Tag

3d Genome

All articles tagged with #3d genome

biology4 days ago•75 min saved

Pre-ZGA 3D genome architecture emerges modularly in Drosophila embryos

Using Pico-C, a low-input Micro-C method, the study maps high-resolution 3D genome architecture across NC9–NC14 in early Drosophila embryos and reveals that chromatin loops and boundaries emerge in an ordered, modular fashion before major ZGA. Transcriptional elongation inhibition preserves some early loops but weakens promoter insulation, while sequence-based models show orthogonal motif-driven contributions to architecture. Co-depleting Zelda and GAF confirms locus-specific regulatory inputs, supporting a layered regulatory logic for genome establishment prior to ZGA.

via Nature|

#3d-genome #biology #chromatin-architecture

science25 days ago•83 min saved

Transient HDAC inhibition imprints lasting gene and genome architecture memory in stem cells

A four-hour pulse of the HDAC inhibitor TSA in mouse embryonic stem cells transiently boosts H3K27ac and shifts transcription from pluripotency toward development; genome folding also rewires with more interchromosomal contacts and weaker A-compartment interactions. Most changes reverse after washout, but a subset of genes remains misregulated and the 3D genome stays perturbed, constituting a memory that is strengthened by a second TSA pulse and linked to Polycomb-mediated looping. Disrupting canonical PRC1 (PCGF2/PCGF4) reduces this memory, indicating Polycomb topology contributes to transcriptional memory.

via Nature|

#3d-genome #embryonic-stem-cells #epigenetics

science-and-technology2 years ago•6 min saved

Revolutionary Technique Provides Unprecedented View of Gene Regulation in 3D Genome.

MIT researchers have developed a new technique called Region Capture Micro-C (RCMC) that can map the interactions between regulatory elements and genes in the 3D genome with 100 times higher resolution than previously possible. The researchers found that many genes interact with dozens of different regulatory elements, and that DNA appears to coil itself into nested “microcompartments” that facilitate these interactions. The new method is able to inexpensively generate maps 100 times richer in information than other published techniques for a fraction of the cost.

via MIT News|

#3d-genome #enhancers #gene-regulation