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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Positive and negative selection in murine ultraconserved noncoding elements.

Daniel L Halligan¹, Fiona Oliver, Jack Guthrie

¹Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.

Molecular Biology and Evolution

|April 12, 2011

Summary

Conserved noncoding elements (CNEs) in mouse genomes show high rates of adaptation, suggesting widespread evolutionary innovation in non-coding DNA. These elements are crucial for development and exhibit unique selection patterns compared to protein-coding genes.

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Area of Science:

Genomics
Evolutionary Biology
Molecular Biology

Background:

Mammalian genomes contain numerous selectively constrained noncoding nucleotides, with hundreds of conserved noncoding elements (CNEs) over 200 bp identified across mammalian orders.
Evidence suggests CNEs are under selective constraint and play roles in developmental regulation, not merely mutational cold spots.

Purpose of the Study:

To quantify negative and positive selection acting on murine CNEs.
To compare selection pressures on CNEs with protein-coding genes and other regulatory elements.

Main Methods:

Analysis of within-species nucleotide variation and between-species divergence of murine CNEs.
Identification of CNEs using a phylogenetically independent comparison.

Main Results:

CNEs experience a higher load of strongly selected deleterious mutations and fewer nearly neutral mutations than protein-coding sites.
CNEs exhibit a significantly higher proportion of adaptive substitutions compared to other genomic sites in murids.
The rate of adaptation in CNEs is comparable to that of amino acid sites in proteins.

Conclusions:

Mammalian conserved noncoding DNA demonstrates widespread adaptation.
CNEs are key sites for evolutionary innovation, with implications for understanding the regulation of critical biological processes like development.