Research Briefing

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  • In the zebrafish heart, several transient fibroblast types appear after injury. High-throughput lineage tracing revealed that injury-responsive fibroblasts are derived from two distinct lineage origins: the epicardium and the endocardium. Targeted cell-type-specific depletion showed that at least one fibroblast type has a critical role in heart regeneration.

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  • Assemblies of hexaploid cultivated oat, and of close relatives of its diploid and tetraploid progenitors, have revealed its polyploid formation and subgenome evolution. These high-quality oat reference genomes will facilitate the discovery of candidate genes that underlie beneficial traits such as hulless grain and disease resistance.

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  • Genetic and phenotypic analyses of data from over 400,000 participants in the UK Biobank identified 10 new loci associated with the development of clonal hematopoiesis and implicated DNA damage, oncogene signaling, telomere maintenance and blood cell homing in its pathogenesis. These findings can help to decipher the pathogenesis of clonal hematopoiesis and develop therapeutic approaches.

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  • Systematic CRISPR screens in primary human T cells uncovered the upstream regulators of crucial immune genes — IL2RA, IL2 and CTLA4. Then, using RNA-seq and ATAC-seq in knockout T cells, we mapped the downstream target genes and non-coding cis-regulatory elements of key regulators, thereby revealing a regulatory network enriched for immune disease-associated genes.

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  • By integrating single-cell and bulk transcriptomic analyses, we found that malignant cells belong to two major intrinsic epithelial subtypes. We propose a refined, three-tiered classification of colorectal cancer subtypes based on intrinsic epithelial subtypes, microsatellite instability status and the presence of fibrosis.

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  • The largest GWAS for kidney function so far provided the starting point for integrated multi-stage annotation of genetic loci. Whole kidney and single-cell epigenomic information is crucial for translating GWAS information to the identification of causal genes and pathogenetic (and potentially targetable) cellular and molecular mechanisms of kidney disease.

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  • A study using single-cell transcriptomics and mapping of expression quantitative trait loci (eQTLs) in a dynamic model of CD4+ T cell activation reveals novel, context-specific eQTLs linked to genes associated with immune diseases such as inflammatory bowel disease.

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  • A large-scale single-nucleus chromatin accessibility profiling study in coronary artery samples from patients with coronary artery disease generated a landscape of the regulatory activity during the disease. These data highlight cell type-specific gene programs that can improve the interpretation of human genome-wide association studies findings for cardiovascular diseases.

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  • 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.

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