Marie Zufferey, Marco Mina, Yuanlong Liu, Giovanni Ciriello |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Transcription
Genetic Co-regulation QH301-705.5 Datasets as Topic Computational biology Biology QH426-470 Genetic Heterogeneity Structure-Activity Relationship 03 medical and health sciences 0302 clinical medicine Transcription (biology) Hi-C Neoplasms Transcriptional regulation Genetics Humans Gene Regulatory Networks Biology (General) Gene 030304 developmental biology 0303 health sciences Research Chromatin Assembly and Disassembly Chromatin Human genetics Neoplasm Proteins Gene Expression Regulation Neoplastic Differentially expressed genes 030220 oncology & carcinogenesis Gene co-regulation Chromatin compartment domains Algorithms Function (biology) |
| Zdroj: | Genome Biology, Vol 22, Iss 1, Pp 1-24 (2021) Genome Biology |
| Popis: | BackgroundSpatial interactions and insulation of chromatin regions are associated with transcriptional regulation. Domains of frequent chromatin contacts are proposed as functional units, favoring and delimiting gene regulatory interactions. However, contrasting evidence supports the association between chromatin domains and transcription.ResultHere, we assess gene co-regulation in chromatin domains across multiple human cancers, which exhibit great transcriptional heterogeneity. Across all datasets, gene co-regulation is observed only within a small yet significant number of chromatin domains. We design an algorithmic approach to identify differentially active domains (DADo) between two conditions and show that these provide complementary information to differentially expressed genes. Domains comprising co-regulated genes are enriched in the less active B sub-compartments and for genes with similar function. Notably, differential activation of chromatin domains is not associated with major changes of domain boundaries, but rather with changes of sub-compartments and intra-domain contacts.ConclusionOverall, gene co-regulation is observed only in a minority of chromatin domains, whose systematic identification will help unravel the relationship between chromatin structure and transcription. |
| Databáze: | OpenAIRE |
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