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Single-nucleus ATAC-seq characterization of chromatin accessibility in human coronary artery disease samples identifies cell-type- and state-specific regulatory mechanisms underlying disease risk, highlighting the roles of TBX2 and PRDM16.
The genome of the SunUp transgenic papaya cultivar includes a complex 1.64-Mb insertion that contains 3 transgenic fragments integrated with 61 nuclear genome fragments from the progenitor Sunset cultivar and 13 organelle genome fragments. Population genomic analyses yielded 147 selective sweeps during papaya domestication, which include essential genes that are involved in fruit flesh color formation and sugar content.
Orca is a sequence-based deep-learning algorithm that predicts 3D genome architecture from kilobase to whole-chromosome scale, including the impact of structural variants. In silico modeling identifies a putative sequence basis for chromatin compartment formation.
Genome-wide epigenomic profiling of liver tissue from one surface and two independent cave populations of Astyanax mexicanus sheds light on regulatory changes underlying metabolic adaptations to the nutrient-deprived cave environment.
Genome assemblies for the SunUp transgenic papaya and its progenitor Sunset identify three transgene-insertions in SunUp. Resequencing of 86 papaya genomes highlights the impacts of breeding and geographic origin.
A deep-learning model called DeepSTARR quantitatively predicts enhancer activity on the basis of DNA sequence. The model learns relevant motifs and syntax rules, allowing for the design of synthetic enhancers with specific strengths.
Genome-wide association and fine-mapping analyses in ancestrally diverse populations implicate candidate causal genes and mechanisms underlying type 2 diabetes. Trans-ancestry genetic risk scores enhance transferability across populations.
A new study demonstrates that the disordered N-terminal domain of DNMT3A1 binds PRC1-catalyzed H2AK119ub, targeting DNA methylation to bivalent promoters in mouse brain cortical cells. Methylation around bivalent genes is critical for mouse postnatal development, and could be equally important in other cell types and in disease.
To leverage the genetic diversity in Nigeria, we established the Non-Communicable Diseases Genetic Heritage Study (NCD-GHS) consortium to help produce a comprehensive catalog of human genetic variation in Nigeria and assess the burden and etiological characteristics of non-communicable diseases in 100,000 adults in Nigeria.
The long isoform of DNMT3A is essential for mouse postnatal development and regulates bivalent genes in the brain, likely via a PRC1-mediated mechanism.
Within-sibship genome-wide association analyses using data from 178,076 siblings illustrate differences between population-based and within-sibship GWAS estimates for phenotypes influenced by demographic and indirect genetic effects.
The Cardiometabolic Disorders in African-Ancestry Populations (CARDINAL) study site is a well-powered, first-of-its-kind resource for developing, refining and validating methods for research into polygenic risk scores that accounts for local ancestry, to improve risk prediction in diverse populations.
Integrating methods that assess allele-specific regulatory activity and chromatin accessibility in T cells identifies putative causal variants for five autoimmune diseases.
Genomic and transcriptomic analyses of chronic lymphoproliferative disorder of natural killer cells identifies somatic gain-of-function mutations in the chemokine gene CCL22 with cell-extrinsic effects. Mutations caused biased signaling downstream of the G-protein-coupled receptor for CCL22 and deregulated interactions with the hematopoietic microenvironment.
PRS-CSx is a polygenic risk score construction method that improves cross-population polygenic prediction by integrating GWAS summary statistics from multiple populations.
Joint analysis of 11 major psychiatric disorders identifies four broad factor underlying genetic correlations among the disorders. Association analyses detect 152 loci acting on these factors and identify 9 loci that act heterogeneously across disorders.
Systematic phenotyping of 58,101 mutants of the model eukaryotic alga Chlamydomonas reinhardtii under 121 environmental and chemical stress conditions provides a large resource for characterizing gene function.
Analyses of cis-genetic regulation of the plasma proteome in European and African American populations lead to the identification of shared and unique cis-protein quantitative trait loci and models for proteome-wide association studies of complex traits.
