Loop extrusion: theory meets single-molecule experiments |
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| Institution: | 1. Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA;2. The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA;3. Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA;4. Gene Regulation, Laboratory of Pathology, NCI, NIH, Bethesda, MD 20892, USA;5. Department of Computer Science, Stanford University, Stanford, CA 94305, USA;6. Laboratory of Genome Integrity, NCI, NIH, Bethesda, MD 20892, USA;7. The Jackson Laboratory for Genomic Medicine and Department of Genetic and Development Biology, University of Connecticut, Farmington, CT 06030, USA;8. Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD 20852, USA;9. Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA;10. Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA;11. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China;1. Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy;2. Berlin Institute of Health (BIH), MDC-Berlin, Germany;1. European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany;2. Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Germany;3. Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;1. Division of Cell Biology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands;2. Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands;3. Division of Biochemistry, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands;4. Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands;5. Cancer Genomics Center, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands |
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| Abstract: | Chromosomes are organized as chromatin loops that promote segregation, enhancer-promoter interactions, and other genomic functions. Loops were hypothesized to form by ‘loop extrusion,’ by which structural maintenance of chromosomes (SMC) complexes, such as condensin and cohesin, bind to chromatin, reel it in, and extrude it as a loop. However, such exotic motor activity had never been observed. Following an explosion of indirect evidence, recent single-molecule experiments directly imaged DNA loop extrusion by condensin and cohesin in vitro. These experiments observe rapid (kb/s) extrusion that requires ATP hydrolysis and stalls under pN forces. Surprisingly, condensin extrudes loops asymmetrically, challenging previous models. Extrusion by cohesin is symmetric but requires the protein Nipbl. We discuss how SMC complexes may perform their functions on chromatin in vivo. |
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| Keywords: | Chromosomes Chromatin Loop extrusion Cohesin Condensin SMC Polymers Simulations Molecular motors Nuclear organization Single-molecule experiments |
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