Chromatin folding motifs define the basic grammar of TAD architecture in single alleles
Messina, O.; Fiche, J.-B.; Elkhoury Youhanna, C.; Ganesh, G.; Kemkem, Y.; Mesnager, A.; Akerman, I.; Hodson, D.; Schaeffer, M.; Nollmann, M.
Show abstract
Chromatin structure varies dramatically among single cells, yet the specific motifs underpinning this organization remain poorly understood. Using imaging-based spatial genomics, we visualized 3D chromatin organization across seven mouse tissues. We demonstrate that single chromatin traces can be decomposed into loop and domain Chromatin Folding Motifs (CFMs). Polymer simulations revealed that loop-extrusion reproduces loop CFMs, while cis-regulatory interactions are primarily responsible for domain CFMs. Notably, a unique set of CFMs describes single-cell chromatin architecture across multiple cell types, underscoring the universality of CFMs in organizing chromatin. In the pancreas, cells with different transcriptional programs exhibited distinct CFM usage, highlighting the functional relevance of CFMs. Perturbation of transcription and CTCF levels in a type 2 diabetes model altered CFM usage, demonstrating that disease induction affects both architectural and cis-regulatory interactions. Our results uncover how chromatin is organized in single cells and reveal the alterations that occur during disease.
Matching journals
The top 6 journals account for 50% of the predicted probability mass.
Similar papers in this journal
Similar papers in this journal
- Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not 97%
- Boosting the detection of enhancer-promoter loops via novel normalization methods for chromatin interaction data 96%
- Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions 96%
Similar papers in this journal
- A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model 96%
- Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator 95%
- High-resolution, genome-wide mapping of positive supercoiling in chromosomes 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.