Nanometer condensate organization in live cells derived from partitioning measurements

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 27, 2025

Biomolecules associate, forming condensates that house essential biochemical processes, including ribosome biogenesis. Unraveling how shape macromolecular assembly and transport requires cellular measurements of nanoscale structure. Here, we determine the organization around between specific proteins at nanometer resolution within condensates, deploying thermodynamic principles to interpret partitioning designed protein probes. When applied nucleolus as a proof principle, data reveals considerable inhomogeneity, deviating from expected liquid-like phase. The inhomogeneity can be attributed biogenesis, with local meshwork weakening biogenesis progresses, facilitating transport. Beyond introducing an innovative modality for biophysical interrogation, our results suggest are far uniform, simple liquids, property conjecture enables regulation proofreading.

Language: Английский

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Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 22, 2025

We present a genome-scale method to map the single-molecule co-occupancy of structurally distinct nucleosomes, subnucleosomes, and other protein-DNA interactions via long-read high-resolution adenine methyltransferase footprinting. I teratively D efined L engths Inaccessibility (IDLI) classifies nucleosomes on basis shared patterns intranucleosomal accessibility, into: i.) minimally-accessible chromatosomes; ii.) octasomes with stereotyped DNA accessibility from superhelical locations (SHLs) ±1 through ±7; iii.) highly-accessible unwrapped nucleosomes; iv.) subnucleosomal species, such as hexasomes, tetrasomes, short protections. Applying IDLI mouse embryonic stem cell (mESC) chromatin, we discover widespread nucleosomal distortion individual mammalian chromatin fibers, >85% surveyed displaying degrees intranucleosomally accessible DNA. observe epigenomic-domain-specific distorted nucleosome positioning, including at enhancers, promoters, satellite repeat sequences. Nucleosome is programmed by presence bound transcription factors (TFs) cognate motifs; occupied TF binding sites are differentially decorated compared unbound sites, degradation experiments establish direct roles for TFs in structuring binding-site proximal nucleosomes. Finally, apply context primary hepatocytes, observing evidence pervasive vivo. Further genetic reveal role hepatocyte master regulator FOXA2 directly impacting hepatocyte-specific regulatory elements vivo . Our work suggests extreme-but regulated-plasticity level. Further, our study offers an essential new framework model factor binding, remodeling, cell-type specific gene regulation across biological contexts.

Language: Английский

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A chromatin mesh model for compaction of chromatin by PRC1 in condensates

Nature Structural & Molecular Biology, Journal Year: 2025, Volume and Issue: unknown

Published: March 3, 2025

Language: Английский

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