Hybrid mice reveal parent-of-origin and Cis- and trans-regulatory effects in the retina.

Susan Q Shen,Joseph C Corbo,Ernest Turro

doi:10.1371/journal.pone.0109382

Abstract

A fundamental challenge in genomics is to map DNA sequence variants onto changes in gene expression. Gene expression is regulated by cis-regulatory elements (CREs, i.e., enhancers, promoters, and silencers) and the trans factors (e.g., transcription factors) that act upon them. A powerful approach to dissecting cis and trans effects is to compare F1 hybrids with F0 homozygotes. Using this approach and taking advantage of the high frequency of polymorphisms in wild-derived inbred Cast/EiJ mice relative to the reference strain C57BL/6J, we conducted allele-specific mRNA-seq analysis in the adult mouse retina, a disease-relevant neural tissue. We found that cis effects account for the bulk of gene regulatory divergence in the retina. Many CREs contained functional (i.e., activating or silencing) cis-regulatory variants mapping onto altered expression of genes, including genes associated with retinal disease. By comparing our retinal data with previously published liver data, we found that most of the cis effects identified were tissue-specific. Lastly, by comparing reciprocal F1 hybrids, we identified evidence of imprinting in the retina for the first time. Our study provides a framework and resource for mapping cis-regulatory variants onto changes in gene expression, and underscores the importance of studying cis-regulatory variants in the context of retinal disease.

Highlights

Photoreceptors mediate vision by converting light into an electrical signal, which is processed by the inner retina and sent to the brain as visual information
Whole-genome sequencing of thousands of individuals [57] and genome-wide association studies (GWAS) have catalogued thousands of disease-associated variants, many of which fall within regulatory regions [58]
We have taken a first step toward understanding the role of regulatory variants in retinal disease by dissecting cisand trans-regulatory effects in the mouse retina, a tissue that models many key aspects of human retinal biology [59]

Summary

Introduction

Photoreceptors mediate vision by converting light into an electrical signal, which is processed by the inner retina and sent to the brain as visual information. Many of the key transcriptional regulators in photoreceptor development are known, and the transcriptomes of these cells have been profiled over normal development as well as in disease states [3,4,5]. A transregulatory difference (‘‘trans effect’’) manifests as conserved expression between the two alleles in the F1 hybrids, despite differential expression of the gene in the F0 homozygotes. A cis-regulatory difference (‘‘cis effect’’) manifests as an allelic expression imbalance (AEI)—i.e., differential expression between the two alleles of a gene in the F1 hybrids, with an allelic ratio that recapitulates the ratio of gene expression levels in the F0 homozygotes. By measuring allele-specific gene expression, the relative contributions of cis and trans effects can be dissected genome-wide. By conducting reciprocal crosses, parentof-origin effects can be identified and filtered to avoid confounding the analysis of cis and trans effects

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