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Chromatin is a flexibly joined chain of nucleosomes that exists inside the nucleus of eukaryotic cells and has been described as a 'bead on a string'. Chromatin organization strengthens DNA for mechanically stressful processes like mitosis, helps protect DNA from damage and is important in the control of gene expression and DNA replication.
Goel et al. produce high-resolution three-dimensional genome structure mapping from mitosis to G1 phase to show unseen interactions between enhancers and promoters in prometaphase. Polymer modeling indicates the interactions are facilitated by chromosome compaction.
G2E3-catalysed H3K14 mono-ubiquitination is crucial for SUV39H compartmentalization and H3K9 trimethylation in pericentromeric heterochromatin, which is essential for proper euchromatin organization and transcriptional regulation in mammalian cells.
Embedding is a key step in single-cell Hi-C analysis to identify cell states. Here, the authors benchmark 13 embedding methods in 10 scHi-C datasets. They find that data representation, preprocessing options, and biological settings are often more important considerations than the actual methods.
There are many open questions around the mechanism of sex chromosome dosage compensation in birds. In this study, Papanicolaou et al. show that female avian cells upregulate their single Z chromosome via increased transcriptional burst frequency and enhanced translation, revealing parallels with mammalian dosage compensation.
Heart failure can be caused by cardiac fibroblasts replacing myocytes. Here, the authors use functional genomic data from fibroblasts, genetic signals enriched in people with heart disease, and gene perturbation analyses to link disease-associated regulatory elements to protein-coding genes.
Rhythms in chromatin state guide circadian gene expression. Here, the authors show that histone H3.3 coordinates BMAL1 activity along with cBAF/PBAF remodelers. Circadian disruption promotes remodeler reorganization and fragile H3.3 nucleosome accumulation, enhancing chromatin accessibility.
The effector fates of innate lymphoid cells (ILCs) are epigenetically imprinted early in ontogeny through the selective loss of DNA methylation at signature genes encoding fate-determining regulators — a process that is important for functional diversification of barrier immunity.
We developed an efficient transposon-based approach to create a panel of large genomic rearrangements between lamina associated domains (LADs) and inter-LAD sequences. This work demonstrates that LAD–nuclear lamina interactions involve multiple contacts of varying strength. Moreover, changes in nuclear lamina association are often accompanied by transcriptional repression and heterochromatin histone mark deposition.
The transcription factor GAGA factor (GAF) recruits chromatin remodelers to establish and maintain open chromatin for transcription in Drosophila melanogaster. In searching for DNA targets, GAF undergoes one-dimensional (1D) diffusion on linear DNA; however, 1D diffusion is constrained when DNA is wrapped around histones, necessitating 3D diffusion to locate cognate GAGAG sequences embedded within nucleosomes.
H3.14, a histone variant of unknown role, has a dual transcriptional function in the abiotic stress response in plants: activation of stress response genes and inhibition of growth genes.
Francesca Mattiroli leads a research group at the Hubrecht Institute in Utrecht in the Netherlands, delving into the dynamics of chromatin during DNA synthesis. Here we ask her about her research ethos, experience and interests.
