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De novo genome assemblies of 22 Brassica oleracea accessions and pan-genome analyses highlight the effects of structural variation on gene expression and its contribution to morphotype diversification.
Gestational diabetes is a complex metabolic condition thought to have a strong genetic predisposition. A large genome-wide association study of participants from Finland sheds light on the genetic contributors, opening avenues for research into mechanisms that underlie glucose regulation in pregnancy to improve the health of mothers and babies.
A common architectural feature of the genome in many organisms is chromatin domains. A synthetic biology approach now builds chromatin domains from scratch and identifies some of the minimal components needed for their formation.
Spatial omics enables the molecular profiling of cells with the tissue context preserved. A new analytic approach shows how cellular neighborhood analysis and feature augmentation can spatially connect and cluster millions of cells into higher-order functional units.
Mutational signatures help to deconvolve the different processes that shape cancer genomes. A new tool now alleviates some of the persistent challenges in the field.
Genome-wide CRISPR screening coupled with ATAC-see uncovered modulators that influence global chromatin accessibility. Notably, TFDP1 emerged as a pivotal modulator of chromatin accessibility that acts by controlling histone transcription. Depletion of TFDP1 induced a global elevation in accessibility, enhancing the efficiency of genome editing and iPS cell reprogramming.
We constructed a pan-genome using 27 high-quality representative Brassica oleracea genomes. Using this pan-genome, together with multi-omics datasets from large-scale populations, we uncovered the important role of structural variations as dosage regulators of gene expression, which drives the morphotype diversification in B. oleracea.
An approach combining infection of primary human epithelial cells with a barcoded lentiviral-based library followed by engraftment into mice yields biologically relevant models of bladder and prostate cancer harboring complex genetic perturbations.
Genome-wide association analyses identify 13 loci associated with gestational diabetes, showing partial overlap with type 2 diabetes risk loci but also distinct genetic architecture predominantly influencing pregnancy-related mechanisms.
Fluorescence-activated nuclear sorting combined with deep profiling shows that Huntington’s disease repeat expansions arise in specific cell types and are associated with elevated MSH2 and MSH3, which promote expansions in vitro by inhibiting excision of CAG slip-outs by FAN1.
Digenic inheritance of deleterious variants in serine/arginine protein kinase 3 (SRPK3) and titin (TTN) leads to a progressive early onset skeletal muscle myopathy. Zebrafish double mutants exhibit a similar myopathy phenotype accompanied by myofibrillar disorganization.
Epigenetic profiles can be predictive of macrophage transcriptional responses to influenza A virus infection in individuals of European and African ancestry. Ancestry-linked epigenetic differences appear to be genetically controlled.
Lentiviral massively parallel reporter assay (lentiMPRA) analysis of cardiac cis-regulatory elements characterizes the effects of noncoding de novo variants identified in congenital heart disease. EpiCard is a model for variant prioritization.
BANKSY is an algorithm with R and Python implementations that identifies both cell types and tissue domains from spatially resolved omics data by incorporating spatial kernels capturing microenvironmental information. It is applicable to a range of technologies and is scalable to millions of cells.
Multi-omic analysis of 100 clear cell renal cell carcinomas identifies four transcriptomic subgroups (IM1–IM4). IM4 is a high-risk subtype characterized by specific metabolic changes and a loss of lipid droplets.
Analysis of colorectal cancer bulk gene expression data at the pathway level identifies a poor-prognosis subtype associated with cell differentiation. The subtypes are reproducible in single-cell data and offer biological insights beyond existing stratification strategies.
A genome-wide CRISPR knockout screen in eHAP cells using ATAC-see to fluorescently label chromatin identifies novel regulators of accessibility, such as the transcription factor TFDP1 via regulation of canonical histone expression.
Bottom-up in vitro reconstitution of ~10-kb chromatin domains shows that nucleosome positioning, rather than loop extrusion or transcription, determines domain formation in yeast.
In vivo tracing of the single-cell 3D structure at the Hoxa cluster shows that Polycomb-associated domains in individual cells are flexible and often decompact while maintaining a repressive transcriptional state.
Near-gapless and haplotype-resolved genome assemblies of the dwarfing ‘M9’ and semi-vigorous ‘MM106’ rootstocks and a major apple cultivar ‘Fuji’ provide insights into the genetic basis of rootstock-induced dwarfing traits.
De novo genome assemblies of 22 Brassica oleracea accessions and pan-genome analyses highlight the effects of structural variations on gene expression and their contributions to morphotype diversification.
Resequencing of 390 peanut accessions provides insights into peanut migration and diversity in China. Genome-wide association analysis identifies loci associated with 28 agronomic traits.
MuSiCal is a mutational signature analysis tool combining minimum-volume nonnegative matrix factorization with other algorithmic innovations. Applied to PCAWG data, MuSiCal gives more accurate results, including resolving ambiguous flat signatures.