Bidirectional action of the Igf2r imprint control element on upstream and downstream imprinted genes

Abstract

Imprinting of the maternally-expressed Igf2r gene is controlled by an intronic imprint control element (ICE) known as Region2 that contains the promoter of the noncoding Air RNA, whose transcript overlaps the silenced paternal Igf2r promoter in an antisense orientation. Two novel imprinted genes, Slc22a2 and Slc22a3 are described here that lie 110 and 155 kb 3 to Igf2r and that are not overlapped by the Air transcript but are regulated by the Igf2r-ICE, as previously shown for Igf2r. These results identify a new cluster of imprinted genes whose repression by the bidirectional action of the Region2-ICE is independent of transcript overlap by the Air RNA. Cis-acting epigenetic mechanisms that regulate gene expression are of critical importance in understanding how gene regulation is controlled in development and disease, but are currently understood only at a basic level. Of the many mammalian systems currently used to investigate epigenetic mechanisms, parental-specific gene expression induced by genomic imprinting has the best potential to identify relevant DNA sequences and modifications, since both the active and silent parental alleles are retained in the same nuclear environment and can be directly compared (for reviews, see Reik and Walter 2001;Sleutels and Barlow 2001). At present, 50 imprinted genes have been identified with approximately equal numbers of maternally and paternally expressed examples . This may represent a near complete collection, since the total number of imprinted genes, predicted to be in the range of 200, should now be reduced by 60%, following the reappraisal of the total number of genes in the mammalian genome (Claverie 2001).A large body of evidence indicates that imprinted genes are regulated by cis-linked DNA imprint control elements (ICEs) that are epigenetically modified by an imprint in either the maternal germ line (for maternally imprinted genes) or paternal germ line (for paternally imprinted genes). Experimental data also indicate that DNA methylation is the imprint or at least is involved in maintaining the imprint for most but not all genes (Caspary et al. 1998;Jackson-Grusby et al. 2001). In contrast to early expectations, the data clearly show that imprints can act either as epigenetic activators to activate one allele of an imprinted gene, or as epigenetic repressors to silence one allele (Obata et al. 1998;Kato et al. 1999;Jackson-Grusby et al. 2001). The observation that imprinted genes are clustered within a chromosomal region has led to the suggestion that the ICE may also serve as an epigenetic domain regulator that controls the imprinted expression of more than one imprinted gene. To date, seven clusters have been identified in the mouse genome that are also conserved in the human genome . The clusters show generally similar behavior whereby a majority of the clustered genes are expressed from one parental chromosome and only a minority from the reciprocal parental chromosome. Two well-known examples are the Prader-Willi syndrome (PWS) region (human 15q11-15 syn...

Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrum

“…A differentially methylated region-2 (DMR2) within the second intron of Igf2r constitutes a critical, bidirectional element controlling silencing of the paternal allele of three protein-coding imprinted genes, Igf2r, Slc22a2, and Slc22a3 (Zwart et al 2001). DMR2 resides in a promoter that drives the transcription of a nonprotein-coding antisense transcript, Air, which partially overlaps with Igf2r.…”

Long-range DNase I hypersensitivity mapping reveals the imprinted Igf2r and Air promoters share cis-regulatory elements

“…The expression profile of the Slc22a2 and Slc22a3 genes is very different, as these genes show restricted tissuespecific and developmental expression. Both are repressed in preand post-implantation embryos but show maternal-specific expression in the placenta that switches to biparental expression before birth in Slc22a3 but continues until birth for Slc22a2 (Zwart et al 2001a). Another characteristic feature of imprinted genes is that most are distinguished by a CpG island-type promoter that is associated with only 50% of nonimprinted mammalian genes.…”

“…This has been verified for the Igf2r/Air cluster, where a single imprint control element (ICE) that maps to Igf2r intron 2 has been shown to control allele-specific silencing of all imprinted genes in this 513-kb cluster (Zwart et al 2001a). The Igf2r intron 2 ICE contains the Air ncRNA promoter .…”

Imprinting centers, chromatin structure, and disease

“…The major organizational features of the PWS/AS region and the KIP2/ LIT1 domain resemble those of another intensively studied imprinted region, the Igf2r region in mouse (Fig. 1) [Zwart et al, 2001;Fournier et al, 2002] (in humans, IGF2R and nearby genes are not imprinted in most individuals [Riesewijk et al, 1996]). …”