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Genome Research Papers Tackle Primate Gene Regulation, C. Elegans Transcriptome, More

Investigators in the US, Switzerland, and Spain share findings from an analysis of gene expression and DNA methylation in several tissue types from humans, chimpanzees, and rhesus macaques. After sequencing RNA and DNA isolated from heart, liver, kidney, and lung samples for four representatives from each species, the team compared gene expression, methylation, and related gene regulation features within and between species and tissue types. "[W]e aim to provide a new and more accurate comparative catalog of inter-tissue and interspecies differences in gene regulation between humans and other primates," the researchers report, noting that "this catalog can be useful for many future applications and can serve as a new benchmark for regulatory divergence in primates."

A Johns Hopkins University team reports on results from a direct RNA sequencing analysis of the worm model organism Caenorhabditis elegans. Using nanopore long read sequencing, the team did direct RNA-seq on duplicate worm representatives spanning different stages of C. elegans development. The resulting transcriptome sequence revealed messenger RNA transcripts stemming from more than 14,600 genes, uncovering thousands of new and known splice isoforms compared to the C. elegans annotation. "Combining [3' untranslated regions (UTR)] and splice isoforms, we identified 28,858 full-length transcript isoforms," the authors write, noting that the transcriptome provide a look at variable transcript polyadenylated tail lengths and corresponding expression and 3'-UTR features.

Researchers from the US and Germany examine alternative polyadenylation-based gene regulation in pancreatic ductal adenocarcinoma (PDAC). "Pan-cancer analyses have revealed common [alternative polyadenylation] events across the tumor landscape," they write, though "little is known about tumor-specific alterations that may uncover novel events and vulnerabilities." The team's analysis of available RNA sequence data for almost 150 PDAC tumors revealed recurrent alternative polyadenylation events, coinciding with shifts in mRNA 3'-UTR lengths, gene expression, microRNA regulation, and more. The alternative polyadenylation events were over-represented in genes and pathways previously linked to PDAC, the authors note, while a subset of patients with 3'-UTR changes appeared to have particularly poor outcomes in a subsequent survival analysis.