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This Week in Genome Biology: Aug 9, 2017

Researchers from Weill Cornell Medical College and elsewhere present findings from a prostate cancer analysis performed with a computational tool called RegNetDriver, designed to uncover cancer driver mutations based on integrated genomic and epigenomic data. For its proof-of-principle analyses, the team used RegNetDriver to analyze structural variant, transcription factor, variant, promoter, enhancer, and other data gleaned from 521 prostate cancer tumors. The search led to known prostate cancer drivers, along with a handful of candidate driver genes coding for transcription factors. 

A team from China, France, and the UK describes gut microbial features that seem to coincide with the presence of an autoinflammatory disease called ankylosing spondylitis. Using shotgun metagenomic sequencing, the researchers examined microbial genes and representatives present in stool samples from 211 Chinese individuals, including 97 with ankylosing spondylitis and 114 without. In the process, they identified a dozen microbial species and tens of thousands of genes with altered representation in the guts of affected individuals — from declining Bacteroides species to rising levels of some bacteria in the Prevotella and Bifidobacterium genera.

Finally, a Swiss-lead team takes a look at structure-function interactions between development genes in the HoxD cluster, nearby topically associating domains, and related regulatory elements in centromeric sequences and beyond. With the help of RNA sequencing, combination of chromosome conformation (4C) sequencing, fluorescence in situ hybridization, and other approaches, the researchers assessed tissue samples from wild-type and HoxD-mutant mice, along with mice carrying deletions and inversions that altered native chromatin topology in this model of development. "We report multi-partite associations between HoxD gene and up to three enhancers," the authors say, noting that "loss of native chromatin topology leads to the remodeling of [topologically associating domain] structure following distinct parameters."