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Single-cell transcriptomics and expression quantitative trait locus mapping in 114 lung tissue samples, including 66 with interstitial lung disease, highlight the cell-type-specific functions of risk variants contributing to disease pathobiology.
Single-cell RNA sequencing analysis of over 800,000 human adult breast cells from 55 female donors identifies 41 cell subtypes and highlights age- and parity-dependent effects. Samples from healthy women with germline mutations in BRCA1 or BRCA2 showed signs of T cell exhaustion.
Single-cell ATAC + RNA linking (SCARlink) predicts gene expression by jointly modeling local tiled chromatin accessibility using regularized Poisson regression on multi-ome data. SCARlink predictions can be used to identify cell-type-specific enhancers and perform chromatin potential analysis.
Single-nucleus RNA sequencing from the dorsolateral prefrontal cortex of 424 aging individuals, and mapping the effect of genetic variation on gene expression, identified a large number of cis-expression quantitative trait loci at the level of cell types and cell subtypes.
A catalog of enhancer–promoter (E–P) interactions across ten mouse embryonic tissues, supported by in vivo functional experiments, shows that E–P proximity increases upon enhancer activation during development.
The transcription factor double homeobox protein (DUX) induces a totipotency-specific regulatory program, including the upregulation of DUXBL. DUXBL subsequently accesses DUX-bound regions and interacts with TRIM24 and TRIM33, thus contributing to totipotency exit.
Chromosome-level genome assemblies of 11 bamboo species comprising lineages from diploid (herbaceous) to tetraploid and hexaploid (woody) provide insights into dynamic subgenome dominance in bamboos.
Analysis of enhancer–promoter (E–P) interactions during Drosophila embryogenesis suggests that the relationship between E–P proximity and activity depends on the developmental stage. Increased E–P proximity is associated with activity during differentiation but not specification.
This paper highlights the mechanisms underlying MYC-dependent gene regulation from transcriptional enhancers, which are distinct to the function of MYC at promoters. This process takes place in a cancer type-specific way, and the resulting transcriptional programs can predict prognosis.
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.
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.
This study examines karyotypic selection and evolution in vitro using immortalized mammary and kidney epithelial cell lines, observing aneuploidy patterns specific to each origin tissue that are correlated with frequencies in patient tumors and independent of drivers such as TP53 mutation.
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.
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.
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.
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.
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.
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.
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.