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Joint analyses of multi-tissue Hi-C and eQTL data demonstrate close spatial proximity between eQTLs and their target genes.
Yu, Jingting; Hu, Ming; Li, Chun.
Afiliação
  • Yu J; Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
  • Hu M; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA. hum@ccf.org.
  • Li C; Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA. cxl791@case.edu.
BMC Genet ; 20(1): 43, 2019 04 30.
Article em En | MEDLINE | ID: mdl-31039743
BACKGROUND: Gene regulation is important for cells and tissues to function. It has been studied from two aspects at the genomic level, the identification of expression quantitative trait loci (eQTLs) and identification of long-range chromatin interactions. It is important to understand their relationship, such as whether eQTLs regulate their target genes through physical chromatin interaction. Although chromatin interactions have been widely believed to be one of the main mechanisms underlying eQTLs, most evidence came from studies of cell lines and yet no direct evidence exists for tissues. RESULTS: We performed various joint analyses of eQTL and high-throughput chromatin conformation capture (Hi-C) data from 11 human primary tissue types and 2 human cell lines. We found that chromatin interaction frequency is positively associated with the number of genes that have eQTLs and that eQTLs and their target genes tend to fall into the same topologically associating domain (TAD). These results are consistent across all tissues and cell lines we evaluated. Moreover, in 6 out of 11 tissues (aorta, dorsolateral prefrontal cortex, hippocampus, pancreas, small bowel, and spleen), tissue-specific eQTLs are significantly enriched in tissue-specific frequently interacting regions (FIREs). CONCLUSIONS: Our data have demonstrated the close spatial proximity between eQTLs and their target genes among multiple human primary tissues.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Cromatina / Regulação da Expressão Gênica / Locos de Características Quantitativas / Sequenciamento de Nucleotídeos em Larga Escala Idioma: En Ano de publicação: 2019 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Cromatina / Regulação da Expressão Gênica / Locos de Características Quantitativas / Sequenciamento de Nucleotídeos em Larga Escala Idioma: En Ano de publicação: 2019 Tipo de documento: Article