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Peer-reviewedCC BYPLOS One

Coupling between adhesome assembly and 3D chromatin organization

  • Louis Vincent Cammarata1,2
  • Duhita Sengupta3
  • Rajshikhar Gupta3,4
  • Caroline Uhler2,5,6
  • G V Shivashankar3,4
6 affiliations
  1. 1Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America.
  2. 2Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center, Cambridge, Massachusetts, United States of America.
  3. 3Paul Scherrer Institut, Villigen, Switzerland.
  4. 4Department of Health Science and Technology, ETH Zürich, Zürich, Switzerland.
  5. 5Massachusetts Institute of Technology, Laboratory for Information and Decision Systems, Cambridge, Massachusetts, United States of America.
  6. 6Massachusetts Institute of Technology, Institute for Data, Systems, and Society, Cambridge, Massachusetts, United States of America.
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Abstract

Proteins on the cell membrane cluster to respond to extracellular signals; for example, adhesion proteins cluster to enhance extracellular matrix sensing. The maturation of such receptor clusters may require additional adhesome proteins to adapt and reinforce extracellular signal sensing. However, it has been unclear whether the genes encoding these proteins share a spatial organization in the nucleus. Using the adhesome as an example, we show that subsets of genes that code for adhesome proteins exhibit relative spatial clustering and co-regulation in distinct locations within the nucleus. We use Hi-C maps and RNA-seq data from adherent cells to map the correspondence between adhesome gene localization and their expression. Interestingly, we find that the genes encoding several transcription factors, cofactors, and chromatin regulators that regulate these genes are also co-localized with the adhesome gene loci, thereby potentially suggesting a link between the extracellular matrix sensing machinery and gene expression. Additionally, we validate the spatial sub-clustering of adhesome gene loci using MERFISH data and DNA-FISH experiments. Collectively, our results support an association between adhesome gene organization and regulatory state, with a possible role in cellular signal sensing.

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Cite

BibTeXRIS
BibTeX
@article{cammarata2026coupling,
  title = {{Coupling between adhesome assembly and 3D chromatin organization}},
  author = {Louis Vincent Cammarata and Duhita Sengupta and Rajshikhar Gupta and Caroline Uhler and G V Shivashankar},
  journal = {PLOS One},
  year = {2026},
  month = oct,
  doi = {10.1371/journal.pone.0361202},
  url = {https://doi.org/10.1371/journal.pone.0361202},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Coupling between adhesome assembly and 3D chromatin organization
AU  - Louis Vincent Cammarata
AU  - Duhita Sengupta
AU  - Rajshikhar Gupta
AU  - Caroline Uhler
AU  - G V Shivashankar
PY  - 2026
DA  - 2026/10/29
JO  - PLOS One
DO  - 10.1371/journal.pone.0361202
UR  - https://doi.org/10.1371/journal.pone.0361202
AB  - Proteins on the cell membrane cluster to respond to extracellular signals; for example, adhesion proteins cluster to enhance extracellular matrix sensing. The maturation of such receptor clusters may require additional adhesome proteins to adapt and reinforce extracellular signal sensing. However, it has been unclear whether the genes encoding these proteins share a spatial organization in the nucleus. Using the adhesome as an example, we show that subsets of genes that code for adhesome proteins exhibit relative spatial clustering and co-regulation in distinct locations within the nucleus. We use Hi-C maps and RNA-seq data from adherent cells to map the correspondence between adhesome gene localization and their expression. Interestingly, we find that the genes encoding several transcription factors, cofactors, and chromatin regulators that regulate these genes are also co-localized with the adhesome gene loci, thereby potentially suggesting a link between the extracellular matrix sensing machinery and gene expression. Additionally, we validate the spatial sub-clustering of adhesome gene loci using MERFISH data and DNA-FISH experiments. Collectively, our results support an association between adhesome gene organization and regulatory state, with a possible role in cellular signal sensing.
SN  - 1932-6203
ER  -