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Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Mitchelmore, Joanna 
Grinberg, Nastasiya F 
Spivakov, Mikhail 

Abstract

Identifying DNA cis-regulatory modules (CRMs) that control the expression of specific genes is crucial for deciphering the logic of transcriptional control. Natural genetic variation can point to the possible gene regulatory function of specific sequences through their allelic associations with gene expression. However, comprehensive identification of causal regulatory sequences in brute-force association testing without incorporating prior knowledge is challenging due to limited statistical power and effects of linkage disequilibrium. Sequence variants affecting transcription factor (TF) binding at CRMs have a strong potential to influence gene regulatory function, which provides a motivation for prioritizing such variants in association testing. Here, we generate an atlas of CRMs showing predicted allelic variation in TF binding affinity in human lymphoblastoid cell lines and test their association with the expression of their putative target genes inferred from Promoter Capture Hi-C and immediate linear proximity. We reveal >1300 CRM TF-binding variants associated with target gene expression, the majority of them undetected with standard association testing. A large proportion of CRMs showing associations with the expression of genes they contact in 3D localize to the promoter regions of other genes, supporting the notion of 'epromoters': dual-action CRMs with promoter and distal enhancer activity.

Description

Keywords

Chromatin, Transcription Factors, Transcription, Genetic, Gene Expression Regulation, Binding Sites, Base Sequence, Protein Binding, Genes, Reporter, Quantitative Trait Loci, Promoter Regions, Genetic

Journal Title

Nucleic acids research

Conference Name

Journal ISSN

0305-1048
1362-4962

Volume Title

48

Publisher

Oxford University Press (OUP)