The potential role of a retrotransposed gene and a long noncoding RNA in regulating an X‐linked chromatin gene (KDM5C): Novel epigenetic mechanism in autism

Abstract

A growing body of evidence supports the potential role of the circadian system and chromatin remodeling genes in autism. Considering the heterogeneity and gender discrepancy in autism, and the complex nature of the epigenetic landscape, identification of biologically relevant epigenetic factors requires reducing heterogeneity using proper subtyping. For this study, we used X chromosome inactivation (XCI) status in females with autism as an epigenetic marker for subtyping and examined the expression level of members of KDM5, a chromatin remodeling gene family. KDM5 are histone demethylases involved in the circadian molecular machinery. We used human blood samples to characterize alternatively spliced KDM5 isoforms and noticed that KDM5C undergoes a complex splicing process. We also identified a KDM5C isoform (KDM5C‐3′UTR‐lncRNA) containing a novel 3′UTR originated from a retrotransposed gene (retro‐SUV39H2) of an autosomal methyltransferase (SUV39H2). This 3′UTR shows 84% sequence homology with long ncRNAs (lncRNAs) and is located 32 kb downstream of KDM5C. The KDM5C‐3′UTR‐lncRNA isoform was differentially expressed in autistic females with XCI skewness compared with controls. KDM5C plays a crucial role in balancing histone H3K4 methylation states. The identified retro‐SUV39H2 originated lncRNA also shows H3K4 marks. By assessing the expression level of alternatively spliced Kdm5 isoforms at different circadian time‐points, we showed that some isoforms follow a circadian oscillation pattern in wild type mouse brain.This study provides the first evidence and a suggestive model for the potential role of retrotransposed elements in autism through linking methylases and demethylases, two functionally complementary components of chromatin remodeling, which may collectively contribute to disease etiology through lncRNAs. Autism Res 2019, 12: 1007–1021. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. Lay Summary Genes do not function in isolated conditions and their proper expression level also depends on a mechanism called gene regulation. An example of gene regulation is when changes outside DNA sequences influence the function of autism susceptibility genes. Alternative splicing is one type of gene regulation, which produces several versions of a gene (called variants) that may slightly differ from each other and be expressed at different levels in response to environmental changes. The circadian clock is an essential timing mechanism that enables organisms to maintain internal processes in sync with the dynamic environment brought about by the day–night cycle. The goal of this study was to assess if a subset of females with autism with certain genetic marker had a unique pattern of alternative splicing of three circadian genes. We identified a novel variant that is differentially expressed in this subset. Our study provides a novel subject stratification strategy, and a suggestive model of how biologically relevant components of a gene regulatory process may be linked and, possibly, collecti...

EHMT2 (G9a) activation in mantle cell lymphoma and its associated DNA methylation and gene expression

“…There are also functional links between H3K9 methylation and DNA methylation in mammals 24 , 25 . SUV39H1/2 catalyzes the trimethylation of H3K9 and is necessary to maintain DNA methylation 26 , 27 . Dimethylation of H3K9 plays an equally important role in gene silencing and is catalyzed by distinct H3K9 methyltransferases, EHMT2 and EHMT2-like protein (EHMT1/GLP) 28 , 29 .…”

The Molecular Basis of Depression: Implications of Sex-Related Differences in Epigenetic Regulation

“…Overexpression of X-linked genes may be a common mechanism underlying the development of psychiatric disorders in patients with these rare genetic diseases and in the general population of female psychiatric patients with XIST overexpression. Among the four X-linked escapee genes stated above, KDM5C is especially known to be related to psychiatric disorders including X-linked syndrome, autism, and depression (Ji et al, 2015 ; Vallianatos and Iwase, 2015 ; Talebizadeh et al, 2019 ). Indeed, female patients with MDD show increased expression of the XIST gene and KDM5C in lymphoblastoid cells (Ji et al, 2015 ).…”

“…Indeed, female patients with MDD show increased expression of the XIST gene and KDM5C in lymphoblastoid cells (Ji et al, 2015 ). In addition, a recent clinical study has reported that, in blood samples, the expression levels of KDM5C-3’UTR-lncRNA isoform were different in autistic females with XCI skewness compared with controls (Talebizadeh et al, 2019 ). Intriguingly, a study of human postmortem brains supported overexpression of the XIST gene in female psychiatric patients (Ji et al, 2015 ).…”

Bioinformatics analysis of genomic and immune infiltration patterns in autism spectrum disorder

“…Previous study has also shown the importance of chromatin genes in ASD. Biologically relevant components of gene regulatory processes may collectively contribute to the etiology of ASD ( 10 ). However, no exact ASD causative genes have been identified, and the mechanisms linking them remain unclear.…”