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This Week in Genome Research: Jan 3, 2018

A team from the University of British Columbia and the University of California, Santa Cruz, presents information on genome sequences generated for the model organism Caenorhabditis elegans using the MinION nanopore long read sequencer. With MinION sequencing and de novo assembly, the researchers tackled the genomes of wild type and rearrangement-containing C. elegans strains. In the wild-type strain, they report, the resulting assembly spanned more than 99 percent of the existing reference genome, while stretching it out by more than two million bases and highlighting sequences for co-occurring bacteria. Along with analyses of complex rearrangements revealed in the MinION-sequenced mutant C. elegans genome, the authors improved the accuracy of the wild type assembly by incorporating Illumina short reads.

Researchers from the University of Texas Southwestern Medical Center, Baylor College of Medicine, and elsewhere explore enhancer patterns and related expression activity in breast cancer cell lines, using a combination of RNA sequencing, global run-on sequencing, and chromatin immunoprecipitation sequencing. With the help of a computational pipeline that brings together enhancer transcription magnitude, transcription factor expression, and telltale binding and chromatin motifs, the team profiled more than a dozen breast cancer cell lines from five molecular subtypes, uncovering enhancers and related transcription factors active within specific breast cancer subtypes.

A Swiss team takes a look at transcription factor dynamics and transcriptional regulation in various mouse tissue types over time to untangle circadian clock features. In mice with or without circadian clock disruptions, the researchers analyzed new and available RNA sequence patterns in up to 11 tissue types tested every few hours for multiple time points. Together with transcription factor binding site information, chromosome conformation capture sequencing, and/or DNase-seq experiments to explore chromatin accessibility, the transcriptomic data provided clues to the regulatory features such as chromatin folding that mediate tissue-specific circadian rhythms.