A Downstream CpG Island Controls Transcript Initiation and Elongation and the Methylation State of the Imprinted Airn Macro ncRNA Promoter

Abstract

A CpG island (CGI) lies at the 5′ end of the Airn macro non-protein-coding (nc) RNA that represses the flanking Igf2r promoter in cis on paternally inherited chromosomes. In addition to being modified on maternally inherited chromosomes by a DNA methylation imprint, the Airn CGI shows two unusual organization features: its position immediately downstream of the Airn promoter and transcription start site and a series of tandem direct repeats (TDRs) occupying its second half. The physical separation of the Airn promoter from the CGI provides a model to investigate if the CGI plays distinct transcriptional and epigenetic roles. We used homologous recombination to generate embryonic stem cells carrying deletions at the endogenous locus of the entire CGI or just the TDRs. The deleted Airn alleles were analyzed by using an ES cell imprinting model that recapitulates the onset of Igf2r imprinted expression in embryonic development or by using knock-out mice. The results show that the CGI is required for efficient Airn initiation and to maintain the unmethylated state of the Airn promoter, which are both necessary for Igf2r repression on the paternal chromosome. The TDRs occupying the second half of the CGI play a minor role in Airn transcriptional elongation or processivity, but are essential for methylation on the maternal Airn promoter that is necessary for Igf2r to be expressed from this chromosome. Together the data indicate the existence of a class of regulatory CGIs in the mammalian genome that act downstream of the promoter and transcription start.

Human PPP1R26P1 Functions as cis-Repressive Element in Mouse Rb1

“…The capability of mESCs to be genetically modified by homologous recombination and to be differentiated into several lineages makes them a useful tool to dissect imprinting mechanisms during development and to modify and study the genetic elements involved, as was exemplified at the murine Igf2r/Airn locus [15,17–19]. Most importantly, by the use of mESCs it could be demonstrated recently that it is the transcriptional overlap of Airn with the Igf2r promoter and not the Airn transcript itself that induces Igf2r silencing [20], establishing transcriptional interference as imprinting mechanism [21].…”

Noncoding Transcriptional Landscape in Human Aging

“…The IR syndrome is compensated by a hyperinsulinemia which can be considered as a risk factor for age-related diseases (Erol 2007). Epigenetic factors, including the regulatory effects of the noncoding transcriptome, could be potential modulators of this age-dependent decline of the insulin signaling pathway (Koerner et al 2012).…”

Epigenetics: The Language of the Cell?

“…Moreover, short-segment RNA transiently transcribed from the promoter upstream is also involved in the targeting of DNMTs to unique loci, mediating the establishment of DNA methylation [45]. In addition, DNA methylation localized in special ncRNAs sequences often participates in the regulation of these ncRNAs' expression; for example, the methylation state of a downstream CpG island in the imprinted Airn regulates the transcription initiation, elongation and methylation status of its promoter region [46]. In addition, there is also an interdependent relationship between ncRNAs and histone modifications.…”