Genomics & Functional Genomics
The Th1 cell regulatory circuitry is largely conserved between human and mouseComparison of the binding sites of the Th1 lineage-specifying transcription factor T-bet between human and mouse reveals differences in binding sites but that the most of the target genes are shared.
Statistical guidelines for quality control of next-generation sequencing techniquesCondition-specific statistical guidelines and accurate classification trees for quality control of functional genomics NGS files (RNA-seq, ChIP-seq and DNase-seq) have been generated using thousands of reference files from the ENCODE project and made available to the community.
Paralogous synthetic lethality underlies genetic dependencies of the cancer-mutated gene STAG2The context-dependency of genetic interactions of the cohesin gene STAG2, specifically STAG1 and the iron regulatory gene IREB2, are revealed by CRISPR-Cas9 screening in three different cellular backgrounds.
RNA sequencing reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubesRNA sequencing reveals primary myocyte-specific gene-regulatory niche effects for β-hydroxybutyrate but do not support a general signaling of β-hydroxybutyrate role in other primary cells or during cellular differentiation in vitro.
Sequencing of a central nervous system tumor demonstrates cancer transmission in an organ transplantThis study uses DNA sequencing to trace a donor organ transplant–mediated cancer transmission and illustrates how precise molecular pathology profiles might reduce future risk for transplant recipients.
Functional annotation of noncoding mutations in cancerRecurrent regulatory mutations affecting transcription factor binding sites in 2,500 cancer samples.
UVB mutagenesis differs in Nras- and Braf-mutant mouse models of melanomaA single, neonatal UVB exposure drives greater UV-signature production in Braf- than Nras-mutant murine melanomas.
Deletion of a pseudogene within a fragile site triggers the oncogenic expression of the mitotic CCSER1 geneFrequent deletions impacting the FRA4F fragile site leads to the oncogenic overexpression of the corresponding CCSER1 gene, through the deletion of the TMSB4XP8 pseudogene. The ensuing CCSER1 overexpression elicits mitotic instability, targetable with aurora kinase inhibitors.
Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detectionATAC-seq reveals unique neutrophil chromatin architecture changes in response to different stimuli before transcriptional activation, possibly regulating downstream gene expression.
HCV poly U/UC sequence–induced inflammation leads to metabolic disorders in vulvar lichen sclerosisMulti-omics analysis reveals the elevation of HCV poly U/UC sequences, which induces abnormal inflammation and related metabolic disorder in vulvar lichen sclerosis.