An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder

Sarah M. Williams,Joon Yong An,Colin J. Jackson,Michelle Watts,Valentine Murigneux,Mark A. Bellgrove,Alexandre S. Cristino,Andrew J. O. Whitehouse,Charles Claudianos,Janette Edson

doi:10.1038/s41380-018-0049-x

Abstract

A number of genetic studies have identified rare protein-coding DNA variations associated with autism spectrum disorder (ASD), a neurodevelopmental disorder with significant genetic etiology and heterogeneity. In contrast, the contributions of functional, regulatory genetic variations that occur in the extensive non-protein-coding regions of the genome remain poorly understood. Here we developed a genome-wide analysis to identify the rare single nucleotide variants (SNVs) that occur in non-coding regions and determined the regulatory function and evolutionary conservation of these variants. Using publicly available datasets and computational predictions, we identified SNVs within putative regulatory regions in promoters, transcription factor binding sites, and microRNA genes and their target sites. Overall, we found that the regulatory variants in ASD cases were enriched in ASD-risk genes and genes involved in fetal neurodevelopment. As with previously reported coding mutations, we found an enrichment of the regulatory variants associated with dysregulation of neurodevelopmental and synaptic signaling pathways. Among these were several rare inherited SNVs found in the mature sequence of microRNAs predicted to affect the regulation of ASD-risk genes. We show a paternally inherited miR-873-5p variant with altered binding affinity for several risk-genes including NRXN2 and CNTNAP2 putatively overlay maternally inherited loss-of-function coding variations in NRXN1 and CNTNAP2 to likely increase the genetic liability in an idiopathic ASD case. Our analysis pipeline provides a new resource for identifying loss-of-function regulatory DNA variations that may contribute to the genetic etiology of complex disorders.

Highlights

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with heterogeneous genetic origins
The whole-exome sequencing (WES) data used in this study was from our previous study of Australian ASD families (n = 128; 48 ASD cases, and 80 parents) [7], and we considered the single nucleotide variants (SNVs) for this analysis as there were no large copy number variations (CNVs) detected in this sample
To examine the captured non-coding regions, we developed a computational pipeline to systematically analyze WES data in non-coding regulatory contexts: proximal promoter regions, transcription start site (TSS), untranslated regions (5′ and 3′ untranslated regions (3′UTR)), transcription-factor-binding sites (TFBS), microRNA regulatory elements (MREs), and miRNA genes (Fig. 1)

Summary

Introduction

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with heterogeneous genetic origins. Recent genome sequencing studies have identified many risk genes from the loss-of-function protein-coding variants, which has Francisco, San Francisco, USA 5 Telethon Kids Institute, University of Western Australia, Perth, Australia 6 Cooperative Research Centre for Living with Autism, Brisbane, Australia 7 Research School of Chemistry, Australian National University, Canberra, Australia 8 Monash Institute of Cognitive and Clinical Neuroscience, Monash. University, Canberra, Australia driven a move toward analysis of convergent risk pathways [1,2,3,4]. In a recent landmark-autism study, non-coding de novo DNA variations were found to be enriched in the untranslated regions of genes, gene boundaries, and DNase I hypersensitive regions [6]. A number of previous exomesequencing studies including our own [7] have shown that there are many DNA variations that occur in the non-coding regulatory regions of genes, albeit of unknown functional significance

Methods

Results

Conclusion