Defining the Transcriptional Ecosystem
2018; Elsevier BV; Volume: 72; Issue: 6 Linguagem: Inglês
10.1016/j.molcel.2018.11.022
ISSN1097-4164
AutoresMaruhen Amir Datsch Silveira, Steve Bilodeau,
Tópico(s)Gene Regulatory Network Analysis
ResumoFine tuning of the transcriptional program requires the competing action of multiple protein complexes in a well-organized environment. Genome folding creates proximity between genes, leading to accumulation of regulatory factors and formation of local microenvironments. Many roles of this complex organization controlling gene transcription remain to be explored. In this Perspective, we are proposing the existence of a transcriptional ecosystem equilibrium: a mechanism balancing transcriptional regulation between connected genes during environmental disturbances. This model is derived from chromosome architecture studies assigning genes to specific DNA structures and evidence establishing that the transcription machinery and coregulators create dynamic phase separation droplets surrounding active genes. Defining connected genes as ecosystems rather than individuals will cement that transcriptional regulation is a biochemical equilibrium and force a reassessment of direct and indirect responses to environmental disturbances. Fine tuning of the transcriptional program requires the competing action of multiple protein complexes in a well-organized environment. Genome folding creates proximity between genes, leading to accumulation of regulatory factors and formation of local microenvironments. Many roles of this complex organization controlling gene transcription remain to be explored. In this Perspective, we are proposing the existence of a transcriptional ecosystem equilibrium: a mechanism balancing transcriptional regulation between connected genes during environmental disturbances. This model is derived from chromosome architecture studies assigning genes to specific DNA structures and evidence establishing that the transcription machinery and coregulators create dynamic phase separation droplets surrounding active genes. Defining connected genes as ecosystems rather than individuals will cement that transcriptional regulation is a biochemical equilibrium and force a reassessment of direct and indirect responses to environmental disturbances. Genome folding creates physical structures and organizes gene activities within the nucleus. Groups of genes are secluded within larger domains called topologically associating domains (TADs), creating insulated neighborhoods to self-contain chromosome contacts and gene regulation (Dixon et al., 2012Dixon J.R. Selvaraj S. Yue F. Kim A. Li Y. Shen Y. Hu M. Liu J.S. Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions.Nature. 2012; 485: 376-380Crossref PubMed Scopus (3955) Google Scholar, Dowen et al., 2014Dowen J.M. Fan Z.P. Hnisz D. Ren G. Abraham B.J. Zhang L.N. Weintraub A.S. Schujiers J. Lee T.I. Zhao K. Young R.A. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.Cell. 2014; 159: 374-387Abstract Full Text Full Text PDF PubMed Scopus (579) Google Scholar, Nora et al., 2012Nora E.P. Lajoie B.R. Schulz E.G. Giorgetti L. Okamoto I. Servant N. Piolot T. van Berkum N.L. Meisig J. Sedat J. et al.Spatial partitioning of the regulatory landscape of the X-inactivation centre.Nature. 2012; 485: 381-385Crossref PubMed Scopus (1807) Google Scholar, Nora et al., 2017Nora E.P. Goloborodko A. Valton A.-L. Gibcus J.H. Uebersohn A. Abdennur N. Dekker J. Mirny L.A. Bruneau B.G. 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Dorschner M.O. et al.Comprehensive mapping of long-range interactions reveals folding principles of the human genome.Science. 2009; 326: 289-293Crossref PubMed Scopus (4868) Google Scholar, Wang et al., 2016Wang S. Su J.H. Beliveau B.J. Bintu B. Moffitt J.R. Wu C. Zhuang X. Spatial organization of chromatin domains and compartments in single chromosomes.Science. 2016; 353: 598-602Crossref PubMed Scopus (321) Google Scholar). Compartmentalization of active genes is supported by imaging studies depicting the transcriptional process in distinct nuclear foci scattered throughout the nucleoplasm, often referred to as transcription factories (Feuerborn and Cook, 2015Feuerborn A. Cook P.R. Why the activity of a gene depends on its neighbors.Trends Genet. 2015; 31: 483-490Abstract Full Text Full Text PDF PubMed Scopus (59) Google Scholar, Rieder et al., 2012Rieder D. Trajanoski Z. McNally J.G. Transcription factories.Front. Genet. 2012; 3: 221Crossref PubMed Scopus (67) Google Scholar). The number of sites with active transcription in the nucleus is smaller than the number of transcribed coding and noncoding genes, supporting the presence of multiple genes in each defined area (Chakalova and Fraser, 2010Chakalova L. Fraser P. Organization of transcription.Cold Spring Harb. Perspect. Biol. 2010; 2: a000729Crossref PubMed Scopus (58) Google Scholar, Feuerborn and Cook, 2015Feuerborn A. Cook P.R. Why the activity of a gene depends on its neighbors.Trends Genet. 2015; 31: 483-490Abstract Full Text Full Text PDF PubMed Scopus (59) Google Scholar, Rieder et al., 2012Rieder D. Trajanoski Z. McNally J.G. Transcription factories.Front. Genet. 2012; 3: 221Crossref PubMed Scopus (67) Google Scholar). These pieces of physical evidence are corroborated by the observation that connected genes are transcriptionally coregulated (Boudaoud et al., 2017Boudaoud I. Fournier É. Baguette A. Vallée M. Lamaze F.C. Droit A. Bilodeau S. Connected gene communities underlie transcriptional changes in Cornelia de Lange syndrome.Genetics. 2017; 207: 139-151Crossref PubMed Scopus (20) Google Scholar, Fanucchi et al., 2013Fanucchi S. Shibayama Y. Burd S. Weinberg M.S. Mhlanga M.M. Chromosomal contact permits transcription between coregulated genes.Cell. 2013; 155: 606-620Abstract Full Text Full Text PDF PubMed Scopus (141) Google Scholar, Osborne et al., 2004Osborne C.S. Chakalova L. Brown K.E. Carter D. Horton A. Debrand E. Goyenechea B. Mitchell J.A. Lopes S. Reik W. Fraser P. Active genes dynamically colocalize to shared sites of ongoing transcription.Nat. Genet. 2004; 36: 1065-1071Crossref PubMed Scopus (819) Google Scholar). This high level of organization is important for different aspects of gene regulation, but questions remain regarding the dynamic regulation of genes sharing the same physical environment. There are interesting parallels between transcriptional regulation and the ecological organization found in nature. An ecosystem is defined as a biological community including multiple populations of living organisms and non-living components, creating dynamic interplays between individuals and their physical environment (Figure 1; Odum and Barrett, 2006Odum E.P. Barrett G.W. Fundamentals of Ecology. Brooks Cole, 2006Google Scholar). In this Perspective, we are considering the DNA elements important for gene transcription (coding regions, promoters, enhancers, etc.) as individual species or the biotic component of the ecosystem. The association of similar individuals (or DNA elements) in a defined area creates populations. As we and others have shown, the interplay between these populations of DNA elements defines communities (Boudaoud et al., 2017Boudaoud I. Fournier É. Baguette A. Vallée M. Lamaze F.C. Droit A. Bilodeau S. Connected gene communities underlie transcriptional changes in Cornelia de Lange syndrome.Genetics. 2017; 207: 139-151Crossref PubMed Scopus (20) Google Scholar, Fanucchi et al., 2013Fanucchi S. Shibayama Y. Burd S. Weinberg M.S. Mhlanga M.M. Chromosomal contact permits transcription between coregulated genes.Cell. 2013; 155: 606-620Abstract Full Text Full Text PDF PubMed Scopus (141) Google Scholar, Li et al., 2012Li G. Ruan X. Auerbach R.K. Sandhu K.S. Zheng M. Wang P. Poh H.M. Goh Y. Lim J. Zhang J. et al.Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.Cell. 2012; 148: 84-98Abstract Full Text Full Text PDF PubMed Scopus (850) Google Scholar). Each member of a natural ecosystem shares nutrients, air, water, and all essential abiotic components to survive and maintain homeostasis. For transcriptional regulation, abiotic components are represented by available transcriptional resources (as defined by the sum of transcription factors, coregulators, and machinery found in a designated area) and the local environment surrounding connected genes (i.e., the physical structure). We are proposing that genes found in the same nuclear environment are part of a transcriptional ecosystem equilibrium, where they are expressed at a steady-state level. Following an environmental disturbance, each natural ecosystem will react differently. For the transcriptional ecosystem, external stimuli will trigger specific but transient gene responses while ensuring restoration of the normal cell state, or equilibrium, afterward. The blending of these different ecosystems creates the biosphere in which we are living or a functional cell. Availability of resources is a critical feature of ecosystems, as it allows them to react to disturbances and maintain homeostasis. Following environmental perturbations, cells must respond quickly, including through activation of a specific set of transcription factors (López-Maury et al., 2008López-Maury L. Marguerat S. Bähler J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation.Nat. Rev. Genet. 2008; 9: 583-593Crossref PubMed Scopus (642) Google Scholar, de Nadal et al., 2011de Nadal E. Ammerer G. Posas F. Controlling gene expression in response to stress.Nat. Rev. Genet. 2011; 12: 833-845Crossref PubMed Scopus (453) Google Scholar, Voss and Hager, 2014Voss T.C. Hager G.L. Dynamic regulation of transcriptional states by chromatin and transcription factors.Nat. Rev. Genet. 2014; 15: 69-81Crossref PubMed Scopus (314) Google Scholar). These induced transcription factors reassign resources as they redistribute chromatin-remodeling complexes, coregulators, and the machinery required for the transcription of specific coding mRNA and noncoding RNA species (Lee and Young, 2013Lee T.I. Young R.A. Transcriptional regulation and its misregulation in disease.Cell. 2013; 152: 1237-1251Abstract Full Text Full Text PDF PubMed Scopus (846) Google Scholar, Schmidt et al., 2016Schmidt S.F. Larsen B.D. Loft A. Mandrup S. Cofactor squelching: artifact or fact?.BioEssays. 2016; 38: 618-626Crossref PubMed Scopus (28) Google Scholar, Spitz and Furlong, 2012Spitz F. Furlong E.E.M. Transcription factors: from enhancer binding to developmental control.Nat. Rev. Genet. 2012; 13: 613-626Crossref PubMed Scopus (1168) Google Scholar, Voss and Hager, 2014Voss T.C. Hager G.L. Dynamic regulation of transcriptional states by chromatin and transcription factors.Nat. Rev. Genet. 2014; 15: 69-81Crossref PubMed Scopus (314) Google Scholar). A fundamental property of gene transcription is that it is "bursty," which is defined by periods of high expression separated by refractory periods (Nicolas et al., 2017Nicolas D. Phillips N.E. Naef F. What shapes eukaryotic transcriptional bursting?.Mol. Biosyst. 2017; 13: 1280-1290Crossref PubMed Google Scholar). Transcription-factor-dependent recruitment of multiple RNA polymerase II (Pol II) molecules (known as "convoys" or "pelotons") is necessary for genes to be transcribed in bursts (van den Berg and Depken, 2017van den Berg A.A. Depken M. Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes.Nucleic Acids Res. 2017; 45: 7623-7632Crossref PubMed Scopus (9) Google Scholar, Tantale et al., 2016Tantale K. Mueller F. Kozulic-Pirher A. Lesne A. Victor J.M. Robert M.C. Capozi S. Chouaib R. Bäcker V. Mateos-Langerak J. et al.A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting.Nat. Commun. 2016; 7: 12248Crossref PubMed Scopus (149) Google Scholar). Therefore, access to a pool of transcriptional regulators, including the transcription machinery, is essential to respond to environmental disturbances. Transcriptional disturbances are created by cellular responses to environmental signals (López-Maury et al., 2008López-Maury L. Marguerat S. Bähler J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation.Nat. Rev. Genet. 2008; 9: 583-593Crossref PubMed Scopus (642) Google Scholar, de Nadal et al., 2011de Nadal E. Ammerer G. Posas F. Controlling gene expression in response to stress.Nat. Rev. Genet. 2011; 12: 833-845Crossref PubMed Scopus (453) Google Scholar, Vihervaara et al., 2018Vihervaara A. Duarte F.M. Lis J.T. Molecular mechanisms driving transcriptional stress responses.Nat. Rev. Genet. 2018; 19: 385-397Crossref PubMed Scopus (123) Google Scholar). From yeast to human, activation of transcription factors leads to transcriptional activation and repression within minutes (López-Maury et al., 2008López-Maury L. Marguerat S. Bähler J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation.Nat. Rev. Genet. 2008; 9: 583-593Crossref PubMed Scopus (642) Google Scholar, de Nadal et al., 2011de Nadal E. Ammerer G. Posas F. Controlling gene expression in response to stress.Nat. Rev. Genet. 2011; 12: 833-845Crossref PubMed Scopus (453) Google Scholar, Vihervaara et al., 2018Vihervaara A. Duarte F.M. Lis J.T. Molecular mechanisms driving transcriptional stress responses.Nat. Rev. Genet. 2018; 19: 385-397Crossref PubMed Scopus (123) Google Scholar). During this time frame, genomic binding is detected at the regulatory regions of activated but typically not repressed genes, suggesting an indirect effect on gene repression (Schmidt et al., 2016Schmidt S.F. Larsen B.D. Loft A. Mandrup S. Cofactor squelching: artifact or fact?.BioEssays. 2016; 38: 618-626Crossref PubMed Scopus (28) Google Scholar). For example, estrogen stimulation activates the estrogen receptor (ER), which binds rapidly to target sites (Shang et al., 2000Shang Y. Hu X. DiRenzo J. Lazar M.A. Brown M. Cofactor dynamics and sufficiency in estrogen receptor-regulated transcription.Cell. 2000; 103: 843-852Abstract Full Text Full Text PDF PubMed Scopus (1446) Google Scholar). Interestingly, although an equal ratio of activated and repressed genes was observed after 40 min, ER was enriched only at activated genes (Hah et al., 2011Hah N. Danko C.G. Core L. Waterfall J.J. Siepel A. Lis J.T. Kraus W.L. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.Cell. 2011; 145: 622-634Abstract Full Text Full Text PDF PubMed Scopus (366) Google Scholar). Another example, in yeast, shows that the stress-induced transcription factor Msn2 quickly occupies activated genes, although downregulated genes are not bound (Elfving et al., 2014Elfving N. Chereji R.V. Bharatula V. Björklund S. Morozov A.V. Broach J.R. A dynamic interplay of nucleosome and Msn2 binding regulates kinetics of gene activation and repression following stress.Nucleic Acids Res. 2014; 42: 5468-5482Crossref PubMed Scopus (34) Google Scholar). These observations are in accordance with results showing that transcriptional regulators, including Pol II, the mediator complex, P300/CBP, SRC3, BRD4, and likely many others, are relocalized to induced transcription factors within minutes (Cho et al., 2016Cho W.K. Jayanth N. English B.P. Inoue T. Andrews J.O. Conway W. Grimm J.B. Spille J.H. Lavis L.D. Lionnet T. Cisse I.I. RNA polymerase II cluster dynamics predict mRNA output in living cells.eLife. 2016; 5: 1-31Crossref Scopus (153) Google Scholar, Schmidt et al., 2016Schmidt S.F. Larsen B.D. Loft A. Mandrup S. Cofactor squelching: artifact or fact?.BioEssays. 2016; 38: 618-626Crossref PubMed Scopus (28) Google Scholar, Vihervaara et al., 2018Vihervaara A. Duarte F.M. Lis J.T. Molecular mechanisms driving transcriptional stress responses.Nat. Rev. Genet. 2018; 19: 385-397Crossref PubMed Scopus (123) Google Scholar). Accordingly, inducing a new gene expression program has a negative effect on the original cell-type-specific program (Schmidt et al., 2015Schmidt S.F. Larsen B.D. Loft A. Nielsen R. Madsen J.G.S. Mandrup S. Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers.Genome Res. 2015; 25: 1281-1294Crossref PubMed Scopus (49) Google Scholar). Therefore, transcriptional responses to environmental disturbances include primary direct and indirect effects triggered by the responsive transcription factor. This model postulates that environmental disturbances trigger an internal competition for limited transcriptional resources. A healthy ecosystem is dynamic but maintains an equilibrium to allow all individuals to thrive, forcing adaptation to respond to a disturbance and a recovery phase to return to steady state. From prokaryotes to humans, a transcriptional response to environmental perturbations is linked to feedback mechanisms forcing the cells toward returning to the equilibrium (López-Maury et al., 2008López-Maury L. Marguerat S. Bähler J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation.Nat. Rev. Genet. 2008; 9: 583-593Crossref PubMed Scopus (642) Google Scholar). For example, following estrogen stimulation, genes are bursting for 10–40 min and eventually return to basal level after 160 min when the estrogen receptor is degraded (Hah et al., 2011Hah N. Danko C.G. Core L. Waterfall J.J. Siepel A. Lis J.T. Kraus W.L. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells.Cell. 2011; 145: 622-634Abstract Full Text Full Text PDF PubMed Scopus (366) Google Scholar). These observations demonstrate that mechanisms are in place to disengage the transcriptional disturbance and restore the equilibrium. To be defined as an ecosystem, groups of genes need to be sharing a common physical space and the same transcriptional resources. At a higher level, the physical boundaries of the ecosystem could be represented by the entire nucleus or cell. However, molecular crowding within the nucleus makes diffusion of molecules through the nucleoplasm difficult, and distances in the whole cell could hinder the capacity to quickly adapt to disturbances. If neither the nucleus nor the whole cell is the physical boundary of the ecosystem, what about the three-dimensional chromosome structures, such as TADs and compartments? TADs are dynamic, with boundaries and intra-TAD interactions being constantly restructured (Hansen et al., 2018Hansen A.S. Cattoglio C. Darzacq X. Tjian R. Recent evidence that TADs and chromatin loops are dynamic structures.Nucleus. 2018; 9: 20-32Crossref PubMed Scopus (122) Google Scholar). Furthermore, disruption of TADs through degradation of cohesin (Canela et al., 2017Canela A. Maman Y. Jung S. Wong N. Callen E. Day A. Kieffer-Kwon K.R. Pekowska A. Zhang H. Rao S.S.P. et al.Genome organization drives chromosome fragility.Cell. 2017; 170: 507-521.e18Abstract Full Text Full Text PDF PubMed Scopus (217) Google Scholar, Schwarzer et al., 2017Schwarzer W. Abdennur N. Goloborodko A. Pekowska A. Fudenberg G. Loe-Mie Y. Fonseca N.A. Huber W. H Haering C. Mirny L. Spitz F. Two independent modes of chromatin organization revealed by cohesin removal.Nature. 2017; 551: 51-56Crossref PubMed Scopus (571) Google Scholar), CTCF (Nora et al., 2017Nora E.P. Goloborodko A. Valton A.-L. Gibcus J.H. Uebersohn A. Abdennur N. Dekker J. Mirny L.A. Bruneau B.G. Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.Cell. 2017; 169: 930-944.e22Abstract Full Text Full Text PDF PubMed Scopus (812) Google Scholar), or deletion of the cohesin-loader NIPBL (Remeseiro et al., 2013Remeseiro S. Cuadrado A. Kawauchi S. Calof A.L. Lander A.D. Losada A. 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Supporting the model, transcription leads to local RNA accumulation, creation of architectural microenvironments, and more physical contacts (Beagrie et al., 2017Beagrie R.A. Scialdone A. Schueler M. Kraemer D.C.A. Chotalia M. Xie S.Q. Barbieri M. de Santiago I. Lavitas L.-M. Branco M.R. et al.Complex multi-enhancer contacts captured by genome architecture mapping.Nature. 2017; 543: 519-524Crossref PubMed Scopus (354) Google Scholar, Hug et al., 2017Hug C.B. Grimaldi A.G. Kruse K. Vaquerizas J.M. Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription.Cell. 2017; 169: 216-228.e19Abstract Full Text Full Text PDF PubMed Scopus (257) Google Scholar, Tsai et al., 2017Tsai A. Muthusamy A.K. Alves M.R.P. Lavis L.D. Singer R.H. Stern D.L. Crocker J. Nuclear microenvironments modulate transcription from low-affinity enhancers.eLife. 2017; 6: 1-18Crossref Scopus (74) Google Scholar). These microenvironments surrounding neighboring genes would represent the physical space in which genes share resources. For genes in close proximity to share resources, the transcription machinery and associated coregulators need to be able to diffuse, be reassigned, and be present in sufficient numbers. High-resolution live imaging established that Pol II clusters form transiently, are modified rapidly following a disturbance, and directly linked to the production of nascent transcripts (Cho et al., 2016Cho W.K. Jayanth N. English B.P. Inoue T. Andrews J.O. Conway W. Grimm J.B. Spille J.H. Lavis L.D. Lionnet T. Cisse I.I. RNA polymerase II cluster dynamics predict mRNA output in living cells.eLife. 2016; 5: 1-31Crossref Scopus (153) Google Scholar, Cisse et al., 2013Cisse I.I. Izeddin I. Causse S.Z. Boudarene L. Senecal A. Muresan L. Dugast-Darzacq C. Hajj B. Dahan M. Darzacq X. Real-time dynamics of RNA polymerase II clustering in live human cells.Science. 2013; 341: 664-667Crossref PubMed Scopus (290) Google Scholar). Similar properties are also shared by many other transcriptional coregulators, including the mediator complex subunit MED1 and BRD4 (Cho et al., 2018Cho W.-K. Spille J.-H. Hecht M. Lee C. Li C. Grube V. Cisse I.I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.Science 361. 2018; : 412-415Crossref Scopus (612) Google Scholar, Chong et al., 2018Chong S. Dugast-Darzacq C. Liu Z. Dong P. Dailey G.M. Cattoglio C. Heckert A. Banala S. Lavis L. Darzacq X. et al.Imaging dynamic and selective low-complexity domain interactions that control gene transcription.Science. 2018; 361: eaar2555Crossref PubMed Scopus (473) Google Scholar, Sabari et al., 2018Sabari B.R. Dall'Agnese A. Boija A. Klein I.A. Coffey E.L. Shrinivas K. Abraham B.J. Hannett N.M. Zamudio A.V. Manteiga J.C. et al.Coactivator condensation at super-enhancers links phase separation and gene control.Science. 2018; 361: eaar3958Crossref PubMed Google Scholar). In an ecosystem, Liebig's law of the minimum applies (Odum and Barrett, 2006Odum E.P. Barrett G.W. Fundamentals of Ecology. Brooks Cole, 2006Google Scholar). The law states that it is not the total resources but the scarcest resource (or limiting factor) that dictates growth. In the nucleus, while mobile, accessibility to the transcription machinery could be an issue. In fact, the number of Pol II molecules is estimated between 4 and 30 within a transcription factory of up to 30 genes (Chakalova and Fraser, 2010Chakalova L. Fraser P. Organization of transcription.Cold Spring Harb. Perspect. Biol. 2010; 2: a000729Crossref PubMed Scopus (58) Google Scholar, Feuerborn and Cook, 2015Feuerborn A. Cook P.R. 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From prokaryotes to eukaryotes, phase separation is a key principle in cell biology concentrating biomolecules into membraneless compartments to promote interactions and facilitate signaling and communication (Boeynaems et al., 2018Boeynaems S. Alberti S. Fawzi N.L. Mittag T. Polymenidou M. Rousseau F. Schymkowitz J. Shorter J. Wolozin B. Van Den Bosch L. et al.Protein Phase Separation: A New Phase in Cell Biology.Trends Cell Biol. 2018; 28: 420-435Abstract Full Text Full Text PDF PubMed Scopus (915) Google Scholar, Hyman et al., 2014Hyman A.A. Weber C.A. Jülicher F. Liquid-liquid phase separation in biology.Annu. Rev. Cell Dev. Biol. 2014; 30: 39-58Crossref PubMed Scopus (1451) Google Scholar). The binding of transcription factors with unstructured domains to DNA, the recruitment of the transcription machinery, and transcription itself have all been implicated in creating phase-separated local microenvironments, thereby facilitating transcription (Chong et al., 2018Chong S. Dugast-Darzacq C. Liu Z. Dong P. Dailey G.M. Cattoglio C. Heckert A. Banala S. Lavis L. Darzacq X. et al.Imaging dynamic and selective low-complexity domain interactions that control gene transcription.Science. 2018; 361: eaar2555Crossref PubMed Scopus (473) Google Scholar, Liu and Tjian, 2018Liu Z. Tjian R. Visualizing transcription factor dynamics in living cells.J. Cell Biol. 2018; 217: 1181-1191Crossref PubMed Scopus (100) Google Scholar, Boija et al., 2018Boija A. Klein I.A. Sabari B.R. Dall'Agnese A. Coffey E.L. Zamudio A.V. Li C.H. Shrinivas K. Manteiga J.C. Hannett N.M. et al.Transcription factors activate genes through the phase-separation capacity of their activation domains.Cell. 2018; (Published online November 8, 2018)Abstract Full Text Full Text PDF PubMed Scopus (707) Google Scholar, Shin et al., 2018Shin Y. Chang Y.C. Lee D.S.W. Berry J. Sanders D.W. Ronceray P. Wingreen N.S. Haataja M. Brangwynne C.P. Liquid nuclear condensates mechanically sense and restructure the genome.Cell. 2018; 175 (1481–1491.e13)Abstract Full Text Full Text PDF PubMed Scopus (317) Google Scholar). Interestingly, imaging studies suggest that these phase separation droplets are highly dynamic and constantly exchanging with the environment, having the ability to fuse and combine resources (Cho et al., 2018Cho W.-K. Spille J.-H. Hecht M. Lee C. Li C. Grube V. Cisse I.I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.Science 361. 2018; : 412-415Crossref Scopus (612) Google Scholar, Chong et al., 2018Chong S. Dugast-Darzacq C. Liu Z. Dong P. Dailey G.M. Cattoglio C. Heckert A. Banala S. Lavis L. Darzacq X. et al.Imaging dynamic and selective low-complexity domain interactions that control gene transcription.Science. 2018; 361: eaar2555Crossref PubMed Scopus (473) Google Scholar, Sabari et al., 2018Sabari B.R. Dall'Agnese A. Boija A. Klein I.A. Coffey E.L. Shrinivas K. Abraham B.J. Hannett N.M. Zamudio A.V. Manteiga J.C. et al.Coactivator condensation at super-enhancers links phase separation and gene control.Science. 2018; 361: eaar3958Crossref PubMed Google Scholar). These droplets appear in different size, shape, and form containing multiple transcription-related activities (Cho et al., 2018Cho W.-K. Spille J.-H. Hecht M. Lee C. Li C. Grube V. Cisse I.I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.Science 361. 2018; : 412-415Crossref Scopus (612) Google Scholar, Sabari et al., 2018Sabari B.R. Dall'Agnese A. Boija A. Klein I.A. Coffey E.L. Shrinivas K. Abraham B.J. Hannett N.M. Zamudio A.V. Manteiga J.C. et al.Coactivator condensation at super-enhancers links phase separation and gene control.Science. 2018; 361: eaar3958Crossref PubMed Google Scholar). What would be the role of these soluble droplets filled with transcriptional components in an ecosystem? We speculate that large stable clusters found imaging the Mediator coactivator and Pol II (Cho et al., 2018Cho W.-K. Spille J.-H. Hecht M. Lee C. Li C. Grube V. Cisse I.I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.Science 361. 2018; : 412-415Crossref Scopus (612) Google Scholar) correspond to local microenvironments associated with one or multiple genes and their associated regulatory regions engaged in active transcription. On the other hand, we postulate that smaller droplets, which tend to be transient (Cho et al., 2018Cho W.-K. Spille J.-H. Hecht M. Lee C. Li C. Grube V. Cisse I.I. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.Science 361. 2018; : 412-415Crossref Scopus (612) Google Scholar), are used as cargos to move molecules from one gene to the next to respond to environmental disturbances. Therefore, in the ecosystem model, large phase-separated clusters are found surrounding active genes and smaller droplets filled with transcriptional resources transit between them. This mode of transportation would be advantageous over random diffusion, as one droplet could transfer the required transcription machinery and coregulators to carry a gene response. Therefore, the physical proximity between genes and the creation of confined environment, combined with mobile but limited transcriptional resources, make the establishment of a transcriptional ecosystem a strong possibility. We are proposing that the association of multiple genes is a prerequisite to maintain an ecosystem equilibrium, providing the ability to quickly adapt to environmental perturbations (Figure 2). In the proposed model, each gene has a transcriptional steady state defining the transcriptional ecosystem equilibrium. When responding to an external signal or disturbance, the status quo will be changed with the activation of one or multiple transcription factors, requiring extra transcription machinery and coregulators to induce specific genes. Concentration of components of the transcription regulators into highly mobile phase separation droplets would allow the transfer between genes found in larger clusters. These small cargos could be physically constrained to sub-nuclear areas, for example, by the chromosome architecture or molecular crowding, to participate in the transcription of a specific group of genes. In absence of a constraining architecture, responses to environmental disturbances could be hampered as cargos would drift from the defined area. Following the transcriptional disturbance, feedback mechanisms will return the system to the steady-state transcriptional program dictated by the core transcription factors (Voss and Hager, 2014Voss T.C. Hager G.L. Dynamic regulation of transcriptional states by chromatin and transcription factors.Nat. Rev. Genet. 2014; 15: 69-81Crossref PubMed Scopus (314) Google Scholar). The existence of a complex transcriptional ecosystem equilibrium therefore forces genes to respond to disturbances with two types of primary effects, direct and indirect, created by the competition for resources. Our model states that, when an acute transcriptional response is solicited, available transcriptional resources are reassigned to new genes, potentially sacrificing other important functions. To some extent, similar mechanisms of action are observed in natural ecosystems. For example, introduction of a predator or invasive species into an ecosystem will lead to direct and indirect competitions for local resources. An important question that follows is where is the additional machinery, which is required to sustain the transcriptional activity, coming from? Although any free or engaged molecules found at genes connected to need-to-be-induced genes could provide transcription machinery and coregulators, we speculate that highly transcribed genes could be used as a reservoir within each ecosystem. Indeed, Pol II accumulates at the promoter of early response genes although its levels decrease at housekeeping genes during stress responses (Cook and O'Shea, 2012Cook K.E. O'Shea E.K. Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae.G3 (Bethesda). 2012; 2: 1129-1136Crossref PubMed Scopus (31) Google Scholar, Vanacloig-Pedros et al., 2015Vanacloig-Pedros E. Bets-Plasencia C. Pascual-Ahuir A. Proft M. Coordinated gene regulation in the initial phase of salt stress adaptation.J. Biol. Chem. 2015; 290: 10163-10175Crossref PubMed Scopus (18) Google Scholar) For example, in yeast, salt stress adaptation is directly linked to a loss of gene expression from highly transcribed genes (Vanacloig-Pedros et al., 2015Vanacloig-Pedros E. Bets-Plasencia C. Pascual-Ahuir A. Proft M. Coordinated gene regulation in the initial phase of salt stress adaptation.J. Biol. Chem. 2015; 290: 10163-10175Crossref PubMed Scopus (18) Google Scholar). In mammalian cells, housekeeping genes are well connected with other cell-type-specific and stress response genes (Rao et al., 2014Rao S.S.P. Huntley M.H. Durand N.C. Stamenova E.K. Bochkov I.D. Robinson J.T. Sanborn A.L. Machol I. Omer A.D. Lander E.S. Aiden E.L. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.Cell. 2014; 159: 1665-1680Abstract Full Text Full Text PDF PubMed Scopus (3598) Google Scholar). Furthermore, housekeeping genes have high RNA copy numbers per cell, long half-lives, and efficient translation (Schwanhäusser et al., 2011Schwanhäusser B. Busse D. Li N. Dittmar G. Schuchhardt J. Wolf J. Chen W. Selbach M. Global quantification of mammalian gene expression control.Nature. 2011; 473: 337-342Crossref PubMed Scopus (4059) Google Scholar), making them resilient to temporary transcriptional slowdown. Another potential reservoir could be provided by transcriptional coregulator-rich regions, which are typically clusters of enhancer regions associated with cell-type-specific genes. This model was suggested by evidence that tumor necrosis factor alpha (TNF-α), through the transcription factor RELA, induced a specific gene response by draining cofactors away from clusters of enhancer regions (Schmidt et al., 2015Schmidt S.F. Larsen B.D. Loft A. Nielsen R. Madsen J.G.S. Mandrup S. Acute TNF-induced repression of cell identity genes is mediated by NFκB-directed redistribution of cofactors from super-enhancers.Genome Res. 2015; 25: 1281-1294Crossref PubMed Scopus (49) Google Scholar). Therefore, we postulate that, within a transcriptional ecosystem, highly transcribed regions are used to buffer the transcriptional resource needs of the ecosystem. Our model proposes that genes are part of complex ecosystems, sharing transcriptional resources. This model is supported by recent observations that genes are found in physical environments created by specific chromosome architectures and the availability of highly mobile transcription machinery and coregulators. The demonstration that these environments are enclosed and filled with a limited number of molecules associated with transcriptional regulation remains to be determined. Furthermore, the traveling of these molecules between genes sharing an environment will need to be validated. The existence of cellular transcriptional ecosystems will modify our interpretation of gene regulation experiments. For example, it should come as no surprise that most transcriptomic studies report that a perturbation leads to genes being increased and decreased in similar proportions. On the contrary, this is the expectation of an equilibrium forced by limited available resources. Deciphering which transcriptional consequences triggered by a disturbance are responsible for the observed phenotype will be a challenge. Obviously, cells have the ability to adapt to prolonged disturbances by increasing the level of limiting transcriptional components. However, this would only force the cell into a new equilibrium.
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