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Nucleic Acids Research Studies on Alu Genotyping, Stress Response Histones, Undocumented Small RNAs

A team from Cornell University, the University of Utah, and elsewhere presents a pipeline called TypeTE for genotyping Alu retrotransposon mobile element insertions using whole-genome sequence data based on a combination of known features associated with polymorphic Alu elements and local de novo sequence reassembly approaches. When they applied the TypeTE method to PCR-based genotyping profiles for dozens of 1000 Genomes Project participants, for example, the researchers found that the pipeline could improve genotyping calls for dozens of reference Alu loci and more than 100 non-reference loci compared to Alu genotype calls produced in the past. Moreover, the authors note that the broader TypeTE pipeline strategy "can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics."

Researchers in Spain, Germany, and the US report on histone residues that appear to contribute to reprogramming of transcriptional regulatory networks in a Saccharomyces cerevisiae yeast model of stress response. Using yeast genetic screens, RNA sequencing, and other approaches, the team tracked heat and osmotic stress response in strains with a wide range of histone mutations to narrow in on the histone residues contributing to transcriptional stress responses. "[W]e observed that the histone residues needed depend on the type of gene and/or stress, thereby suggesting a 'personalized,' rather than general subset of histone requirements for each chromatin context," the authors report, adding that the study "offers a new comprehensive global map of the histone requirements for transcriptional reprogramming in yeast in response to stress."

Finally, a Canadian team describes previously undocumented non-coding RNAs identified using an annotation-independent method that relies on a reverse transcriptase enzyme that is known for tolerating a range of RNA structures. When the researchers used a "thermostable, group II intron reverse transcriptase" (TGIRT) sequencing approach to assess small RNAs treated with a structure-tolerant, highly processive reverse transcriptase enzyme, for example, they identified more than 100 new, non-coding small RNAs. "Together," they say, "the results indicate that the catalogue of human non-coding RNA is far from complete and underscore the power of de novo transcript detection in specialized sequencing techniques as a tool for gene definition."