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Nucleic Acids Research Papers on ViMIC, FACT-seq, COVID19db

A Tongji University and Shanghai Eastern Hepatobiliary Surgery Hospital team touts a ViMIC database that houses insights into virus mutation (VM) sites, viral integration sites (VIS), and genes targeted by cis-regulatory effects for viruses linked to dozens of human conditions. In its current iteration, the pilot database contains more than 1.1 million sequences spanning eight viruses known for integrating into host genomes, the researchers note, as well as data on 105,624 viral integration sites, 31,712 viral mutations, more than 16,300 genes targeted by the viruses, and related regulatory data. "[V]iMIC is the first database to provide VMs and virus sequence data annotations retrieved from a large collection of public domains; and ViMIC is the first to visualize VMs harbored in VIS fragments and integrate VIS data with cistrome resources to help researchers who are interested in gene regulation mechanisms to systematically investigate the functional annotation of VISs in the host genome," they write.

Uppsala University researchers report on a relatively low-input sequencing strategy called the "FFPE tissue with antibody-guided chromatin tagmentation with sequencing" (FACT-seq) for profiling histones in formalin-fixed paraffin-embedded (FFPE) samples. The approach relies on in vitro transcription of a fusion protein containing a hyperactive transposase enzyme to boost the sensitivity of the method and make it amenable to assessing histone modifications in a few thousand cell nuclei, the team writes. When they used FACT-seq to profile histone H3K27ac modifications in nuclei from FFPE samples representing colorectal cancer or glioblastoma tissue samples, the authors tracked down super enhancer sites that appeared to be disease-specific. "In summary," the authors say, "FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease."

Finally, a team from the University of Hong Kong-Shenzhen Hospital and other centers in China describes a database for bringing together and analyzing available COVID-19 transcriptomic datasets from resources such as the NCBI Gene Expression Omnibus. The COVID19db currently contains transcriptome profiles for 4,127 human samples spanning more than a dozen parts of the body in relation to several microbial or drug exposures, the researchers note, along with extensive drug target-pathway interaction clues and related analytical tools. For example, the authors tapped into blood transcriptome profiles in the database to search for candidate treatments and potential COVID-19 treatment targets. "For proof of concept, we used COVID19db and identified multiple potential drugs and targets for COVID-19," they write, noting that the platform "provides user-friendly web interfaces to freely analyze, download data, and submit new data for further integration."