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This Week in PNAS: Feb 5, 2013

In the early, online edition of the Proceedings of the National Academy of Sciences, a University of Michigan-led team takes a look at recurrent RNA chimeras in chronic lymphocytic leukemia, or CLL. From transcriptome sequence data for seven CLL tumors, researchers uncovered nine RNA chimera candidates. Chimeras involving transcripts from YPEL5 and PPP1CB genes were particularly common, they found, with YPEL5-PPP1CB or PPP1CB-YPEL5 RNA fusions turning up in 95 percent of the 103 CLL samples screened subsequently. These chimeras appear to stem from RNA splicing events, study authors say, since corresponding DNA fusions weren't found in two chimera-containing tumors tested by whole-genome sequencing. "These results suggest a role for RNA splicing chimeras in the pathogenesis of CLL," they write.

Another PNAS study hints at previously unappreciated ties between long non-coding RNA production and active transcription at neighboring genes. Researchers from the Whitehead Institute for Biomedical Research, the Massachusetts Institute of Technology, and elsewhere used various types of sequencing to track the formation of new messenger RNAs and lncRNAs in mouse and human embryonic stem cells. Results of the analyses indicate that more than 60 percent of lncRNAs arise from divergent transcription in and around promoters of actively expressed genes. Though not all of these newly formed lncRNAs stick around in the cells, levels of lncRNAs and their corresponding mRNAs appear to increase and decrease together as stem cells differentiate, study authors note, "suggesting that coordinated regulation of lncRNA/mRNA gene pairs may be a general feature of differentiation."

Ghent University's Yves Van de Peer and colleagues present evidence that single-copy genes are more common than expected in flowering plants. Using genome sequence data for 20 flowering plant species, the group saw several instances in which single-copy genes had formed via gene loss in this angiosperm lineage, which has undergone historical genome-wide duplication events. Study authors suspect that convergent evolution may be behind many of the single-copy genes, which were more common than usual in essential, housekeeping pathways. "Because the observed number of single-copy families greatly exceeds what can be expected from random gene loss effects," they write, "selection likely promotes convergent evolution of these genes to single-copy status across angiosperms."