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Targeted inactivation, restoration and overexpression of MALAT1 in multiple in vivo models demonstrate that the lncRNA MALAT1 suppresses breast cancer metastasis through binding and inactivation of the pro-metastatic transcription factor TEAD.
Combining 32 genome-wide association studies with high-density imputation provides a comprehensive view of the genetic contribution to type 2 diabetes in individuals of European ancestry with respect to locus discovery, causal-variant resolution, and mechanistic insight.
Sequencing of haploid sugarcane, Saccharum spontaneum, allows assembly of a prototypical version of the sugarcane chromosome set. This new reference genome will serve as a resource to accelerate sugarcane improvement.
Analysis of genetic data and blood lipid measurements from over 300,000 participants in the Million Veteran Program identifies new associations for blood lipid traits.
Sequence assemblies for the genomes of 16 widely used inbred laboratory mouse strains highlight considerable strain-specific haplotype variation and allow for the identification of regions with the greatest sequence diversity between strains.
A Pitx1 enhancer shows activity in forelimbs and hindlimbs but only interacts with Pitx1 in hindlimbs because of its three-dimensional configuration. Structural variants that affect three-dimensional conformation induce Pitx1 expression in forelimbs and cause partial arm-to-leg transformation in mice and humans.
Analysis of genomic and transcriptomic data from 462 patient-derived tumor cell (PDC) samples across 14 cancer types, along with pharmacological responses to 60 agents, indicates that PDC-derived drug sensitivities might be predictive of clinical response to targeted therapies.
The stay-green G gene, which controls seed dormancy, shows evidence of selection in soybean, rice and tomato. G interacts with NCED3 and PSY and modulates abscisic acid synthesis.
Genome-wide and metagenome-wide association study of 92 cardiovascular-diseases-related proteins identifies genetic and microbial factors that explain 76.6% of inter-individual variation, highlighting the role of gut microbiome in cardiovascular disease.
Analyses of 3,514 whole-genome-sequenced individuals from Sardinia indicate that within-island substructure and sex-biased processes have impacted the genetic history of Sardinia, providing new insight into the demography of ancestral Sardinians.
Analysis of bivalent promoters in embryonic stem cells (ESCs) shows that deletion of MLL2 in ESCs leads to increased Polycomb occupancy, reduced promoter accessibility, redistribution of long-range chromatin interactions, and failure to differentiate.
Association analyses in over 1 million individuals identify 535 new loci influencing blood pressure traits. The results provide new insights into blood pressure regulation and highlight shared genetic architecture between blood pressure and lifestyle exposures.
SEEKR is a method that deconstructs linear sequence relationships between lncRNAs and evaluates similarity on the basis of abundance of short motifs called k-mers. LncRNAs of related function often have similar k-mer profiles despite lacking linear homology.
De novo mutations in MSL3 cause an X-linked syndrome affecting both males and females. MSL3 mutations reduce H4K16ac levels and lead to misregulation of cellular pathways involved in morphogenesis, cellular shape, and cell migration.
The authors present an integrative framework for identifying structural variants (SVs) in cancer that applies optical mapping, Hi-C, and whole-genome sequencing. They find SVs affecting distal regulatory sequences, DNA replication, and three-dimensional chromatin structure.
Analysis of sequencing data from 249 cancer patients with clinically annotated outcomes to immune checkpoint therapy identifies correlates of treatment response. The results highlight complexity in identifying events that generate an immunoresponsive tumor environment.
The authors identify copy number signatures from shallow whole-genome sequencing of high-grade serous ovarian cancer (HGSOC) cases. HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in genomic aberration.
Analysis of summary statistics from 32 GWAS datasets using a new likelihood-based approach evaluates polygenicity across different traits. Effect-size distributions predict the sample sizes needed to explain the SNP-based heritability of traits.
Relatedness disequilibrium regression is a new method for estimating heritability that removes environmental bias by taking advantage of variation in relatedness due to random Mendelian segregation.
ASMC is a new method to estimate coalescence times using SNP array or sequencing data. When applied to data from the UK Biobank or Genome of the Netherlands, ASMC detects signals of recent positive selection and background selection.