title: Promoter cross-talk via a shared enhancer explains paternally biased expression of Nctc1 at the Igf2/H19/Nctc1 imprinted locus.
abstract: Developmentally regulated transcription often depends on physical interactions between distal enhancers and their cognate promoters. Recent genomic analyses suggest that promoter-promoter interactions might play a similarly critical role in organizing the genome and establishing cell-type-specific gene expression. The Igf2/H19 locus has been a valuable model for clarifying the role of long-range interactions between cis-regulatory elements. Imprinted expression of the linked, reciprocally imprinted genes is explained by parent-of-origin-specific chromosomal loop structures between the paternal Igf2 or maternal H19 promoters and their shared tissue-specific enhancer elements. Here, we further analyze these loop structures for their composition and their impact on expression of the linked long non-coding RNA, Nctc1. We show that Nctc1 is co-regulated with Igf2 and H19 and physically interacts with the shared muscle enhancer. In fact, all three co-regulated genes have the potential to interact not only with the shared enhancer but also with each other via their enhancer interactions. Furthermore, developmental and genetic analyses indicate functional significance for these promoter-promoter interactions. Altogether, we present a novel mechanism to explain developmental specific imprinting of Nctc1 and provide new information about enhancer mechanisms and about the role of chromatin domains in establishing gene expression patterns.
authors.affiliation: Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Bokkee
authors.initials: B
authors.lastname: Eun
authors.forename: Megan L
authors.initials: ML
authors.lastname: Sampley
authors.forename: Austin L
authors.initials: AL
authors.lastname: Good
authors.forename: Claudia M
authors.initials: CM
authors.lastname: Gebert
authors.forename: Karl
authors.initials: K
authors.lastname: Pfeifer
mesh_terms: D000818:Animals; D033481:Chromosomes, Mammalian / Q000737:chemistry; D004247:DNA / Q000737:chemistry; D004742:Enhancer Elements, Genetic; D056426:Genetic Loci; D018392:Genomic Imprinting; D007335:Insulin-Like Growth Factor II / Q000096:biosynthesis / Q000235:genetics; D051379:Mice; D020297:Mice, Congenic; D018482:Muscle, Skeletal / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000096:biosynthesis / Q000235:genetics*; D015533:Transcriptional Activation
chemical_list: C094335:H19 long non-coding RNA; C513121:IGF2 protein, mouse; D062085:RNA, Long Noncoding; D007335:Insulin-Like Growth Factor II; D004247:DNA; D012319:RNA Polymerase II