三维基因组专栏

生物大分子“液-液相分离”调控染色质三维空间结构和功能

展开
  • 1. 中国科学院北京基因研究所, 基因组科学与技术重点实验室,北京 100101
    2. 中国科学院大学生命科学学院, 北京 100049
高晓萌,硕士研究生,专业方向:三维基因组结构研究。E-mail: gaoxiaomeng2018m@big.ac.cn

收稿日期: 2019-09-04

  修回日期: 2019-11-04

  网络出版日期: 2019-12-05

基金资助

国家重点研发计划编号(2018YFC2000400);国家自然科学基金项目资助编号(31871331);国家自然科学基金项目资助编号(31671342)

Three-dimensional structure and function of chromatin regulated by “liquid-liquid phase separation” of biological macromolecules.

Expand
  • 1. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics. Chinese Academy of Sciences, Beijing 100101, China
    2. Life Sciences College, University of Chinese Academy of Sciences, Beijing 100049, China

Received date: 2019-09-04

  Revised date: 2019-11-04

  Online published: 2019-12-05

Supported by

Supported by the National Key R&D Program of China No(2018YFC2000400);the National Natural Science Foundation of China Nos(31871331);the National Natural Science Foundation of China Nos(31671342)

摘要

生物大分子的相分离聚集(简称相分离)是驱动细胞内无膜细胞器形成的主要机制,参与众多生物学过程并和多种人类疾病密切相关,如神经退行性疾病等。近年来,研究人员围绕相分离现象的分子机制和生物学功能,发现了相分离与信号传导、染色质结构、基因表达、转录调控等一系列生物学过程存在紧密关联,为理解细胞命运决定和疾病发生提供了新的视角,为疾病治疗和新药研发开辟了新的可能途径。本文在回顾了相分离研究的发展过程、相分离现象在生物学中的应用,以及相分离与疾病的关系的基础上,重点分析了近年来相分离与染色质结构关联方面的研究突破,包括相分离如何感知并重塑染色质结构、超级增强子如何通过相分离调节基因表达、共转录激活因子如何通过相分离参与基因表达调控等,以期为进一步理解相分离与染色质空间结构的关系提供参考。

本文引用格式

高晓萌, 张治华 . 生物大分子“液-液相分离”调控染色质三维空间结构和功能[J]. 遗传, 2020 , 42(1) : 45 -56 . DOI: 10.16288/j.yczz.19-266

Abstract

Phase separation drives biomacromolecule condensation (phase separation) and is the main mechanism for the formation of membrane-less organelles in cells. Phase separation is involved in many biological processes and is closely associated to various human diseases, e.g., neurodegenerative diseases. Focusing on the molecular mechanism and functions, researchers have recently revealed close associations s between phase separation and various biological functions, such as signal transduction, chromosome structure, gene expression, and transcriptional regulation. These findings have provided new perspectives in understanding cell fate decisions and disease processes, thereby offering novel approaches for future drug discovery and development of disease treatments in medicine. In this review, we summarized the current progress in the field of phase separation research. We focused on its application on understanding how phase separation remodels the chromatin structure, assembles co-activators and super-enhancers in regulation of gene expression, in order to further understand the relationship between phase separation and chromatin spatial structures. Finally, we also outline the challenges in reference to future research directions in the field.

参考文献

[1] Mitrea DM, Kriwacki RM . Phase separation in biology; functional organization of a higher order. Cell Commun Signal, 2016,14:1.
[2] Uversky VN . Intrinsically disordered proteins in overcrowded milieu: membrane-less organelles, phase separation, and intrinsic disorder . Curr Opin Struct Biol, 2017,44:18-30.
[3] Banani SF, Lee OH, Hyman AA, Rosen MK . Biomolecular condensates: organizers of cellular biochemistry . Nat Rev Mol Cell Biol, 2017,18(5):285-298.
[4] Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Jülicher F, Hyman AA . Germline P granules are liquid droplets that localize by controlled dissolution/condensation . Science, 2009,324(5935):1729-1732.
[5] Brangwynne CP, Mitchison TJ, Hyman AA . Active liquid-like behavior of nucleoli determines their size and shape in xenopus laevis oocytes . Proc Natl Acad Sci USA, 2011,108(11):4334-4339.
[6] Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J, Grishin MV, Frantz DE, Schneider JW, Chen S, Li L, Sawaya MR, Eisenberg D, Tycko R, McKnight SL. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels . Cell, 2012,149(4):753-767.
[7] Nott TJ, Petsalaki E, Farber P, Jervis D, Fussner E, Plochowietz A, Craggs TD, Bazett-Jones DP, Pawson T, Forman-Kay JD, Baldwin AJ . Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles . Mol Cell, 2015,57(5):936-947.
[8] Li P, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF, Russo PS, Jiang QX, Nixon BT, Rosen MK . Phase transitions in the assembly of multivalent signalling proteins . Nature, 2012,483(7389):336-340.
[9] Deichmann U . Chromatin: its history, current research, and the seminal researchers and their philosophy . Perspect Biol Med, 2015,58(2):143-164.
[10] Wu RB, Li PL . Liquid-liquid separation and biomolecular condensation. Chin Sci Bull, 2019,64(22):2285-2291.
[10] 吴荣波, 李丕龙 . 液-液相分离与生物分子凝集体. 科学通报, 2019,64(22):2285-2291.
[11] Ramaswami M, Taylor JP, Parker R . Altered ribostasis: RNA-protein granules in degenerative disorders . Cell, 2013,154(4):727-736.
[12] King OD, Gitler AD, Shorter J . The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease . Brain Res, 2012,1462:61-80.
[13] Alberti S, Halfmann R, King O, Kapila A, Lindquist S . A systematic survey identifies prions and illuminates sequence features of prionogenic proteins . Cell, 2009,137(1):146-158.
[14] Fromm SA, Kamenz J, N?ldeke ER, Neu A, Zocher G, Sprangers R . In vitro reconstitution of a cellular phase- transition process that involves the mRNA decapping machinery . Angew Chem Int Ed Engl, 2014,53(28):7354-7359.
[15] Zeng M, Shang Y, Araki Y, Guo T, Huganir RL, Zhang M. Phase transition in postsynaptic densities underlies formation of synaptic complexes and synaptic plasticity. Cell, 2016, 166(5): 1163-1175.e12.
[16] Shin Y, Chang YC, Lee DSW, Berry J, Sanders DW, Ronceray P, Wingreen NS, Haataja M, Brangwynne CP. Liquid nuclear condensates mechanically sense and sestructure the genome. Cell, 2018, 175(6): 1481-1491.e13.
[17] Huang WYC, Alvarez S, Kondo Y, Lee YK, Chung JK, Lam HYM, Biswas KH, Kuriyan J, Groves JT . A molecular assembly phase transition and kinetic proofreading modulate Ras activation by SOS . Science, 2019,363(6431):1098-1103.
[18] Houtman JC, Yamaguchi H, Barda-Saad M, Braiman A, Bowden B, Appella E, Schuck P, Samelson LE . Oligomerization of signaling complexes by the multipoint binding of GRB2 to both LAT and SOS1 . Nat Struct Mol Biol, 2006,13(9):798-805.
[19] Bandaru P, Kondo Y, Kuriyan J . The interdependent activation of Son-of-Sevenless and Ras . Cold Spring Harb Perspect Med, 2019,9(2):a031534.
[20] Nag A, Monine MI, Faeder JR, Goldstein B . Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system . Biophys J, 2009,96(7):2604-2623.
[21] Huang WYC, Ditlev JA, Chiang HK, Rosen MK, Groves JT . Allosteric modulation of Grb2 recruitment to the intrinsically disordered scaffold protein, LAT, by Remote Site Phosphorylation . . Am Chem Soc, 2017,139(49):18009-18015.
[22] Huang WYC, Chiang HK, Groves JT . Dynamic scaling analysis of molecular motion within the LAT:Grb2:SOS protein network on membranes . Biophys J, 2017,113(8):1807-1813.
[23] Riback JA, Katanski CD, Kear-Scott JL, Pilipenko EV, Rojek AE, Sosnick TR, Drummond DA. Stress-triggered phase separation is an adaptive, evolutionarily tuned response. Cell, 2017, 168(6): 1028-1040.e19.
[24] Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S,. Phase separation of a yeast prion protein promotes cellular fitness. Science, 2018, 359(6371): eaa05654.
[25] Li YR, King OD, Shorter J, Gitler AD . Stress granules as crucibles of ALS pathogenesis. . Cell Biol, 2013,201(3):361-372.
[26] Brundin P, Melki R, Kopito R . Prion-like transmission of protein aggregates in neurodegenerative diseases . Nat Rev Mol Cell Biol, 2010,11(4):301-307.
[27] Shulman JM, De Jager P, Feany MB . Parkinson's disease: genetics and pathogenesis . Annu Rev Pathol, 2011,6(1):193-222.
[28] Robberecht W, Philips T . The changing scene of amyotrophic lateral sclerosis . Nat Rev Neurosci, 2013,14(4):248-264.
[29] Patel A, Lee HO, Jawerth L, Maharana S, Jahnel M, Hein MY, Stoynov S, Mahamid J, Saha S, Franzmann TM, Pozniakovski A, Poser I, Maghelli N, Royer LA, Weigert M, Myers EW, Grill S, Drechsel D, Hyman AA, Alberti S . A liquid-to-solid phase transition of the ALS protein FUS accelerated by disease mutation . Cell, 2015,162(5):1066-1077.
[30] Kim HJ, Kim NC, Wang YD, Scarborough EA, Moore J, Diaz Z, MacLea KS, Freibaum B, Li S, Molliex A, Kanagaraj AP, Carter R, Boylan KB, Wojtas AM, Rademakers R, Pinkus JL, Greenberg SA, Trojanowski JQ, Traynor BJ, Smith BN, Topp S, Gkazi AS, Miller J, Shaw CE, Kottlors M, Kirschner J, Pestronk A, Li YR, Ford AF, Gitler AD, Benatar M, King OD, Kimonis VE, Ross ED, Weihl CC, Shorter J, Taylor JP,. Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS . Nature, 2013,495(7442):467-473.
[31] Murakami T, Qamar S, Lin JQ, Schierle GS, Rees E, Miyashita A, Costa AR, Dodd RB, Chan FT, Michel CH, Kronenberg-Versteeg D, Li Y, Yang SP, Wakutani Y, Meadows W, Ferry RR, Dong L, Tartaglia GG, Favrin G, Lin WL, Dickson DW, Zhen M, Ron D, Schmitt-Ulms G, Fraser PE, Shneider NA, Holt C, Vendruscolo M, Kaminski CF, St George-Hyslop P. ALS/FTD mutation- induced phase transition of FUS liquid droplets and reversible hydrogels into irreversible hydrogels impairs RNP granule function . Neuron, 2015,88(4):678-690.
[32] Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D . The 3D profile method for identifying fibril-forming segments of proteins . Proc Natl Acad Sci USA, 2006,103(11):4074-4078.
[33] Han TW, Kato M, Xie S, Wu LC, Mirzaei H, Pei J, Chen M, Xie Y, Allen J, Xiao J, McKnight SL. Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies . Cell, 2012,149(4):768-779.
[34] Schwartz JC, Wang X, Podell ER, Cech TR . RNA seeds higher-order assembly of FUS protein . Cell Rep, 2013,5(4):918-925.
[35] Schwartz JC, Cech TR, Parker RR . Biochemical properties and biological functions of FET proteins . Annu Rev Biochem, 2015,84:355-379.
[36] Cleary JD, Ranum LP . Repeat-associated non-ATG (RAN) translation in neurological disease . Hum Mol Genet, 2013,22(R1):R45-51.
[37] Mori K, Weng SM, Arzberger T, May S, Rentzsch K, Kremmer E, Schmid B, Kretzschmar HA, Cruts M, Van Broeckhoven C, Haass C, Edbauer D . The C9orf72 GGGGCC repeat is translated into aggregating dipeptide- repeat proteins in FTLD/ALS . Science, 2013,339(6125):1335-1338.
[38] Lin MT, Beal MF . Mitochondrial dysfunction and oxidative stress in neurodegenerative diseases . Nature, 2006,443(7113):787-795.
[39] Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N . The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data . Cancer Discov, 2012,2(5):401-404.
[40] Klokk TI, Kurys P, Elbi C, Nagaich AK, Hendarwanto A, Slagsvold T, Chang CY, Hager GL, Saatcioglu F . Ligand-specific dynamics of the androgen receptor at its response element in living cells . Mol Cell Biol, 2007,27(5):1823-1843.
[41] Bouchard JJ, Otero JH, Scott DC, Szulc E, Martin EW, Sabri N, Granata D, Marzahn MR, Lindorff-Larsen K, Salvatella X, Schulman BA, Mittag T. Cancer mutations of the tumor suppressor SPOP disrupt the formation of active, phase-separated compartments. Mol Cell, 2018, 72(1): 19- 36. e8.
[42] Wojciechowska M, Krzyzosiak WJ . Cellular toxicity of expanded RNA repeats: focus on RNA foci . Hum Mol Genet, 2011,20(19):3811-3821.
[43] Feric M, Vaidya N, Harmon TS, Mitrea DM, Zhu L, Richardson TM, Kriwacki RW, Pappu RV, Brangwynne CP , Coexisting liquid phases underlie nucleolar subcompartments . Cell, 2016,165(7):1686-1697.
[44] Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE . Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state . Nat Biotechnol, 2015,33(11):1165-1172.
[45] Shankaranarayanan P, Mendoza-Parra MA, Walia M, Wang L, Li N, Trindade LM, Gronemeyer H . Single-tube linear DNA amplification (LinDA) for robust ChIP-seq . Nat Methods, 2011,8(7):565-567.
[46] Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J . Comprehensive mapping of long- range interactions reveals folding principles of the human genome . Science, 2009,326(5950):289-293.
[47] Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL . A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping . Cell, 2014,159(7):1665-1680.
[48] Buenrostro JD, Wu BJ, Chang HY, Greenleaf WJ,. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol, 2015, 109: 21.29.1- 21.29. 9.
[49] Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ . Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position . Nat Methods, 2013,10(12):1213-1218.
[50] Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N, Henry L, Gerlich DW, Redding S, Rosen MK. Organization of chromatin by intrinsic and regulated phase separation. Cell, 2019, 179(2): 470-484.e21.
[51] Xu BX, Zhang ZH . Computational inference of physical spatial organization of eukaryotic genomes . Quant Biol, 2016,4(4):302-309.
[52] Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH . Phase separation drives heterochromatin domain formation . Nature, 2017,547(7662):241-245.
[53] Mao YS, Zhang B, Spector DL . Biogenesis and function of nuclear bodies . Trends Genet, 2011,27(8):295-306.
[54] Erdel F, Rippe K . Formation of chromatin subcompartments by phase separation . Biophys J, 2018,114(10):2262-2270.
[55] Ruthenburg AJ, Li H, Patel DJ, Allis CD . Multivalent engagement of chromatin modifications by linked binding modules . Nat Rev Mol Cell Biol, 2007,8(12):983-994.
[56] Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA . Master transcription factors and mediator establish super-enhancers at key cell identity genes . Cell, 2013,153(2):307-319.
[57] Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA . A phase separation model for transcriptional control . Cell, 2017,169(1):13-23.
[58] Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, Malik S, Hnisz D, Lee TI, Cisse II, Roeder RG, Sharp PA, Chakraborty AK, Young PA. Coactivator condensation at super-enhancers links phase separation and gene control. Science, 2018, 361(6400): eaar3958.
[59] Brent R, Ptashne M . A eukaryotic transcriptional activator bearing the DNA specificity of a prokaryotic repressor . Cell, 1985,43(3 Pt 2):729-736.
[60] Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R . TFCat: the curated catalog of mouse and human transcription factors . Genome Biol, 2009,10(3):R29.
[61] Boija A, Klein IA, Sabari BR, Dall'Agnese A, Coffey EL, Zamudio AV, Li CH, Shrinivas K, Manteiga JC, Hannett NM, Abraham BJ, Afeyan LK, Guo YE, Rimel JK, Fant CB, Schuijers J, Lee TL, Taatjes DJ, Young RA. Transcription factors activate genes through the phase- separation capacity of their activation domains. Cell, 2018,175(7): 1842-1855.e16.
[62] Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K . Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming . Cell Stem Cell, 2013,12(6):699-712.
[63] Cramer P . Organization and regulation of gene transcription . Nature, 2019,573(7772):45-54.
[64] Guo YE, Manteiga JC, Henninger JE, Sabari BR, Dall'Agnese A, Hannett NM, Spille JH, Afeyan LK, Zamudio AV, Shrinivas K, Abraham BJ, Boija A, Decker TM, Rimel JK, Fant CB, Lee TI, Cisse II, Sharp PA, Taatjes DJ, Young RA. Pol II phosphorylation regulates a switch between transcriptional and splicing condensates . Nature, 2019,572(7770):543-548.
文章导航

/