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Genome Research Papers Describe Tool to Uncover Alternative Polyadenylation, Way to Find Conserved Non-Coding Sequences, More

Researchers from Baylor College of Medicine and the University of California, Irvine, have developed a bioinformatic algorithm to uncover  instances of alternative polyadenylation at single-cell and single-gene resolution from single-cell RNA-seq data. The researchers applied their Dynamic Analysis of Alternative PolyAdenylation from Single-cell RNA-seq, or scDaPars, tool to real and simulated data to show that it could recover alternative polyadenylation events otherwise missed due to low levels of sequenced mRNA. Further, applying scDaPars to cancer and human endoderm differentiation data enabled the researchers to tease out additional cell subpopulations. "Thus, scDaPars will enable us to understand cellular heterogeneity at the post-transcriptional APA level," the researchers say.

A Cornell University-led team has developed a pipeline to identify conserved non-coding sequences within Andropogoneae in this week's Genome Research. Andropogoneae, they note, includes multiple crop species that descended from a common ancestor about 18 million years ago. With their approach, the researchers found that most conserved non-coding sequences were annotated and include introns, UTRs, putative cis-regulatory elements, and more; exhibit differential DNA methylation; and variants in them were associated with changes in gene expression levels. "Our results provide a quantitative understanding of the molecular processes governing the evolution of CNSs in maize," they add.

Finally, a Clemson University-led team examines the effects of cocaine consumption on gene expression within the brain of the fruit fly Drosophila melanogaster. They examined single-cell transcriptional changes within the brains of flies given either sucrose or sucrose laced with cocaine. Clustering the transcription profiles of 86,224 cells led to the discovery of 36 distinct groups, encompassing neurons and glia. They additionally noted differences by sex, with more profound changes among male flies. Despite differences between fly and human brains, the researchers note there are functional overlaps, and, because of this, they suggest their atlas of transcriptional changes in fruit flies in response to cocaine consumption "can serve as a contextual framework for future human studies.