Selective constraints in experimentally defined primate regulatory regions.

Area of Science:

• Evolutionary biology
• Genomics
• Molecular biology

Background:

• Understanding the evolutionary impact of gene regulatory mutations is crucial but hindered by incomplete functional DNA annotation.
• Transcription factor binding sites (TFBSs) are key regulatory elements, but their short, degenerate nature complicates identification and evolutionary analysis.
• Existing methods using evolutionary conservation to predict TFBSs may introduce bias in estimating selective constraint.

Purpose of the Study:

• To investigate the fitness effects of regulatory mutations using experimentally validated human TFBS datasets.
• To assess selective constraint in regulatory elements and its relationship with gene expression and evolutionary rates.
• To determine the proportion of regulatory mutations fixed by positive selection in humans.

Main Methods:

• Utilized two human TFBS datasets: TRANSFAC literature collection and ChIP-chip data.
• Defined putative cis-regulatory modules (pCRMs) by clustering TFBSs.
• Compared selective constraint across species (human, chimpanzee, macaque) and correlated it with gene expression breadth.

Main Results:

• Approximately 37% of TFBS mutations are strongly deleterious, comparable to 2-fold degenerate protein-coding sites.
• Selective constraint is reduced in human/chimpanzee pCRMs and ChIP-chip sequences compared to macaques.
• No significant evidence for positive selection driving regulatory mutations to fixation in humans.
• Selective constraint in regulatory regions negatively correlates with gene expression breadth, opposite to protein-coding sites.
• Transcription factor protein evolution rate positively correlates with the breadth of gene expression it regulates.

Conclusions:

• Strongly deleterious regulatory mutations are 1.6-fold more likely in tissue-specific genes than housekeeping genes.
• Increased gene expression complexity may incur a fitness cost due to a higher occurrence of deleterious regulatory mutations.
• Regulatory mutation fitness effects vary across evolutionary timescales and gene expression patterns.