Genomics & Functional Genomics
The transcriptional landscape analysis of basal cell carcinomas reveals novel signalling pathways and actionable targetsBasal cell carcinoma (BCC) is the most common skin cancer and human malignancy. By analyzing BCC RNA sequencing data according to clinically important features, we identified novel differentially regulated genes and new targetable pathways. Several biomarkers were validated in patient-derived BCC samples.
Fast but not furious: a streamlined selection method for genome-edited cellsMagnetic-activated genome-edited cell sorting (MAGECS) allows a fast and easy generation of genetically modified cells.
Single-cell RNA sequencing of mouse islets exposed to proinflammatory cytokinesSingle-cell RNA-seq was used to show that islet endocrine cells respond to acute cytokine exposure with an increase in the expression of protective genes and the absence of apoptotic gene expression.
In utero exposure to chlordecone affects histone modifications and activates LINE-1 in cord bloodIn utero exposure to chlordecone affects chromatin and leads to activation of retroelements. This study shows the changes induced by chlordecone in human umbilical cord blood and blood-derived cell line.
CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq dataA systematic comparison of batch effect metrics for single cell data is performed. The new cell-specific mixing score from the R/Bioconductor CellMixS package performs well across various tasks.
Phylo-geo-network and haplogroup analysis of 611 novel coronavirus (SARS-CoV-2) genomes from IndiaEvolution of SARS-CoV-2 in India across 51 haplogroups based on 152 parsimony informative sites revealed B6 and B1 (Pangolin) and A2a (Covidex) as the most prevalent lineage and clade, respectively.
A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWASThis paper describes the economical optimization of DNA extraction, short and long read sequencing, and bioinformatic assembly, which in turn improves mapping and variant resolution of short-read sequenced, same-breed dogs for association studies. This methodology is applicable for any investigators planning a genome-wide association study.
The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cellsUsing ChIP-seq and functional genomic analyses, the study shows that the Paf1 complex occupies transcriptional enhancers and positively regulates their activity.
The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cellsThe RNA-binding protein SRSF6 recognizes a purine-rich consensus motif consisting of GAA triplets, and its downregulation in human pancreatic β-cells affects alternative splicing in a position-dependent manner.
Polycomb mutant partially suppresses DNA hypomethylation–associated phenotypes in ArabidopsisA mutation in Arabidopsis polycomb repressive complex 2 partially suppresses the transposon activity observed in a DNA methylation mutant, challenging expectations.