%0 Journal Article
%T A massively parallel 3กไ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
%A Adam J. Litterman
%A David J. Erle
%A Hani Goodarzi
%A John D. Gagnon
%A K. Mark Ansel
%A Olivier Le Tonqueze
%A Robin Kageyama
%A Wenxue Zhao
%J Genome Research
%D 2019
%R http://www.genome.org/cgi/doi/10.1101/gr.242552.118
%X Abstract Compared to coding sequences, untranslated regions of the transcriptome are not well conserved, and functional annotation of these sequences is challenging. Global relationships between nucleotide composition of 3กไ UTR sequences and their sequence conservation have been appreciated since mammalian genomes were first sequenced, but the functional relevance of these patterns remain unknown. We systematically measured the effect on gene expression of the sequences of more than 25,000 RNA-binding protein (RBP) binding sites in primary mouse T cells using a massively parallel reporter assay. GC-rich sequences were destabilizing of reporter mRNAs and come from more rapidly evolving regions of the genome. These sequences were more likely to be folded in vivo and contain a number of structural motifs that reduced accumulation of a heterologous reporter protein. Comparison of full-length 3กไ UTR sequences across vertebrate phylogeny revealed that strictly conserved 3กไ UTRs were GC-poor and enriched in genes associated with organismal development. In contrast, rapidly evolving 3กไ UTRs tended to be GC-rich and derived from genes involved in metabolism and immune responses. Cell-essential genes had lower GC content in their 3กไ UTRs, suggesting a connection between unstructured mRNA noncoding sequences and optimal protein production. By reducing gene expression, GC-rich RBP-occupied sequences act as a rapidly evolving substrate for gene regulatory interactions
%U https://genome.cshlp.org/content/29/6/896.abstract