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The exact relationship between 3D chromatin interactions and enhancer function is unclear. By probing three-dimensional enhancer interactions in developing embryos, two studies now show nuanced dynamics in tissue-specific contexts and reveal how moderately increased enhancer–promoter interactions coincide with functionality.
In mice, zygotic genome activation occurs at onset of the two-cell stage in embryonic development and coincides with the exit from totipotency. Our work shows that the transcription factor DUXBL participates in silencing part of the stage-specific two-cell-associated transcriptional program and is required for development to proceed.
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.
We show that in addition to promoter activation, MYC drives cancer progression by activating transcriptional enhancers via a distinct mechanism. MYC cooperates with several other proteins at these cis-regulatory regions to change the epigenome and promote recruitment of RNA polymerase II and enhancer transcription.
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.
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.
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.
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.