Genomics & Functional Genomics
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.
Single-cell RNA sequencing of human breast tumour-infiltrating immune cells reveals a γδ T-cell subtype associated with good clinical outcomeSingle-cell sequencing of γδ-T cells from human blood and tumours revealed novel markers of subtypes with distinct effector functions and a subtype that is associated with favourable clinical outcome.
Characterization of ori and parS-like functions in secondary genome replicons in Deinococcus radioduransAn array of direct repeats upstream to parAB operon helps in secondary genome elements’ maintenance independent of primary chromosome in multipartite genome harboring bacterium Deinococcus radiodurans.
Incipient sympatric speciation in wild barley caused by geological-edaphic divergenceSympatric speciation is still contentious but here based on genome-wide analysis; we show incipient sympatric speciation of an emerging new wild barley species from Hordeum spontaneum, the progenitor of all cultivated barleys at “Evolution Plateau” (EP), Upper Galilee, Israel.
Predicting gene regulatory networks from cell atlasesIntegrated single-cell gene regulatory network from three mouse cell atlases captures global and cell type–specific regulatory modules and crosstalk, important for cellular identity.
multicrispr: gRNA design for prime editing and parallel targeting of thousands of targetsA bioinformatics R package for a fast and generic guideRNA design, optimized for large-scale perturbation assays.
Peptide-based quorum sensing systems in Paenibacillus polymyxaDiscovery of conserved communication systems in the agriculturally important Paenibacillus bacteria. These systems are widespread, and some species encode more than 25 different peptide-receptor pairs.