Regulatory Elements Associated with Paternally-Expressed Genes in the Imprinted Murine Angelman/Prader-Willi Syndrome Domain

Abstract

The Angelman/Prader-Willi syndrome (AS/PWS) domain contains at least 8 imprinted genes regulated by a bipartite imprinting center (IC) associated with the SNRPN gene. One component of the IC, the PWS-IC, governs the paternal epigenotype and expression of paternal genes. The mechanisms by which imprinting and expression of paternal genes within the AS/PWS domain – such as MKRN3 and NDN – are regulated by the PWS-IC are unclear. The syntenic region in the mouse is organized and imprinted similarly to the human domain with the murine PWS-IC defined by a 6 kb interval within the Snrpn locus that includes the promoter. To identify regulatory elements that may mediate PWS-IC function, we mapped the location and allele-specificity of DNase I hypersensitive (DH) sites within the PWS-IC in brain cells, then identified transcription factor binding sites within a subset of these DH sites. Six major paternal-specific DH sites were detected in the Snrpn gene, five of which map within the 6 kb PWS-IC. We postulate these five DH sites represent functional components of the murine PWS-IC. Analysis of transcription factor binding within multiple DH sites detected nuclear respiratory factors (NRF's) and YY1 specifically on the paternal allele. NRF's and YY1 were also detected in the paternal promoter region of the murine Mrkn3 and Ndn genes. These results suggest that NRF's and YY1 may facilitate PWS-IC function and coordinately regulate expression of paternal genes. The presence of NRF's also suggests a link between transcriptional regulation within the AS/PWS domain and regulation of respiration. 3C analyses indicated Mkrn3 lies in close proximity to the PWS-IC on the paternal chromosome, evidence that the PWS-IC functions by allele-specific interaction with its distal target genes. This could occur by allele-specific co-localization of the PWS-IC and its target genes to transcription factories containing NRF's and YY1.

A boy with Prader-Willi syndrome: unmasking precocious puberty during growth hormone replacement therapy

“…Mapping of microdeletions associated with PWS has identified a 4.3 kb region of the SNPRN gene that appears to be required for establishment and/or maintenance of the paternal epigenotype across the imprinting center domain (11). Therefore, it has been speculated that deleterious defects such as paternal deletion, maternal uniparental disomy, and methylation abnormalities of the SNPRN probes in the MS-MLPA could lead to the loss of paternal PWS-imprinting center and presumably lose expression of the distal genes, including the makorin ring finger protein 3 (MKRN3) (12).…”

Epigenetic regulation of Newborns’ imprinted genes related to gestational growth: patterning by parental race/ethnicity and maternal socioeconomic status

“…Clearly, severe defects where imprinted status is lost—whether due to genetic defects (eg, loss or gain of the chromosomal region or the entire chromosome) or to epigenetic defects (loss or gain of methylation)—lead to pregnancy failures35 or to severe developmental and neurological disorders, including the Prader-Willi and Angelman syndromes,36 37 Beckwith-Wiedemann syndrome38 and neurodevelopmental disorders such as autism 39 40. Furthermore, given the importance of these genes in directing appropriate prenatal growth,22 DNA methylation profiles of the regulatory regions and expression levels of imprinted genes are often found to be highly deregulated in many types of cancer 41 42.…”

Application of droplet digital PCR in the analysis of genome integration and organization of the transgene in BAC transgenic mice

“…The BAC clone was mapped to the large imprinted domain, where imprinted expression of the genes is regulated by a bipartite cis -acting imprinting centre (IC) located ~2.4 Mb downstream of Mkrn3 . The long-range interactions between the IC and the imprinted genes in the domain are thought to form a chromatin holocomplex structure 16 similar to an active chromatin hub 17 , 18 . Such complexity in the chromatin conformation may affect the fragmentation and integration of the BAC molecule in the mouse genome.…”