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Even though the three-dimensional static organization of chromatin is highly studied, chromatin is a dynamic structure, and time-dependent changes are crucial for biological function. Although it is known that both intrachromatin interaction and loop extrusion are crucial to understanding chromatin organization, what their respective roles are in deciding the nature of spatial and temporal organization is not clear. Simulating a model with active loop extrusion and intrachromatin interactions, we show that under certain conditions, the measurable dynamic quantities are dominated by the loop extrusion, even though the population-averaged contact map (structure) can be dominated by intrachromatin interactions, with loop extrusion playing no major role. Our results show that the dynamic scaling exponents with loop extrusion are consistent with the experimental observations and can be very different from those predicted by existing fractal globule models for chromatin. We argue that one needs to measure both the structure and dynamics simultaneously to unambiguously interpret the organization of chromatin.
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http://dx.doi.org/10.1016/j.bpj.2025.08.018 | DOI Listing |
J Chem Phys
September 2025
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
We study how protein condensates respond to a site of active RNA transcription (i.e., a gene promoter) due to electrostatic protein-RNA interactions.
View Article and Find Full Text PDFStructure
September 2025
Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, SAS Nagar (Mohali), Punjab, India. Electronic address:
The structural maintenance of chromosomes (SMC)-family Wadjet complex restricts plasmid transformation in bacteria through a distinctive mechanism coupling DNA loop extrusion and cleavage. In this issue of Structure, Roisné-Hamelin et al. report the biochemical reconstitution and structure of a type II Wadjet complex, revealing a shared overall mechanism and notable architectural differences compared to related type I complexes.
View Article and Find Full Text PDFFEBS Lett
August 2025
Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
Multidrug and toxin extrusion (MATE) transporters are widely conserved across all domains of life and play diverse roles in plant development. Here, we investigated the role of DETOXIFICATION 51 (DTX51), a MATE transporter in Arabidopsis. Overexpression of DTX51 led to pleiotropic phenotypes resembling those of hls1 hlh1 and amp1 lamp1 loss-of-function mutants, which have disruptions of key developmental regulators that act non-cell-autonomously.
View Article and Find Full Text PDFBiophys J
August 2025
Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India; Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Mumbai, India; Koita Centre for Digital Health, Indian Institute of Technology Bombay, Mumbai, Indi
Even though the three-dimensional static organization of chromatin is highly studied, chromatin is a dynamic structure, and time-dependent changes are crucial for biological function. Although it is known that both intrachromatin interaction and loop extrusion are crucial to understanding chromatin organization, what their respective roles are in deciding the nature of spatial and temporal organization is not clear. Simulating a model with active loop extrusion and intrachromatin interactions, we show that under certain conditions, the measurable dynamic quantities are dominated by the loop extrusion, even though the population-averaged contact map (structure) can be dominated by intrachromatin interactions, with loop extrusion playing no major role.
View Article and Find Full Text PDFResearch (Wash D C)
August 2025
Department of Gynecologic Oncology, Women's Hospital, School of Medicine and MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
Mitotic chromosome formation depends on coordinated SMC complex activities, yet how condensin engages cohesin during this process remains unclear. Samejima et al. combined synchronized mitotic entry, auxin-inducible degrons, high-resolution Hi-C, live-cell imaging, quantitative proteomics, and polymer simulations to dissect condensin I, condensin II, and cohesin interplay in vertebrate cells.
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