Imaging dynamic and selective low-complexity domain interactions that control gene transcription
Shasha Chong,Claire Dugast-Darzacq,Zhe Liu,Peng Dong,Gina M. Dailey,Claudia Cattoglio,Alec Heckert,Sambashiva Banala,Luke D. Lavis,Xavier Darzacq,Robert Tjian +10 more
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TLDR
Live-cell single-molecule imaging revealed that TF LCDs interact to form local high-concentration hubs at both synthetic DNA arrays and endogenous genomic loci, suggesting that under physiological conditions, rapid, reversible, and selective multivalent LCD-LCD interactions occur between TFs and the RNA Pol II machinery to activate transcription.Abstract:
Many eukaryotic transcription factors (TFs) contain intrinsically disordered low-complexity sequence domains (LCDs), but how these LCDs drive transactivation remains unclear. We used live-cell single-molecule imaging to reveal that TF LCDs form local high-concentration interaction hubs at synthetic and endogenous genomic loci. TF LCD hubs stabilize DNA binding, recruit RNA polymerase II (RNA Pol II), and activate transcription. LCD-LCD interactions within hubs are highly dynamic, display selectivity with binding partners, and are differentially sensitive to disruption by hexanediols. Under physiological conditions, rapid and reversible LCD-LCD interactions occur between TFs and the RNA Pol II machinery without detectable phase separation. Our findings reveal fundamental mechanisms underpinning transcriptional control and suggest a framework for developing single-molecule imaging screens for drugs targeting gene regulatory interactions implicated in disease.read more
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Long-range enhancer-promoter contacts in gene expression control.
TL;DR: The latest understanding of long-range enhancer–promoter crosstalk is discussed, including target-gene specificity, interaction dynamics, protein and RNA architects of interactions, roles of 3D genome organization and the pathological consequences of regulatory rewiring.
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Organization of Chromatin by Intrinsic and Regulated Phase Separation
Bryan A. Gibson,Lynda K. Doolittle,Maximillian W.G. Schneider,Liv E. Jensen,Nathan Gamarra,Lisa Henry,Daniel W. Gerlich,Sy Redding,Michael K. Rosen +8 more
TL;DR: It is demonstrated that reconstituted chromatin undergoes histone tail-driven liquid-liquid phase separation (LLPS) in physiologic salt and when microinjected into cell nuclei, producing dense and dynamic droplets.
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Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome.
Yongdae Shin,Yongdae Shin,Yi-Che Chang,Daniel S.W. Lee,Joel Berry,David W. Sanders,Pierre Ronceray,Ned S. Wingreen,Mikko Haataja,Clifford P. Brangwynne,Clifford P. Brangwynne +10 more
TL;DR: CasDrop is used, a novel CRISPR-Cas9-based optogenetic technology, to show that various IDPs phase separate into liquid condensates that mechanically exclude chromatin as they grow and preferentially form in low-density, largely euchromatic regions.
Journal ArticleDOI
The molecular language of membraneless organelles
Edward Gomes,James Shorter +1 more
TL;DR: An overview of the molecular underpinnings of the formation and regulation of these membraneless organelles are provided and new light on neurodegenerative diseases is shone on.
Journal ArticleDOI
RNA polymerase II clustering through carboxy-terminal domain phase separation
Marc Boehning,Claire Dugast-Darzacq,Marija Rankovic,Anders S. Hansen,Taekyung Yu,Hervé Marie-Nelly,David T. McSwiggen,Goran Kokic,Gina M. Dailey,Patrick Cramer,Xavier Darzacq,Markus Zweckstetter,Markus Zweckstetter +12 more
TL;DR: It is reported that human and yeast CTDs undergo cooperative liquid phase separation, with the shorter yeast CTD forming less-stable droplets and that CTD phosphorylation liberates Pol II enzymes from hubs for promoter escape and transcription elongation.
References
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Journal ArticleDOI
NIH Image to ImageJ: 25 years of image analysis
TL;DR: The origins, challenges and solutions of NIH Image and ImageJ software are discussed, and how their history can serve to advise and inform other software projects.
Journal ArticleDOI
Genome engineering using the CRISPR-Cas9 system
F. Ann Ran,Patrick D. Hsu,Jason Wright,Vineeta Agarwala,Vineeta Agarwala,David A. Scott,Feng Zhang +6 more
TL;DR: A set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies are described.
Journal ArticleDOI
A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation
Avinash Patel,Hyun O. Lee,Louise Jawerth,Shovamayee Maharana,Marcus Jahnel,Marco Y. Hein,Stoyno S. Stoynov,Julia Mahamid,Shambaditya Saha,Titus M. Franzmann,Andrej Pozniakovski,Ina Poser,Nicola Maghelli,Loic Royer,Martin Weigert,Eugene W. Myers,Stephan W. Grill,David N. Drechsel,Anthony A. Hyman,Simon Alberti +19 more
TL;DR: It is proposed that liquid-like compartments carry the trade-off between functionality and risk of aggregation and that aberrant phase transitions within liquid- like compartments lie at the heart of ALS and, presumably, other age-related diseases.
Journal ArticleDOI
Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization
Amandine Molliex,Jamshid Temirov,Jihun Lee,Maura Coughlin,Anderson P. Kanagaraj,Hong Joo Kim,Tanja Mittag,J. Paul Taylor +7 more
TL;DR: It is demonstrated that the disease-related RBP hnRNPA1 undergoes liquid-liquid phase separation (LLPS) into protein-rich droplets mediated by a low complexity sequence domain (LCD), and suggested that LCD-mediated LLPS contributes to the assembly of stress granules and their liquid properties.
Journal ArticleDOI
Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels
Masato Kato,Tina W. Han,Shanhai Xie,Kevin Y. Shi,Xinlin Du,Leeju C. Wu,Hamid Mirzaei,Elizabeth J. Goldsmith,Jamie Longgood,Jimin Pei,Jimin Pei,Nick V. Grishin,Douglas E. Frantz,Jay W. Schneider,She Chen,Lin Li,Michael R. Sawaya,David Eisenberg,Robert Tycko,Steven L. McKnight +19 more
TL;DR: It is discovered that exposure of cell or tissue lysates to a biotinylated isoxazole (b-isox) chemical precipitated hundreds of RNA-binding proteins with significant overlap to the constituents of RNA granules, offering a framework for understanding the function of LC sequences as well as an organizing principle for cellular structures that are not membrane bound.
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