In a paper published online in advance in Genome Research this week, investigators at The Wistar Institute report their generation of a "genome-wide inventory of non-coding and protein-coding transcripts, their promoters, and histone modification states for developing and adult cerebella using integrative, massive[ly] parallel sequencing and [a] bioinformatics approach," with which they elucidated "alternative promoters and transcriptional terminations as major sources of transcriptome diversity." Rather than H3K27me3, the team found that H3K4me3 "defined the use of alternative promoters," though it "observed strong bias of both … for CpG-rich promoters." Overall, the team reports that "the majority of genes associated with neurological diseases expressed multiple transcripts through alternative promoters" in the study.
In another Genome Research paper recently published online in advance, a public-private collaborative team of researchers at the University of Utah and Omicia Inc. present their Variant Annotation, Analysis and Search Tool — or VAAST, a probabilistic tool "for identifying damaged genes and their disease-causing variants in personal genome sequences." VAAST prioritizes variants within a "single unified likelihood framework that allows users to identify damaged genes and deleterious variants with greater accuracy" and ease-of-use, the authors write. As it can score both coding and non-coding variants, the team adds that VAAST can not only "identify rare variants causing rare genetic diseases," but can also "use both rare and common variants to identify genes responsible for common diseases."
The University of Washington's Evan Eichler and his colleagues report more than 7,665 structural changes within the gorilla lineage, which they discovered when comparing human and great ape genomes. Eichler et al. show that "the gorilla genome has been subjected to the highest rate of segmental duplication," and overall, that the "chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes."
Researchers at the University of California, San Francisco, and Wesleyan University in Connecticut show in a recent Genome Research advance online publication that, in mouse, "genomic neighborhood, rather than promoter sequence, correlates with the probability of different OR [olfactory receptor] genes to be expressed in the same olfactory cell." More specifically, in mapping and analyzing the transcription start sites of 1,085 of the 1,400 total murine OR genes, the team identified "potential transcription factor binding sites shared by the majority of these promoters," revealing "an intriguing correlation between promoter AT content and evolutionary plasticity."