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Nucleic Acids Research Papers on VirusViz, Methylation Sub-Population Analysis, BRCA2 Survival Screen

Investigators in Italy outline a method for visualizing, comparing, and analyzing variants in SARS-CoV-2 and other viral species at the nucleotide and amino acid level. The platform, known as VirusViz, includes a bioinformatics pipeline for analyzing viral data from the ViruSurf database or other sources, the team says, and provides variant visualization, metadata, and more on the viral populations and sub-populations considered. "The VirusViz system is a new powerful tool for supporting comparative virtual analysis of variants, both of nucleotides and of amino acids, accepting input from both public sequences and user-provided sequences, integrated with a curated knowledge base of variants of interest," the authors write, calling it "the only tool currently supporting user-defined grouping of sequences for the comparative inspection of variant distributions across groups."

A Washington University School of Medicine-led team describes a computational approach for looking at methylation patterns within cellular sub-populations or cancer clones. The researchers note that their "deconvolution of sub-populations existing in methylation data," or DXM, method is designed for detecting allelic sub-populations with distinct methylation marks based on bisulfite sequencing data. After comparing the tool with other methylation analysis methods, they applied DXM to data from dozens of diffuse large B-cell lymphoma samples, uncovering relapse-related allelic sub-populations with distinct methylation features. "We expect that DXM will have high applicability and utility for the analysis of sub-population methylation in any heterogeneous sample and in the future similar approach could be adapted to the analysis of cell-free DNA," the authors write.

Finally, investigators at the University of Texas MD Anderson Cancer Center and University of Texas Health Science Center at Houston present a role for cyclin C (CCNC) and other components of the RNA Polymerase II transcription mediator complex in survival in cells with lower-than-usual levels of BRCA2, providing clues to potential mechanisms of PARP inhibitor (PARPi) resistance. Using a whole-genome CRISPR screening strategy, the team searched for pathways that are required in the absence of BRCA2, uncovering reliance on CCNC in cells with inducible BRCA2 depletion — results that were subsequently assessed using RNA sequencing and other experiments. "Taken together, our data reveal CCNC as a critical genetic determinant upon BRCA2 loss of function, which may help the development of novel therapeutic strategies that overcome PARPi resistance," the authors write.

The Scan

Panel Votes for COVID-19 Pill

A US Food and Drug Administration panel has voted to support the emergency use authorization of an antiviral pill for COVID-19 from Merck and Ridgeback Biotherapeutics, CNN says.

But Not Harm

New Scientist reports that UK bioethicists say that though gene editing may improve food production, it should not harm livestock welfare.

Effectiveness Drop Anticipated

Moderna's Stéphane Bancel predicts that that current SARS-CoV-2 vaccines may be less effective against the Omicron variant, the Financial Times reports.

Cell Studies of Human Chromatin Accessibility, SARS-CoV-2 Variants, Cell Signaling Networks

In Cell this week: chromatin accessibility maps of adult human tissues, modeling to track SARS-CoV-2 variants of concern, and more.