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Evolutionary divergence of 3' UTRs in cichlid fishes.

ABSTRACT: BACKGROUND:Post-transcriptional regulation is crucial for the control of eukaryotic gene expression and might contribute to adaptive divergence. The three prime untranslated regions (3' UTRs), that are located downstream of protein-coding sequences, play important roles in post-transcriptional regulation. These regions contain functional elements that influence the fate of mRNAs and could be exceptionally important in groups such as rapidly evolving cichlid fishes. RESULTS:To examine cichlid 3' UTR evolution, we 1) identified gene features in nine teleost genomes and 2) performed comparative analyses to assess evolutionary variation in length, functional motifs, and evolutionary rates of 3' UTRs. In all nine teleost genomes, we found a smaller proportion of repetitive elements in 3' UTRs than in the whole genome. We found that the 3' UTRs in cichlids tend to be longer than those in non-cichlids, and this was associated, on average, with one more miRNA target per gene in cichlids. Moreover, we provided evidence that 3' UTRs on average have evolved faster in cichlids than in non-cichlids. Finally, analyses of gene function suggested that both the top 5% longest and 5% most rapidly evolving 3' UTRs in cichlids tended to be involved in ribosome-associated pathways and translation. CONCLUSIONS:Our results reveal novel patterns of evolution in the 3' UTRs of teleosts in general and cichlids in particular. The data suggest that 3' UTRs might serve as important meta-regulators, regulators of other mechanisms governing post-transcriptional regulation, especially in groups like cichlids that have undergone extremely fast rates of phenotypic diversification and speciation.

SUBMITTER: Xiong P

PROVIDER: S-EPMC5987618 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Evolutionary divergence of 3' UTRs in cichlid fishes.

Xiong Peiwen P Hulsey C Darrin CD Meyer Axel A Franchini Paolo P

BMC genomics 20180605 1

<h4>Background</h4>Post-transcriptional regulation is crucial for the control of eukaryotic gene expression and might contribute to adaptive divergence. The three prime untranslated regions (3' UTRs), that are located downstream of protein-coding sequences, play important roles in post-transcriptional regulation. These regions contain functional elements that influence the fate of mRNAs and could be exceptionally important in groups such as rapidly evolving cichlid fishes.<h4>Results</h4>To exam ...[more]

PMID: 29866078

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Project description:Divergence within cis-regulatory sequences may contribute to the adaptive evolution of gene expression, but functional alleles in these regions are difficult to identify without abundant genomic resources. Among African cichlid fishes, the differential expression of seven opsin genes has produced adaptive differences in visual sensitivity. Quantitative genetic analysis suggests that cis-regulatory alleles near the SWS2-LWS opsins may contribute to this variation. Here, we sequence BACs containing the opsin genes of two cichlids, Oreochromis niloticus and Metriaclima zebra. We use phylogenetic footprinting and shadowing to examine divergence in conserved non-coding elements, promoter sequences, and 3'-UTRs surrounding each opsin in search of candidate cis-regulatory sequences that influence cichlid opsin expression.We identified 20 conserved non-coding elements surrounding the opsins of cichlids and other teleosts, including one known enhancer and a retinal microRNA. Most conserved elements contained computationally-predicted binding sites that correspond to transcription factors that function in vertebrate opsin expression; O. niloticus and M. zebra were significantly divergent in two of these. Similarly, we found a large number of relevant transcription factor binding sites within each opsin's proximal promoter, and identified five opsins that were considerably divergent in both expression and the number of transcription factor binding sites shared between O. niloticus and M. zebra. We also found several microRNA target sites within the 3'-UTR of each opsin, including two 3'-UTRs that differ significantly between O. niloticus and M. zebra. Finally, we examined interspecific divergence among 18 phenotypically diverse cichlids from Lake Malawi for one conserved non-coding element, two 3'-UTRs, and five opsin proximal promoters. We found that all regions were highly conserved with some evidence of CRX transcription factor binding site turnover. We also found three SNPs within two opsin promoters and one non-coding element that had weak association with cichlid opsin expression.This study is the first to systematically search the opsins of cichlids for putative cis-regulatory sequences. Although many putative regulatory regions are highly conserved across a large number of phenotypically diverse cichlids, we found at least nine divergent sequences that could contribute to opsin expression differences in cis and stand out as candidates for future functional analyses.

Dataset Information

Evolutionary divergence of 3' UTRs in cichlid fishes.

Publications

Evolutionary divergence of 3' UTRs in cichlid fishes.

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