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Mapping long-range chromatin interactions in 27 human cell/tissue types identifies candidate target genes of 70,329 putative regulatory elements. Further analysis suggests potential regulatory function for 27,325 noncoding variants associated with 2,117 traits and diseases.
A new method for inferring genealogical histories from large-scale genetic data is used to characterize population structure using data from the 1000 Genomes Project, the UK Biobank and the Simons Genome Diversity Project.
An approach to estimate the contribution of all alleles to phenotypic variation is applied to transcription regulation using whole-genome sequencing and transcriptome data. Ultrarare variants contribute approximately 46% of cis heritability across genes.
A new technique called NET-CAGE identifies 5′ ends of nascent RNAs with high sensitivity, including enhancer-derived RNAs. This approach shows that enhancer–promoter pairs are generally activated simultaneously.
Relate is a new method for evolutionary analysis of large genetic datasets that can estimate branch lengths, mutational ages and variable historical population sizes.
The first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model, provides insights into legume genome evolution and the molecular basis of agricultural traits for pea improvement.
The authors generate cell lines deficient for 22 BAF subunits, studying effects on complex composition, chromatin accessibility and gene expression. They identify synthetic lethal interactions between SMARCA4–ARID2, SMARCA4–ACTB and SMARCC1–SMARCC2.
Systematic analyses of large-scale genome-wide association data provide an overview of pleiotropy and genetic architecture for hundreds of human complex traits and diseases.
Genetic deletion or transcriptional silencing of HERV-H elements in human pluripotent stem cells (hPSCs) eliminates nearby topologically associating domain boundaries, while de novo insertion of HERV-H elements can introduce new ones. Mutations of specific HERV-H elements can impact hPSC differentiation.
Single-cell DNA replication profiling shows that A/B compartments change coordinately with replication timing (RT) during mouse embryonic stem cell differentiation, with B to A changes preceding late to early RT changes and transcriptional activation.
Genomic analysis of 906 Clostridium difficile strains shows that this enteropathogen is undergoing speciation, which is linked to the selection of genes involved in sporulation and in the metabolism of simple dietary sugars.
A mutation in RAS oncogene family-like 3 (RABL3) is discovered in a family with multiple cases of pancreatic cancer. Zebrafish modeling and biochemical approaches suggest that truncated RABL3 elevates KRAS activity via accelerated prenylation.
Inactivation of DNA cross-link repair in mouse primordial germ cells makes them vulnerable to endogenously produced genotoxic aldehydes and leads to genetic instability.
An integrative three-dimensional genomic and transcriptional profiling of four human neural cell types links regulatory elements to their target genes and elucidates the function of noncoding variants in neuropsychiatric disorders.
The authors use theoretical justifications coupled with extensive simulations to accurately estimate SNP-heritability for 22 complex traits and diseases from the UK Biobank data, irrespective of the underlying genetic architecture of the trait.
Exome sequencing identifies loss-of-function CELA2A mutations in families with early-onset atherosclerosis and metabolic syndrome. Functional studies show that CELA2A is a circulating enzyme that reduces platelet activation, triggers insulin secretion and degradation, and increases insulin sensitivity.
Removal of boundary and intra-TAD CTCF-binding sites at the Sox9–Kcnj2 locus in mice leads to TAD fusion but no major changes in gene expression. Gene misexpression and disease phenotypes were obtained through inversions and/or repositioning of TAD boundaries.
Whole-genome sequencing identifies noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and oculopharyngeal myopathy with leukoencephalopathy, three disorders with overlapping clinical features and neuroimaging findings.
Long-read sequencing identifies a GGC repeat expansion in NOTCH2NLC that is associated with neuronal intranuclear inclusion disease, a progressive neurodegenerative disorder. The expansion results in abnormal anti-sense transcripts that could contribute to disease pathogenesis.