Chinese Journal of Nature ›› 2023, Vol. 45 ›› Issue (1): 33-44.doi: 10.3969/j.issn.0253-9608.2022.05.010
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HAO Li, JIANG Ting, FAN Jun
Received:
2022-07-13
Online:
2023-02-25
Published:
2023-02-21
HAO Li, JIANG Ting, FAN Jun. Advances in single-molecule investigation of dynamic DNA transcription regulation by RNA polymerase[J]. Chinese Journal of Nature, 2023, 45(1): 33-44.
[1] SHANDILYA J, ROBERTS S G. The transcription cycle in eukaryotes: from productive initiation to RNA polymerase II recycling [J]. Biochimica et Biophysica Acta, 2012, 1819(5): 391-400. [2] CRAMER P. Organization and regulation of gene transcription [J]. Nature, 2019, 573(7772): 45-54. [3] CHEN J, BOYACI H, CAMPBELL E A. Diverse and unified mechanisms of transcription initiation in bacteria [J]. Nature Reviews Microbiology, 2021, 19(2): 95-109. [4] BROWNING D F, BUSBY S J. Local and global regulation of transcription initiation in bacteria [J]. Nature Reviews Microbiology, 2016, 14(10): 638-650. [5] ROEDER R G. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms [J]. Nature Structural & Molecular Biology, 2019, 26(9): 783-791. [6] WERNER F, GROHMANN D. Evolution of multisubunit RNA polymerases in the three domains of life [J]. Nature Reviews Microbiology, 2011, 9(2): 85-98. [7] LIU X, BUSHNELL D A, KORNBERG R D. RNA polymerase II transcription: structure and mechanism [J]. Biochimica et Biophysica Acta, 2013, 1829(1): 2-8. [8] LOUDER R K, HE Y, LOPEZ-BLANCE J R, et al. Structure of promoter-bound TFIID and model of human pre-initiation complex assembly [J]. Nature, 2016, 531(7596): 604-609. [9] JOHNSON D S, MORTAZAVI A, MYERS R M, et al. Genomewide mapping of in vivo protein-DNA interactions [J]. Science, 2007, 316(5830): 1497-1502. [10] RHEE H S, PUGH B F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution [J]. Cell, 2011, 147(6): 1408-1419. [11] ZHANG Z, TJIAN R. Measuring dynamics of eukaryotic transcription initiation: challenges, insights and opportunities [J]. Transcription, 2018, 9(3): 159-165. [12] HOBOTH P, SEBESTA O, HOZAK P. How single-molecule localization microscopy expanded our mechanistic understanding of RNA polymerase II transcription [J]. International Journal of Molecular Sciences, 2021, 22(13): 6694. [13] LI G W, XIE X S. Central dogma at the single-molecule level in living cells [J]. Nature, 2011, 475(7356): 308-315. [14] LIU Z, LAVIS L D, BETZIG E. Imaging live-cell dynamics and structure at the single-molecule level [J]. Molecular Cell, 2015, 58(4): 644-659. [15] WANG Z H, DENG W L. Dynamic transcription regulation at the single-molecule level [J]. Developmental Biology, 2022, 482: 67-81. [16] KREUTZBERGER A J B, JI M, AARON J, et al. Rhomboid distorts lipids to break the viscosity-imposed speed limit of membrane diffusion [J]. Science, 2019, 363(6426): eaao0076. [17] WANG X H, LI X J, DENG X, et al. Single-molecule fluorescence imaging to quantify membrane protein dynamics and oligomerization in living plant cells [J]. Nature Protocols, 2015, 10(12): 2054-2063. [18] CUI Y, YU M, YAO X, et al. Single-particle tracking for the quantification of membrane protein dynamics in living plant cells [J]. Molecular Plant, 2018, 11(11): 1315-1327. [19] TOKUNAGA M, IMAMOTO N, SAKATA-SOGAWA K. Highly inclined thin illumination enables clear single-molecule imaging in cells [J]. Nature Methods, 2008, 5(2): 159-161. [20] GEBHARDT J C, SUTER D M, ROY R, et al. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells [J]. Nature Methods, 2013, 10(5): 421-426. [21] CHEN B C, LEGANT W R, WANG K, et al. Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution [J]. Science, 2014, 346(6208): 1257998. [22] SHIMOMURA O, JOHNSON F H, SAIGA Y. Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea [J]. Journal of Cellular and Comparative Physiology, 1962, 59: 223-239. [23] 邢晶晶, 林金星. 活细胞单分子荧光标记——点亮生命微观世界的繁星[J]. 生命世界, 2015(12): 48-53. [24] WANG S, MOFFITT J R, DEMPSEY G T, et al. Characterization and development of photoactivatable fluorescent proteins for singlemolecule-based superresolution imaging [J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(23): 8452-8457. [25] XIA T, LI N, FANG X. Single-molecule fluorescence imaging in living cells [J]. Annual Review of Physical Chemistry, 2013, 64: 459-480. [26] FERNANDEZ-SUAREZ M, TING A Y. Fluorescent probes for super-resolution imaging in living cells [J]. Nature Reviews Molecular Cell Biology, 2008, 9(12): 929-943. [27] BETZIG E, PATTERSON G H, SOUGRAT R, et al. Imaging intracellular fluorescent proteins at nanometer resolution [J]. Science, 2006, 313(5793): 1642-1645. [28] LIPPINCOTT-SCHWARTZ J, PATTERSON G H. Photoactivatable fluorescent proteins for diffraction-limited and super-resolution imaging [J]. Trends in Cell Biology, 2009, 19(11): 555-565. [29] GRIMM J B, ENGLISH B P, CHEN J, et al. A general method to improve fluorophores for live-cell and single-molecule microscopy [J]. Nature Methods, 2015, 12(3): 244-250. [30] ZHANG M, CHANG H, ZHANG Y, et al. Rational design of true monomeric and bright photoactivatable fluorescent proteins [J]. Nature Methods, 2012, 9(7): 727-729. [31] LANDGRAF D, OKUMUS B, CHIEN P, et al. Segregation of molecules at cell division reveals native protein localization [J]. Nature Methods, 2012, 9(5): 480-482. [32] LOS G V, ENCELL L P, MCDOUGALL M G, et al. HaloTag: a novel protein labeling technology for cell imaging and protein analysis [J]. ACS Chemical Biology, 2008, 3(6): 373-382. [33] GAUTIER A, JUILLERAT A, HEINIS C, et al. An engineered protein tag for multiprotein labeling in living cells [J]. Chemistry & Biology, 2008, 15(2): 128-136. [34] CHEN Z, JING C, GALLAGHER S S, et al. Second-generation covalent TMP-tag for live cell imaging [J]. Journal of the American Chemical Society, 2012, 134(33): 13692-13699. [35] LAVIS L D. Teaching old dyes new tricks: biological probes built from fluoresceins and rhodamines [J]. Annual Review of Biochemistry, 2017, 86: 825-843. [36] GRIMM J B, ENGLISH B P, CHOI H, et al. Bright photoactivatable fluorophores for single-molecule imaging [J]. Nature Methods, 2016, 13(12): 985-988. [37] BERTRAND E, CHARTRAND P, SCHAEFER M, et al. Localization of ASH1 mRNA particles in living yeast [J]. Molecular Cell, 1998, 2(4): 437-445. [38] CHAO J A, PATSKOVSKY Y, ALMO S C, et al. Structural basis for the coevolution of a viral RNA-protein complex [J]. Nature Structural & Molecular Biology, 2008, 15(1): 103-105. [39] HOCINE S, RAYMOND P, ZENKLUSEN D, et al. Single-molecule analysis of gene expression using two-color RNA labeling in live yeast [J]. Nature Methods, 2013, 10(2): 119-121. [40] 常振仪, 严维, 刘东风, 等. CRISPR/Cas技术研究进展[J]. 农业生物技术学报, 2015, 23(9): 1196-1206. [41] YANG L Z, WANG Y, LI S Q, et al. Dynamic imaging of RNA in living cells by CRISPR-Cas13 systems [J]. Molecular Cell, 2019, 76(6): 981-997.e7. [42] OUELLET J. RNA fluorescence with light-up aptamers [J]. Frontiers in Chemistry, 2016, 4: 29. [43] TRACHMAN R J 3RD, AUTOUR A, JENG S C Y, et al. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer [J]. Nature Chemical Biology, 2019, 15(5): 472-479. [44] 周子琦, 张洋子, 兰欣悦, 等. 发光核酸适配体的筛选及应用[J]. 生物技术通报, 2022, 38(5): 240-247. [45] LIONNET T, WU C. Single-molecule tracking of transcription protein dynamics in living cells: Seeing is believing, but what are we seeing? [J]. Current Opinion in Genetics & Development, 2021, 67, 94-102. [46] RUST M J, BATES M, ZHUANG X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) [J]. Nature Methods, 2006, 3(10): 793-795. [47] HELL S W, WICHMANN J. Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion fluorescence microscopy [J]. Optics Letters, 1994, 19(11): 780-782. [48] GUSTAFSSON M G L. Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy [J]. Journal of Microscopy, 2000, 198: 82-87. [49] SMALL A, STAHLHEBER S. Fluorophore localization algorithms for super-resolution microscopy [J]. Nature Methods, 2014, 11(3): 267-279. [50] JAQAMAN K, LOERKE D, METTLEN M, et al. Robust singleparticle tracking in live-cell time-lapse sequences [J]. Nature Methods, 2008, 5(8): 695-702. [51] CARRERO G, MCDONALD D, CRAWFORD E, et al. Using FRAP and mathematical modeling to determine the in vivo kinetics of nuclear proteins [J]. Methods, 2003, 29(1): 14-28. [52] DIGMAN M A, GRATTON E. Lessons in fluctuation correlation spectroscopy [J]. Annual Review of Physical Chemistry, 2011, 62: 645-668. [53] 曲绍峰, 林金星, 李晓娟. FCS/FCCS技术及其在植物细胞生物学中的应用[J]. 电子显微学报, 2014, 33(5): 461-468. [54] MICHELMAN-RIBEIRO A, MAZZA D, ROSALES T, et al. Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy [J]. Biophysical Journal, 2009, 97(1): 337-346. [55] WHITE M D, ANGIOLINI J F, ALVAREZ Y D, et al. Long-lived binding of Sox2 to DNA predicts cell fate in the four-cell mouse embryo [J]. Cell, 2016, 165(1): 75-87. [56] BERLAND K M, SO P T, GRATTON E. Two-photon fluorescence correlation spectroscopy: method and application to the intracellular environment [J]. Biophysical Journal, 1995, 68(2): 694-701. [57] SCHIER A C, TAATJES D J. Structure and mechanism of the RNA polymerase II transcription machinery [J]. Genes & Development, 2020, 34(7/8): 465-488. [58] VERA M, BISWAS J, SENECAL A, et al. Single-cell and singlemolecule analysis of gene expression regulation [J]. Annual Review of Genetics, 2016, 50: 267-291. [59] MUELLER F, STASEVICH T J, MAZZA D, et al. Quantifying transcription factor kinetics: at work or at play? [J]. Critical Reviews in Biochemistry and Molecular Biology, 2013, 48(5): 492-514. [60] HAGER G L, MCNALLY J G, MISTELI T. Transcription dynamics [J]. Molecular Cell, 2009, 35(6): 741-753. [61] BROUWER I, LENSTRA T L. Visualizing transcription: key to understanding gene expression dynamics [J]. Current Opinion in Chemical Biology, 2019, 51: 122-129. [62] COOK P R. The organization of replication and transcription [J]. Science, 1999, 284(5421): 1790-1795. [63] DARZACQ X, SHAV-TAL Y, DE TURRIS V, et al. In vivo dynamics of RNA polymerase II transcription [J]. Nature Structural & Molecular Biology, 2007, 14(9): 796-806. [64] ZHAO Z W, ROY R, GEBHARDT J C, et al. Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy [J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (2): 681-686. [65] CISSE I I, IZEDDIN I, CAUSSE S Z, et al. Real-time dynamics of RNA polymerase II clustering in live human cells [J]. Science, 2013, 341(6146): 664-667. [66] CHO W K, JAYANTH N, ENGLISH B P, et al. RNA Polymerase II cluster dynamics predict mRNA output in living cells [J]. Elife, 2016, 5: e13617. [67] LI J R, DONG A K, SAYDAMINOVA K, et al. Single-molecule nanoscopy elucidates RNA polymerase II transcription at single genes in live cells [J]. Cell, 2019, 178(2): 491-506.e28. [68] NGUYEN V Q, RANJAN A, LIU S, et al. Spatiotemporal coordination of transcription preinitiation complex assembly in live cells [J]. Molecular Cell, 2021, 81(17): 3560-3575.e6. [69] BOEYNAEMS S, ALBERTI S, FAWZI N L, et al. Protein phase separation: a new phase in cell biology [J]. Trends in Cell Biology, 2018, 28(6): 420-435. [70] HYMAN A A, WEBER C A, JULICHER F. Liquid-liquid phase separation in biology [J]. Annual Review of Cell and Developmental Biology, 2014, 30: 39-58. [71] LI P, BANJADE S, CHENG H C, et al. Phase transitions in the assembly of multivalent signalling proteins [J]. Nature, 2012, 483(7389): 336-340. [72] 吴荣波, 李丕龙. 液-液相分离与生物分子凝集体[J]. 科学通报, 2019, 64(22): 2285-2291. [73] ZABOROWSKA J, EGLOFF S, MURPHY S. The pol II CTD: new twists in the tail [J]. Nature Structural & Molecular Biology, 2016, 23(9): 771-777. [74] MEINHART A, KAMENSKI T, HOEPPNER S, et al. A structural perspective of CTD function [J]. Genes & Development, 2005, 19(12): 1401-1415. [75] HSIN J P, MANLEY J L. The RNA polymerase II CTD coordinates transcription and RNA processing [J]. Genes & Development, 2012, 26(19): 2119-2137. [76] LU F Y, PORTZ B, GILMOUR D S. The C-terminal domain of RNA polymerase II is a multivalent targeting sequence that supports drosophila development with only consensus heptads [J]. Molecular Cell, 2019, 73(6): 1232-1242.e4. [77] SAWICKA A, VILLAMIL G, LIDSCHREIBER M, et al. Transcription activation depends on the length of the RNA polymerase II C-terminal domain [J]. The EMBO Journal, 2021, 40(9): e107015. [78] BOEHNING M, DUGAST-DARZACQ C, RANKOVIC M, et al. RNA polymerase II clustering through carboxy-terminal domain phase separation [J]. Nature Structural & Molecular Biology, 2018, 25(9): 833-840. [79] CHEN X Z, WEI M, ZHENG M M, et al. Study of RNA polymerase II clustering inside live-cell nuclei using bayesian nanoscopy [J]. Acs Nano, 2016, 10(2): 2447-2454. [80] CHO W K, SPILLE J H, HECHT M, et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates [J]. Science, 2018, 361(6400): 412-415. [81] BOIJA A, KLEIN I A, SABARI B R, et al. Transcription factors activate genes through the phase-separation capacity of their activation domains [J]. Cell, 2018, 175(7): 1842-1855.e16. [82] SABARI B R, DALL'AGNESE A, BOIJA A, et al. Coactivator condensation at super-enhancers links phase separation and gene control [J]. Science, 2018, 361(6400): eaar3958. [83] VOJNOVIC I, WINKELMEIER J, ENDESFELDER U. Visualizing the inner life of microbes: practices of multi-color single-molecule localization microscopy in microbiology [J]. Biochemical Society Transactions, 2019, 47(4): 1041-1065. [84] CABRERA J E, JIN D J. Active transcription of rRNA operons is a driving force for the distribution of RNA polymerase in bacteria: Effect of extrachromosomal copies of rrnB on the in vivo localization of RNA polymerase [J]. Journal of Bacteriology, 2006, 188(11): 4007-4014. [85] JIN D J, MATA MARTIN C, SUN Z, et al. Nucleolus-like compartmentalization of the transcription machinery in fast-growing bacterial cells [J]. Critical Reviews in Biochemistry and Molecular Biology, 2017, 52(1): 96-106. [86] CABRERA J E, JIN D J. The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues [J]. Molecular Microbiology, 2003, 50(5): 1493-1505. [87] STRACY M, LESTERLIN C, GARZA DE LEON F, et al. Livecell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid [J]. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(32): E4390-E4399. [88] WENG X, BOHRER C H, BETTRIDGE K, et al. Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli [J]. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(40): 20115-20123. [89] LADOUCEEUR A M, PARMAR B S, BIEDZINSKI S, et al. Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation [J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(31): 18540-18549. [90] BREMER H, DENNIS P P. Modulation of chemical composition and other parameters of the cell at different exponential growth rates [J]. EcoSal Plus, 2008, 3(1). DOI: 10.1128/ecosal.5.23. [91] SHIN Y, BRANGWYNNE C P. Liquid phase condensation in cell physiology and disease [J]. Science, 2017, 357(6357): eaaf4382. [92] 江海燕, 吴旻昊. 生物大分子相分离研究进展和发展建议[J]. 科学通报, 2020, 65(20): 2085-2093. [93] SHRINIVAS K, SABARI B R, COFFEY E L, et al. Enhancer features that drive formation of transcriptional condensates [J]. Molecular Cell, 2019, 75(3): 549-561.e7. [94] STRACY M, KAPANIDIS A N. Single-molecule and superresolution imaging of transcription in living bacteria [J]. Methods, 2017, 120: 103-114. |
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