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This Week in Genome Biology: Jul 16, 2014

A team from the University of Lausanne and the Swiss Institute of Bioinformatics present evidence of conserved microRNA editing sites in the genomes of mammals and other animals. By searching for examples of RNA and DNA mismatches in human, rhesus macaque, mouse, opossum, platypus, and chicken small RNA sequence datasets, the researchers determined that adenosine-to-inosine editing in miRNAs tends to occur at deeply conserved sites. Even so, editing status seems to vary by tissue type, age, and disease state, they report, noting that placental mammals appear to have undergone edited miRNA family expansions that have altered some of the messenger RNAs targeted during processes such as development and aging.

A form of sequencing that focuses on RNA transcribed in vitro from RNA clones is highlighting the biases that may be introduced during typical RNA sequencing experiments. Researchers from the US and Turkey performed in vitro transcription sequencing, or IVT-seq, on more than 1,000 RNAs transcribed in vitro from a human complementary DNA library. Their results indicate that standard RNA sequencing methods may vary in their coverage, both across a given transcript and between samples representing the same transcript, due to ribosomal RNA depletion.

University of Virginia researchers describe an algorithm for finding new structural variants in whole-genome sequencing data. The breakpoint prediction approach, called LUMPY, integrates several types of structural variant information in read data — from split reads and read pairs in alignment data to read depth — in multiple sample datasets, the study's authors say. Their comparison suggests LUMPY compares favorably with other structural variant detection methods. In a previously sequenced human genome, for example, the method identified more than 4,500 new or known structural variant breakpoints.