The Origin of the RB1 Imprint

Abstract

The human RB1 gene is imprinted due to a differentially methylated CpG island in intron 2. This CpG island is part of PPP1R26P1, a truncated retrocopy of PPP1R26, and serves as a promoter for an alternative RB1 transcript. We show here by in silico analyses that the parental PPP1R26 gene is present in the analysed members of Haplorrhini, which comprise Catarrhini (Old World Monkeys, Small apes, Great Apes and Human), Platyrrhini (New World Monkeys) and tarsier, and Strepsirrhini (galago). Interestingly, we detected the retrocopy, PPP1R26P1, in all Anthropoidea (Catarrhini and Platyrrhini) that we studied but not in tarsier or galago. Additional retrocopies are present in human and chimpanzee on chromosome 22, but their distinct composition indicates that they are the result of independent retrotransposition events. Chimpanzee and marmoset have further retrocopies on chromosome 8 and chromosome 4, respectively. To examine the origin of the RB1 imprint, we compared the methylation patterns of the parental PPP1R26 gene and its retrocopies in different primates (human, chimpanzee, orangutan, rhesus macaque, marmoset and galago). Methylation analysis by deep bisulfite sequencing showed that PPP1R26 is methylated whereas the retrocopy in RB1 intron 2 is differentially methylated in all primates studied. All other retrocopies are fully methylated, except for the additional retrocopy on marmoset chromosome 4, which is also differentially methylated. Using an informative SNP for the methylation analysis in marmoset, we could show that the differential methylation pattern of the retrocopy on chromosome 4 is allele-specific. We conclude that the epigenetic fate of a PPP1R26 retrocopy after integration depends on the DNA sequence and selective forces at the integration site.

Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites

“…In our study, the GFP CGI retrotransposed into Chromosome 2 was not imprinted since no change in methylation patterns was observed when it was transmitted through either the female (B1712) or male (B1718) germline. This result is not unexpected because it has been suggested that the epigenetic fate of the retrotransposed DNA depends on its sequence and selective forces at the integration site (Kanber et al 2013). …”

“…Many pseudogenes are imprinted, manifesting parent-of-origin specific methylation in the overlapping CGIs. In several cases, the imprinted intronic pseudogenes are also responsible for the imprinting of the corresponding genes that contain them (Cowley and Oakey 2010;Kanber et al 2013). In our study, the GFP CGI retrotransposed into Chromosome 2 was not imprinted since no change in methylation patterns was observed when it was transmitted through either the female (B1712) or male (B1718) germline.…”

Phenotypic Spectrum and Extent of DNA Methylation Defects Associated with Multilocus Imprinting Disturbances

“…The RB1 region in ID28 has been analyzed by deep bisulfite sequencing on the Roche/454 GS junior system as described previously in Kanber et al [24]. The PCR amplicon designed to CGI85 incorporates 11 CpG dinucleotides (chr13:48,893,503-48,893,690, hg19) and the average methylation value has been determined at a read depth of 3017 reads.…”

Genome-wide methylation analysis of retrocopy-associated CpG islands and their genomic environment

“…The integration of this retrocopy led to RB1 imprinting as its expression is skewed in favor of the maternal allele. 16,17 RPS2P32 on chromosome 7 is derived from the gene RPS2 on chromosome 16 (Fig. 6).…”

“…Parent-of-origin-specific methylation of CpG85 has been confirmed by other studies. [15][16][17][18] At present, nearly 100 imprinted human genes have been identified, and several studies have taken a genome-wide look at parent-of-origin-specific DNA methylation in order to identify novel imprinted genes. 18,19 Retrocopies are instructive genomic elements for studying the evolutionary dynamics and constraints of DNA methylation.…”