Transcription is required for establishment of germline methylation marks at imprinted genes

Abstract

Genomic imprinting requires the differential marking by DNA methylation of genes in male and female gametes. In the female germline, acquisition of methylation imprint marks depends upon the de novo methyltransferase Dnmt3a and its cofactor Dnmt3L, but the reasons why specific sequences are targets for Dnmt3a and Dnmt3L are still poorly understood. Here, we investigate the role of transcription in establishing maternal germline methylation marks. We show that at the Gnas locus, truncating transcripts from the furthest upstream Nesp promoter disrupts oocyte-derived methylation of the differentially methylated regions (DMRs). Transcription through DMRs in oocytes is not restricted to this locus but occurs across the prospective DMRs at many other maternally marked imprinted domains, suggesting a common requirement for transcription events. The transcripts implicated here in gametic methylation are protein-coding, in contrast to the noncoding antisense transcripts involved in the monoallelic silencing of imprinted genes in somatic tissues, although they often initiate from alternative promoters in oocytes. We propose that transcription is a third essential component of the de novo methylation system, which includes optimal CpG spacing and histone modifications, and may be required to create or maintain open chromatin domains to allow the methylation complex access to its preferred targets.[Keywords: Genomic imprinting; DNA methylation; oocytes; transcription] Supplemental material is available at http://www.genesdev.org.

A maternal deletion upstream of the imprint control region 2 in 11p15 causes loss of methylation and familial Beckwith–Wiedemann syndrome

“…That KCNQ1 is expressed in human and murine oocytes has already been shown. 28,29 Furthermore, Chotalia et al 24 also detected oocyte-specific start sites for Kcnq1.…”

“…12 There is recent evidence for imprinted loci on chromosomes 20 and 15 that transcription through the DMR is required for the establishment of the methylation imprint in the maternal germline. [24][25][26] It is possible that this is also true for the ICR2 on chromosome 11. We therefore suggest that transcription of KCNQ1 through the ICR2 in the maternal germline is required for the imprint establishment in humans ( Figure 6).…”

Genomic imprinting and its relevance to congenital disease, infertility, molar pregnancy and induced pluripotent stem cell

“…63 At least some of these deletions could affect transcription of NESP55 in oocytes, which is presumed to proceed through AS1, XL and exon A/B. In light of the study on the mouse Gnas locus, 26 it is conceivable that the absence of NESP55 transcription leads to a failure in imprint establishment.…”

“…Factors and features identified so far as specificity determinants for imprinting in oocytes include: (1) transcription traversing ICRs (Figure 1), 26 (2) unmethylated lysine-4 of histone H3 (H3K4), 27 (3) 10-bp CpG spacing, 28 (4) a histone H3K4 demethylase Kdm1b (Figure 1) 29 and (5) a Krüppel-associated box (KRAB) zinc finger protein Zfp57 (Figure 1). 30 Among these, the first three seem common to all oocyte-methylated ICRs and could be prerequisites for imprint establishment.…”

“…30 Among these, the first three seem common to all oocyte-methylated ICRs and could be prerequisites for imprint establishment. Transcription through ICRs may make the chromatin more accessible by the Dnmt3a-Dnmt3L complex; 26 unmethylated, but not methylated, H3K4 is the high-affinity binding target of Dnmt3L; 27 two CpG sites located 10-bp apart fit very well with the catalytic centers of the heterotetrameric Dnmt3a-Dnmt3L complex. 28 However, these features can be found elsewhere in the genome and are not specific to ICRs.…”