ArticleScience advances2025
Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.
Article in Science advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Single-molecule chromatin tracing reveals a diversity of megabase heterochromatin domains.Nature structural & molecular biology · 2026Article
- Mechanical regulation of cell memory.Nature structural & molecular biology · 2026Review
- Chromatin Packing Domain Engineering Through the Manipulation of Nuclear Cationic States.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The roles of chromatin remodeling and 3D genome organization in cancers: from mechanistic insights to emerging treatment options.Molecular cancer · 2026Review
- Effect of cellular nutrient economy on the evolution of genome size in phytoplankton.Science advances · 2026Article
- One chromatin, many structures: From ensemble contact maps to single-cell 3D organization.Biophysical journal · 2026Article
- Nucleotide resolution 4-thiouridine sequencing by SNU-Seq and sf4sU-Seq reveals the transcriptional responsiveness of an epigenetically primed human genome.Nucleic acids research · 2026Article
- Transcription and cohesin direct domain boundary spatial positioning and are linked to Friedreich's ataxia.Molecular cell · 2026Article
- Physics-based nucleosome-resolution modeling of epigenetic-driven chromatin domain dynamics.Nucleic acids research · 2026Article
- Gravity as a Boundary Condition for the Evolution of Three-Dimensional Multicellularity.Life (Basel, Switzerland) · 2026Article
- Architecture and regulation of nanoscale chromatin domains.Nature communications · 2026Review
- One Chromatin, Many Structures: From Ensemble Contact Maps to Single-Cell 3D Organization.bioRxiv : the preprint server for biology · 2026Article
- Chromatin architecture and physical constriction cooperate in phenotype switching and cancer cell dissemination.bioRxiv : the preprint server for biology · 2026Article
- Fluorescence Properties and MgChemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- DNA topological regulation in RNA polymerase II transcription.Cellular & molecular biology letters · 2026Review
- ERG phase separation attenuates cellular senescence.iScience · 2026Article
- Selective binding of divalent cations reshapes nucleosome mechanics and unlocks histone tail dynamics.Communications biology · 2026Article
- The emerging paradigms of SETD family enzymes as epigenetic regulators of the immune response in inflammatory diseases.Frontiers in immunology · 2026Review
- Leveraging chromatin packing domains to target chemoevasion in vivo.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multiplexed Chromatin Analysis Using Optical Spectroscopic Statistical Nanosensing.ACS photonics · 2025Article
Corrections and comments
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Authors and funding
24 authors.
Funding
Abstract
In single cells, variably sized nanoscale chromatin structures are observed, but it is unknown whether these form a cohesive framework that regulates RNA transcription. Here, we demonstrate that the human genome is an emergent, self-assembling, reinforcement learning system. Conformationally defined heterogeneous, nanoscopic packing domains form by the interplay of transcription, nucleosome remodeling, and loop extrusion. We show that packing domains are not topologically associated domains. Instead, packing domains exist across a structure-function life cycle that couples heterochromatin and transcription in situ, explaining how heterochromatin enzyme inhibition can produce a paradoxical decrease in transcription by destabilizing domain cores. Applied to development and aging, we show the pairing of heterochromatin and transcription at myogenic genes that could be disrupted by nuclear swelling. In sum, packing domains represent a foundation to explore the interactions of chromatin and transcription at the single-cell level in human health.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.