Changes of gene expression represent one major driving force underlying the evolution of phenotypic differences across different species. Given that the gene expression is a multi-step process, it is conceivable that evolutionary changes at each layer along the process could exert their distinct contributions. Boosted by the advance in the next generation sequencing technologies, recently, global aspect of gene expression level, alternative splicing, RNA decay as well as mRNA translation, and even protein stability are started to be addressed in different system. However, the extent of the evolutionary divergence of alternative polyadenylation (APA), which plays an important role in post-transcriptional gene regulation and is prevalent in mammalian genomes, remains largely unexplored, particularly how such divergence could arise from the change in cis-regulatory elements and/or trans-acting factors is totally unclear.
In this study, to address these questions for the first time in a mammalian system, using deep sequencing based methods, Prof. Wei Chen’s lab globally identified the polyadenylation sites (pAs) expressed in the two mouse inbred strains (Mus musculus C57BL/6J and Mus spretus SPRET/EiJ) and then quantified their usage in both two parental strains and their F1 hybrids （see the figure below）. In F1 hybrids, the nascent RNA transcripts from both parental alleles are subject to the same trans-regulatory environments, thus observed differences in allele-specific APA pattern should only reflect the impact of cis-regulatory divergence. The contribution of trans-regulatory elements can be inferred by comparing the allele-specific differences with the total differences between the parental strains.
In the fibroblasts derived from the two parental strains, they identified a total of 51446 confident pAs, 75% of which were from 13808 genes. Among the 24721 pAs from 7271 genes expressing multiple pAs, 3747 (15.2%) showed significant divergence between the two strains. By comparing them to allele-specific pattern in F1 hybrids, they found predominant contribution from cis-regulatory changes. Further systematic sequence analysis of the regions in proximity to cis-divergent pAs revealed that the local RNA secondary structure and a poly(U) tract in the upstream region could negatively modulate the pAs usage.
Overall, their study represents a first direct measurement of evolutionary divergence of APA in mammals and their results provides novel insights into the molecular mechanisms underlying alternative polyadenylation.
This research article entitled “Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation” was published online in Molecular Systems Biology on 8 December 2016. PhD student Meisheng Xiao from Max-Delbrück Center for Molecular Medicine and postdoc Bin Zhang from SUSTech were the co-first authors. Prof. Wei Chen is the only corresponding author.
Link of the paper: http://msb.embopress.org/content/12/12/890
