Methylation screening of reciprocal genome-wide UPDs identifies novel human-specific imprinted genes†

Abstract

Nuclear transfer experiments undertaken in the mid-80's revealed that both maternal and paternal genomes are necessary for normal development. This is due to genomic imprinting, an epigenetic mechanism that results in parent-of-origin monoallelic expression of genes regulated by germline-derived allelic methylation. To date, ∼100 imprinted transcripts have been identified in mouse, with approximately two-thirds showing conservation in humans. It is currently unknown how many imprinted genes are present in humans, and to what extent these transcripts exhibit human-specific imprinted expression. This is mainly due to the fact that the majority of screens for imprinted genes have been undertaken in mouse, with subsequent analysis of the human orthologues. Utilizing extremely rare reciprocal genome-wide uniparental disomy samples presenting with Beckwith-Wiedemann and Silver-Russell syndrome-like phenotypes, we analyzed ∼0.1% of CpG dinculeotides present in the human genome for imprinted differentially methylated regions (DMRs) using the Illumina Infinium methylation27 BeadChip microarray. This approach identified 15 imprinted DMRs associated with characterized imprinted domains, and confirmed the maternal methylation of the RB1 DMR. In addition, we discovered two novel DMRs, first, one maternally methylated region overlapping the FAM50B promoter CpG island, which results in paternal expression of this retrotransposon. Secondly, we found a paternally methylated, bidirectional repressor located between maternally expressed ZNF597 and NAT15 genes. These three genes are biallelically expressed in mice due to lack of differential methylation, suggesting that these genes have become imprinted after the divergence of mouse and humans.

Loss of Imprinting as an Epigenetic Marker in Bladder Cancer

“…To explain this finding, Buiting et al [144] proposed a model in which the binding of a transcriptional complex in the unmethylated 2B-promoter region (paternal) blocks the transcriptional complex that regulates the expression of an alternate transcript from the promoter located upstream to exon 1, resulting in a low abundance of the paternal allele. Recently, Nakabayashi et al [145] confirmed the maternal methylation of the RB1 DMR in a study of rare reciprocal genome-wide uniparental disomy samples in patients with Beckwith-Wiedemann and SilverRussell syndrome-like phenotypes.…”

Mining Novel Candidate Imprinted Genes Using Genome-Wide Methylation Screening and Literature Review

“…The remaining 27 genes were considered the top candidates for novel IGs from the present work (Table 1). Candidate locus with one probe with maternal methylation exclusively in placenta (HM27K) [13] a Provisional imprinted gene described in the Catalogue of Imprinted Genes and Parent-of-Origin Effects in Humans and Animals. …”

“…In general, the approaches used to identify novel IGs are based on three main features: presence of an epigenetic signature, monoallelic expression dependent on parental origin, and specific characteristics of the DNA sequence (such as Short interspersed nuclear elements-SINE-exclusion) [3]. Currently, large-scale transcriptome and methylome analyses of data obtained by high-throughput technologies, such as microarrays and next-generation sequencing, are enabling the identification of new candidate IGs [11][12][13][14][15][16][17][18][19][20].…”

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

“…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.…”

“…[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. Based on a whole genome methylome data set with single base pair (bp) resolution, we have investigated the methylation status of all human CGIs associated with a retrocopy and of their genomic environment, which we defined as the region 1,000 bp up-and down-stream of a retrocopy.…”