The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus

Abstract

BackgroundGenomic imprinting is the epigenetic marking of genes that results in parent-of-origin monoallelic expression. Most imprinted domains are associated with differentially DNA methylated regions (DMRs) that originate in the gametes, and are maintained in somatic tissues after fertilization. This allelic methylation profile is associated with a plethora of histone tail modifications that orchestrates higher order chromatin interactions. The mouse chromosome 15 imprinted cluster contains multiple brain-specific maternally expressed transcripts including Ago2, Chrac1, Trappc9 and Kcnk9 and a paternally expressed gene, Peg13. The promoter of Peg13 is methylated on the maternal allele and is the sole DMR within the locus. To determine the extent of imprinting within the human orthologous region on chromosome 8q24, a region associated with autosomal recessive intellectual disability, Birk-Barel mental retardation and dysmorphism syndrome, we have undertaken a systematic analysis of allelic expression and DNA methylation of genes mapping within an approximately 2 Mb region around TRAPPC9.ResultsUtilizing allele-specific RT-PCR, bisulphite sequencing, chromatin immunoprecipitation and chromosome conformation capture (3C) we show the reciprocal expression of the novel, paternally expressed, PEG13 non-coding RNA and maternally expressed KCNK9 genes in brain, and the biallelic expression of flanking transcripts in a range of tissues. We identify a tandem-repeat region overlapping the PEG13 transcript that is methylated on the maternal allele, which binds CTCF-cohesin in chromatin immunoprecipitation experiments and possesses enhancer-blocker activity. Using 3C, we identify mutually exclusive approximately 58 and 500 kb chromatin loops in adult frontal cortex between a novel brain-specific enhancer, marked by H3K4me1 and H3K27ac, with the KCNK9 and PEG13 promoters which we propose regulates brain-specific expression.ConclusionsWe have characterised the molecular mechanism responsible for reciprocal allelic expression of the PEG13 and KCNK9 transcripts. Therefore, our observations may have important implications for identifying the cause of intellectual disabilities associated with the 8q24 locus.

In Sickness and in Health: The Role of TRAPP and Associated Proteins in Disease

“…Therefore, it seems reasonable to posit that mutations in TrappC9 may alter its ability to function in this signaling pathway. Indeed, several recent studies further implicated TrappC9 in the NF-κB pathway and in neuronal differentiation (71,72) and, although widely expressed, TRAPPC9 expression appears highest in the cerebellum consistent with the notion that it may have a brain-specific function outside of its role in TRAPP II (73). If this protein functions in both membrane traffic and the NF-κB pathway, then TrappC9 may be viewed as a so-called 'moonlighting' protein (74).…”

A homozygous founder mutation inTRAPPC6Bassociates with a neurodevelopmental disorder characterised by microcephaly, epilepsy and autistic features

“…This protein has been implicated in neural differentiation,15 and inactivation in PC12 cells prevents nerve growth factor-induced neurite outgrowth 14. Its expression is highest in the human cerebellum, suggesting that TrappC9 may have a brain-specific signalling function outside of its general role in membrane trafficking 16. Several children with intellectual disability and microcephaly have been found to carry mutations in TRAPPC9 8–11 17.…”

A role for chromatin topology in imprinted domain regulation

“…Imprinted lncRNAs range in length from ϳ1.6 kb to ϳ1000 kb, and thus, many imprinted lncRNAs are also classified as macro lncRNAs due to their extraordinary length (Guenzl and Barlow 2012). To date, seven imprinted lncRNAs have been identified that are regulated by imprinted gDMRs and are conserved between mice and humans: Airn, Gtl2, H19, Kcnq1ot1, Nespas, Peg13, and Ube3a-as (Brannan et al 1990;Gray et al 1999;Smilinich et al 1999;Lyle et al 2000;Paulsen et al 2001;Coombes et al 2003;Court et al 2014). Similar to Xist, these lncRNAs are thought to have a role in mediating long-range control of imprinted gene transcription.…”