Genomics & Functional Genomics
Drug-induced chromatin accessibility changes associate with sensitivity to liver tumor promotionThis work explores quantitative chromatin accessibility, transcriptional and cis-acting gene regulatory variations underlying mouse strain–specific differences in drug-induced liver tumor promotion sensitivity.
Sufficiency analysis of estrogen responsive enhancers using synthetic activatorsEnhancers bound by synthetic activators can recreate a transcriptional response to estrogen, drive different levels of gene expression, and work independently to regulate transcription.
Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptomeA genome-wide comparative analysis of “cryptic” aslncRNAs decay in RNAi-capable and RNAi-deficient budding yeasts suggests an evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeSBRAPeS is a software for B-cell receptor reconstruction in single cells from very short (25–30 bp) read lengths, which achieves similar success rates and accuracy as applying other methods on long reads.
Targeted variant detection using unaligned RNA-Seq readsThis study introduces km, an approach leveraging k-mer decomposition to identify targeted mutations. It can detect single-base mutations, insertions and deletions, as well as fusions. An analysis of over 10,000 RNA-seq samples shows fast mutation detection via km.
Kinesin-8B controls basal body function and flagellum formation and is key to malaria transmissionThis comprehensive study describes the key role and real-time dynamics of Plasmodium kinesin-8B in microtubule-based basal body and axoneme assembly during flagellum (male gamete) formation and parasite transmission.
TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assayThe authors present a novel method for obtaining chromatin profiles from low cell numbers without prior nuclei isolation. The method is successfully implemented in generating epigenetic profile from 100 cells with high signal-to-noise ratio.
CRISPR-induced double-strand breaks trigger recombination between homologous chromosome armsCRISPR–Cas9 enables recombination between homologous chromosome arms at predefined sites and also underscores the need for caution when applying CRISPR technologies in translational medicine.
Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer’s diseaseThis study describes a gauge for brain aging predictive of cognitive decline and Alzheimer's disease synergistic with the APOE ε4 allele.
A network of human functional gene interactions from knockout fitness screens in cancer cellsThe function of human genes can be strongly inferred from their knockout fitness profiles across hundreds of CRISPR screens, illuminating the modular organization of the cell.