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Genome Biology Papers on Bladder Cancer, PCIP-seq, Structured RNAs in Human Microbiomes

Investigators at Penn State School of Medicine, Northwestern University, and elsewhere explore epigenomic features and three-dimensional genomic interactions in samples from luminal and basal molecular subtypes of muscle-invasive bladder cancer with distinct expression profiles. Using a combination of RNA-sequencing, histone 3 lysine 27 acetylation-focused chromatin immunoprecipitation sequencing, Hi-C chromatin confirmation capture, and ATAC-seq, the team characterized chromatin regulation and interaction patterns in two luminal and two basal bladder cancer cell lines, along with four primary tumor samples from bladder cancer patients. "We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal enhancers of luminal and basal bladder cancers," the authors report, noting that the analysis highlighted a circadian transcription factor called NPAS2 that appears to boost proliferation and cell migration in the luminal bladder cancer subtype.

A Belgian-led team describes a long-read sequencing strategy for interrogating integrated viral genomes and corresponding insertion sites in host genomes — a method that was applied to HIV-1, bovine leukemia virus, human T cell leukemia virus-1, and human papillomaviruses in proof-of-principle experiments. The "pooled CRISPR inverse PCR sequencing," or PCIP-seq, approach relies on multiplexed Oxford Nanopore long-read sequencing to assess stretches of proviral DNA from cleaved circularized DNA that have been subjected to inverse long-range PCR, the researchers say. "Up to now, linking the sequence of the viral genome to a specific integration site and measuring the abundance of the corresponding clone has been difficult," they write, adding that PCIP-seq "can identify integration sites while [sequencing] part and, in many cases, all of the provirus."

Finally, a pair of researchers at Stanford University search for structured RNAs in human microbial communities characterized through phase 2 of the Human Microbiome Project. With the help of informatics and comparative genomics, the duo focused in on almost 3,200 conserved structured RNA candidates in parts of the genome stretching between genes, as well as more than 2,000 candidate structured RNAs in protein-coding regions. A subset of 177 structured RNAs subsequently turned up in gut microbiome bugs in four human fecal samples assessed by small RNA-sequencing, the authors report. "Structured RNAs play varied bioregulatory roles within microbes," they write, concluding that "we hope that this resource of thousands of structured RNAs enables future functional characterization and mechanistic dissection of a wide range of new structured RNAs from previously unexplored microbial genomic regions."