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A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers

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Purifying selection in deeply conserved human enhancers is more consistent than in coding sequences.

Dilrini R De Silva¹, Richard Nichols², Greg Elgar³

¹Systems Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom; School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

|July 26, 2014

Summary

This summary is machine-generated.

Investigating Conserved Non-coding Elements (CNEs) in human DNA reveals that highly conserved regions show strong purifying selection, similar to essential genes. Rare variants in these regulatory regions may indicate widespread deleterious effects.

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Area of Science:

Genomics
Evolutionary Biology
Human Genetics

Background:

Assessing selective constraint in non-coding DNA, particularly Conserved Non-coding Elements (CNEs), is challenging due to the lack of clear distinctions between sites under varying selective pressures.
CNEs, defined by high sequence identity across vertebrates, are implicated in developmental disorders, necessitating an investigation into the widespread impact of their mutations in humans.

Purpose of the Study:

To analyze polymorphism data within human CNEs to determine if deleterious mutations are common.
To compare patterns of genetic variation in CNEs with coding sequences and identify sites under selective constraint.

Main Methods:

Mapped single nucleotide variants from HapMap and 1000 Genomes Projects across nearly 2000 CNEs.
Utilized deep vertebrate alignments to categorize CNE sites into non-variant and substituted categories.
Analyzed allele frequency distributions to infer selective pressures.

Main Results:

The 1000 Genomes data revealed an excess of rare derived alleles in CNEs compared to coding sequences, a pattern obscured in HapMap data due to ascertainment bias.
Two categories of sites were identified within CNEs: highly conserved non-variant stretches and more labile regions with substitutions.
Conserved CNE sites exhibited fewer polymorphisms and a greater excess of rare derived alleles, indicating strong purifying selection comparable to conserved trans-dev genes, while labile CNE sites showed distributions similar to non-synonymous sites.

Conclusions:

A significant proportion of sites within conserved CNEs are under strong purifying selection in humans, suggesting deleterious effects of mutations in these regulatory elements.
Future research should prioritize genome-wide re-sequencing for better non-coding region coverage and validate non-coding variants to identify causal variants in complex disorders.