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Nucleic Acids Research Papers on DAVID Update, ChIP-Atlas, RNA Splicing Assay

Researchers at the Frederick National Laboratory for Cancer Research and the National Institutes of Health describe a 2021 update to the bioinformatics tool DAVID, designed for functional annotation and functional gene enrichment analyses. Along with updates to annotation types and other "Knowledgebase" features, the latest version of the DAVID Gene system covers nearly 55,500 taxonomic groups, the team says, allowing more extensive gene-centered analyses. "[T]his update significantly expands the Knowledgebase and enhances the discovery power of DAVID while hopefully improving the user experience," the authors conclude. "The addition of small molecule-gene and drug-gene interactions to DAVID opens the door for additional discovery and the new update mechanisms developed allows DAVID to stay current and expand in the future."

A Kyoto University-led team shares an online resource called ChIP-Atlas that integrates chromatin immunoprecipitation sequencing data, along with DNase-seq-based chromatin accessibility features, whole-genome bisulfite sequencing on DNA methylation marks, and ATAC-seq data for assessing chromatin accessibility. The ChIP-Atlas currently spans half a dozen species, including humans and several model organisms, the researchers explain, noting that "ChIP-seq data can be visualized with the Peak Browser tool and a genome browser to explore the epigenomic landscape of a query genomic locus, such as its chromatin accessibility, DNA methylation status, and protein-genome interactions."

Yale University investigators outline an RNA splicing assay that relies on fluorescent DNA-based "molecular beacon" probes targeting sites formed after the ligation of spliced exons. After validating the approach, the team used the molecular beacon-based splicing assay to characterize RNA splicing kinetics and assess small molecule inhibition of splicing. "This study focuses on the design and application of molecular beacons that are sensitive to the second and final step of RNA splicing (exon ligation), although the assay can be easily adapted for use in other systems," the team writes, adding that "adaptability of the molecular beacon platform for monitoring various types of RNA splicing under high-throughput conditions will facilitate the screening of small molecules that target specific splicing reactions and isoforms.

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