Chromatin architecture mapping by multiplex proximity tagging Journal Article

  


Authors: Delamarre, A.; Bailey, B.; Yavid, J.; Koche, R.; Mohibullah, N.; Whitehouse, I.
Article Title: Chromatin architecture mapping by multiplex proximity tagging
Abstract: Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a proximity-tagging method to map molecules that associate in 3D space. Using this method—PCP (proximity copy paste)—we mapped the positioning and connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is predominantly organized into regularly spaced nucleosome arrays that can be positioned or delocalized. PCP can also map long-range, multi-way interactions, and we provide direct evidence supporting a model that metaphase chromosomes are compacted by cohesin loop clustering. Analyzing single-molecule nuclease footprinting data, we define distinct chromatin states within a mixed population to show that non-canonical overlapping di-nucleosomes are a stable feature of chromatin. PCP is a versatile method, allowing the detection of the connectivity of individual molecules locally and over large distances to be mapped at high resolution in a single experiment. © 2025 Elsevier Inc.
Keywords: promoter region; nonhuman; protein localization; cohesin; chromosome; chromosome structure; in vivo study; protein interaction; double stranded dna; saccharomyces cerevisiae; epigenetics; chromatin; nuclease; rna polymerase ii; metaphase; ribosome protein; chromatin structure; dna fragment; nucleic acid; nucleosome; molecule; caspase activated deoxyribonuclease; single-molecule; metaphase chromosome; nucleosome arrays; pcp; chromatin remodeling; rna directed dna polymerase; dna sequencing; article; oldn; overlapping di-nucleosome
Journal Title: Molecular Cell
Volume: 85
Issue: 14
ISSN: 1097-2765
Publisher: Cell Press  
Date Published: 2025-07-17
Start Page: 2796
End Page: 2811.e5
Language: English
DOI: 10.1016/j.molcel.2025.06.018
PROVIDER: scopus
PUBMED: 40680724
DOI/URL:

https://www.scopus.com/inward/record.uri?eid=2-s2.0-105010322532&doi=10.1016%2fj.molcel.2025.06.018&partnerID=40&md5=872bd0ddd07ce384f9d0d37fd85503dd
Notes: Source: Scopus
Altmetric
What is Altmetric?
Citation Impact
What is Dimensions Citation Badge?
BMJ Impact Analytics
MSK Authors
  1. Iestyn Whitehouse
    17 Whitehouse
  2. Neeman Mohibullah
    17 Mohibullah
  3. Richard Patrick Koche
    180 Koche
  4. Axel Delamarre
    1 Delamarre
  5. Benton Montgomery Bailey
    1 Bailey
  6. Jennifer A. Yavid
    1 Yavid
Related MSK Work