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Genetic and functional studies implicate allele-specific regulation of OAS1 splicing and nonsense-mediated decay in COVID-19 severity. The OAS1 risk haplotype is also associated with reduced SARS-CoV-2 clearance in a clinical trial with pegIFN-λ1.
YAP upregulates TET1, which physically interacts with TEAD1/4 to demethylate DNA at YAP target genes in the liver. Loss of TET1 reverses YAP-induced chromatin and transcriptional changes and suppresses YAP-induced hepatomegaly and tumorigenesis.
Analysis of whole-exome sequencing data from 200,453 UK Biobank participants identifies loci associated with clonal hematopoiesis and highlights causal links between clonal hematopoiesis and other traits.
A modified fluctuation test applied to colorectal cancer cells shows that EGFR/BRAF inhibitor-induced persisters slowly proliferate and have an increased mutation rate. Error-prone DNA polymerases are identified as potential targets to avoid tumor recurrence following treatment with these drugs.
Genetically dissecting the Epha4–Pax3 topological boundary in mice shows that divergent CTCF binding sites (CBSs) are not essential for insulation and that chromatin loops in nonconvergently oriented CBSs can be driven by a loop interference mechanism.
An analysis of POLE and POLD1 mutations distinguishes driver mutations from passengers and explores their functionality. Driver mutations are associated with specific mutational signatures and correlate with immune checkpoint blockage response.
Pooled loss-of-function CRISPR screens in primary human T cells identify upstream regulators of IL2RA, IL-2 and CTLA4. Individual knockouts of 24 regulators of IL2RA define a central network enriched for genes associated with immune-mediated diseases.
DeepLoop is a modular Hi-C processing workflow that enables kilobase-resolution analysis of sparse data. Reanalysis of published data demonstrates that DeepLoop can identify allele-specific chromatin loops and large heterozygous structural variants.
Sei is a new framework for integrating human genetics data with a sequence-based mapping of predicted regulatory activities to elucidate mechanisms contributing to complex traits and diseases.
The DANIO-CODE consortium leverages a large-scale multiomic dataset to improve zebrafish genome annotation. They identify ~140,000 cis-regulatory elements throughout development and perform a comparison with the mouse regulatory landscape.
A single-cell transcriptomic analysis of 63 patients with colorectal cancer classifies tumor cells into two epithelial subtypes. An improved tumor classification based on epithelial subtype, microsatellite stability and fibrosis reveals differences in pathway activation and metastasis.
Single-cell ATAC-seq and RNA-seq profiling traces the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC). A large proportion of polyp and CRC cells show a stem-like phenotype.
Genome-wide analyses identify hundreds of loci associated with kidney function. Integrated analyses of expression, methylation and single-cell open chromatin and expression data derived from human kidney samples prioritize genes and mechanisms underlying renal disease.
Allelic imbalance analysis applied to ATAC-Seq data from 23 cancer types identifies 7,262 allele-specific accessibility quantitative trait loci, which are enriched for cancer risk heritability and altered transcription factor binding motifs.
Genome-wide analyses of cardiovascular magnetic resonance images identify variants associated with right ventricular structure and function. Polygenic scores for these traits are associated with dilated cardiomyopathy and coronary artery disease.
Genome-wide analyses of cardiac magnetic resonance imaging data identify loci associated with right heart structure and function. A polygenic predictor of right ventricular ejection fraction is associated with dilated cardiomyopathy risk.
A genomic analysis of ductal carcinoma in situ (DCIS) samples with matched ipsilateral invasive breast cancer recurring later shows that around 18% of tumors were unrelated to the DCIS, and had distinct clonal origins.
snipar is a software package for imputing missing parental genotypes and estimating direct genetic effects. Application to UK Biobank data shows that effects estimated by standard genome-wide association study designs have confounding bias for some phenotypes.
SMARCE1 loss destabilizes the canonical BAF complex and increases the formation of BRD9-containing non-canonical (ncBAF) complexes. SMARCE1-deficient cells, which are a model for clear cell meningioma, are sensitive to ncBAF complex inhibition.