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This Week in Genome Research: May 22, 2019

A team from Italy digs into a repetitive element deletion on chromosome 4 that's linked to a form of muscular dystrophy called facioscapulohumeral muscular dystrophy (FSHD). Past research suggests that the chromosome 4q35.2 repeat array deletion is associated with upregulation of specific genes via chromatin structure changes, the investigators note. For the new analysis, they combined a 4C sequencing assay focused on the D4Z4 repeat at 4q35.2 with chromatin immunoprecipitation sequencing and RNA-seq to tease apart chromatin interactions and their transcriptional consequences in muscle samples from two individuals with FSHD1 compared to muscle samples from two unaffected individuals. Results from such experiments suggest that the truncated chromosome 4 repeat has muted methylation, altered chromatin structure, and decreased interaction with the atrophic genes that are upregulated in FSHD.

Based on their large-scale analyses of draft bacterial or archaeal genomes, researchers at Johns Hopkins University suggest that thousands of purported microbial proteins may be the result of human contamination. As it reports in Genome Research, the team brought together nearly 2,300 draft microbial genomes from a publicly available database, identifying some 3,437 bacterial or archaeal proteins that appeared to be spurious, possibly stemming from human sources. "We found that nearly all contaminants occurred on small contigs in draft genome," the authors write, "which suggests that filtering out small contigs from draft genome assembles may mitigate the issue of contamination while still keeping nearly all of the genuine genomic sequences."

Finally, researchers from Baylor College of Medicine and Texas Children's Hospital present a bioinformatics approach for analyzing sequence data from pooled CRISPR target screening strategies. The web-based algorithm — known as the CRISPRBetaBinomial, or CB2 — relies on a so-called beta-binomial distribution, the team says, and includes computational steps to identify CRISPR targets, assess single-guide RNA (sgRNA) levels based on mapping, and dial down the parameters that need fine tuning. The authors applied the algorithm to 10 available biological datasets, comparing CB2 to eight other algorithms used for high-throughput CRISPR screening algorithms. There, they reportedly saw enhanced target identification and sgRNA quantification accuracy for CB2, along with lower-than-usual false-negative or -positive hits.