Distant cis-regulatory elements in human skeletal muscle differentiation

Identifying gene regulatory elements and their target genes in human cells remains a significant challenge. Despite increasing evidence of physical interactions between distant regulatory elements and gene promoters in mammalian cells, many studies consider only promoter-proximal regulatory regions. We identify putative cis-regulatory modules (CRMs) in human skeletal muscle differentiation by combining myogenic TF binding data before and after differentiation with histone modification data in myoblasts. CRMs that are distant (> 20 kb) from muscle gene promoters are common and are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. We find that two of these distant CRMs, known to activate transcription in differentiating myoblasts, interact physically with gene promoters (PDLIM3 and ACTA1) during differentiation. Our results highlight the importance of considering distal CRMs in investigations of mammalian gene regulation and support the hypothesis that distant CRM-promoter looping contacts are a general mechanism of gene regulation.

► We identify proximal and distal putative CRMs for human muscle differentiation. ► Differentiation-specific myogenic TF binding changes are common at distant CRMs. ► Some CRMs distant from muscle genes might regulate muscle-specific microRNAs. ► Distant CRMs loop to contact PDLIM3 and ACTA1 promoters during differentiation.