Enhancer-dependent genes regulated by a shared muscle enhancer at the H19/Igf2 locus

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Authors

• A Mitra
• M Sampley
• K Pfeifer

Abstract

Insulin-like growth factor 2 (Igf2) and H19 are linked genes involved in development – Igf2 promotes growth but is opposed by the non-coding H19 RNA which limits growth. In mice, the expression of these genes in skeletal muscle is controlled by an enhancer (muscle enhancer, ME) whose deletion (ΔME) results in loss of both Igf2 and H19. However, the effect of this deletion on the chromatin structure of the H19/Igf2 locus and on local and global transcriptional status is not known. Genome-wide analysis of histone marks associated with enhancers, promoters and active transcription showed that the deposition of chromatin marks was largely unchanged in ΔME/ΔME cells even while transcription levels were reduced by >300-fold. Thus, the enhancer is not required to establish active chromatin but instead controls the efficacy of transcription from this locus. Further, global mRNA-sequencing revealed that 186 genes in addition to Igf2 and H19 were significantly changed in the mutant cells. To disentangle the primary effects of the enhancer from that of Igf2 and H19, we utilized heterozygous deletion mutants – deletion of the maternal ME results specifically in the loss of H19, while paternal deletion causes Igf2 loss with normal H19 levels. Comparisons of these mutant cells with wild-type revealed a set of 131 putative enhancer-dependent genes that were changed only in the ΔME/ΔME cells, but not in the heterozygous deletions. Thus, the muscle enhancer at the H19/Igf2 locus appears to regulate distal genomic loci, and work is ongoing to further understand this phenomenon.

Scientific Focus Area: Genetics and Genomics

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