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Chromosome conformation capture (3C)-based methods reveal chromosome organization within the nucleus by determining the physical proximity of pairs of points along chromatin. They preserve chromatin interactions by cross-linking followed by fragmentation, ligation and sequencing of interacting regions. Genome organization affects processes such as transcription, repair and DNA replication.
Here the authors develop a single-cell multiomics sequencing method (scCARE-seq), which allows the simultaneous probing of 3D chromatin architecture and transcription for single cells. Using scCARE-seq they explore the relationship between the 3D genome and transcriptome in cell fate transitions and the cell cycle.
Chromosome-wide late replication is an enigmatic hallmark of the inactive X. Here, the authors combined scRepli-seq and 4C-seq to reveal its layered 3D architecture, which could explain local differences in heterochromatin stability.
Here, the authors map chromatin conformation at high resolution after rapid Mediator depletion to show that its loss reduces the frequency of enhancer-promoter interactions and associated gene expression, with a corresponding redistribution of Cohesin.
Existing deep learning-based approaches for the prediction of gene expression by histone modifications (HMs) can only focus on narrow and linear genomic regions around promoters. Here, the authors address these problems by developing a transformer-based deep learning architecture named Chromoformer.
In Drosophila, there are extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 250 kilobases.
Soochit et al. report that the residence time of CTCF on chromatin is controlled by its zinc finger 8 domain and determines chromatin organization, DNA methylation and transcriptional robustness in mouse embryonic stem cells.
A new study in Cell describes how topologically associating domains (TADs) of chromosomes can restructure to resolve the regulatory conflict that arises when a new gene incorporates into an ancestral TAD.
In a paper in Nature, Hua et al. report the Micro-Capture-C method for near-base-pair resolution characterization of chromosomal interactions in mammalian cells.
Two studies in Molecular Cell report fine-scale structural profiles of mammalian genomes using Micro-C, indicating that fine chromosomal structure is regulated by diverse transcription-related features.
A study in Nature Genetics shows that genomic rearrangements that cause extensive changes to chromatin topology do not alter expression for the majority of genes.