Gene expression and adaptive noncoding changes during human evolution

Courtney C Babbitt,William J Nielsen,Gregory A Wray,Ralph Haygood

doi:10.1186/s12864-017-3831-2

Courtney C Babbitt, William J Nielsen + Show 2 more

Open Access

https://doi.org/10.1186/s12864-017-3831-2

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Abstract

BackgroundDespite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear.ResultsHere we present new measurements of gene expression in five tissues of humans and chimpanzees, and use them to assess this relationship. We then compare our results with previous studies of adaptive noncoding changes, analyzing correlations at the level of gene ontology groups, in order to gain statistical power to detect correlations.ConclusionsConsistent with previous studies, we find little correlation between gene expression and adaptive noncoding changes at the level of individual genes; however, we do find significant correlations at the level of biological function ontology groups. The types of function include processes regulated by specific transcription factors, responses to genetic or chemical perturbations, and differentiation of cell types within the immune system. Among functional categories co-enriched with both differential expression and noncoding adaptation, prominent themes include cancer, particularly epithelial cancers, and neural development and function.

Highlights

Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear
Using a multi-factor Generalized Linear Model (GLM) to analyze our measurements of all tissues together [22], we identified 4828 genes whose expression differs between humans and chimpanzees (q-value
We find that adaptation in regulatory regions may have driven many of these changes in gene expression, but that may have had other attendant consequences related to human disease states

Summary

Introduction

Despite evidence for adaptive changes in both gene expression and non-protein-coding, putatively regulatory regions of the genome during human evolution, the relationship between gene expression and adaptive changes in cis-regulatory regions remains unclear. Expression level is for most genes a high-dimensional phenotype: almost without exception it differs among cell types, across the life cycle, and in response to numerous environmental factors [1, 2]. This makes it challenging to link positive selection on regulatory sequences to any particular aspect of a gene’s expression. It has proven difficult to detect a clear relationship at a genomic scale between the distribution

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