Struggle for survival: new insights into NELF condensation for adaptive transcriptional reprogramming

In this issue of Molecular Cell, Rawat et al., 2021Rawat P. Boehning M. Hummel B. Aprile-Garcia F. Pandit A.S. Eisenhardt N. Khavaran A. Niskanen E. Vos S.M. Palvimo J.J. et al.Stress-induced nuclear condensation of NELF drives transcriptional downregulation.Mol. Cell. 2021; (this issue): 1013-1026Abstract Full Text Full Text PDF Scopus (12) Google Scholar characterize novel stress-induced condensates of the negative elongation factor (NELF) as the nuclear counterparts of cytosolic stress granules. This provides a new perspective on transcription repression orchestrated by phase separation. In this issue of Molecular Cell, Rawat et al., 2021Rawat P. Boehning M. Hummel B. Aprile-Garcia F. Pandit A.S. Eisenhardt N. Khavaran A. Niskanen E. Vos S.M. Palvimo J.J. et al.Stress-induced nuclear condensation of NELF drives transcriptional downregulation.Mol. Cell. 2021; (this issue): 1013-1026Abstract Full Text Full Text PDF Scopus (12) Google Scholar characterize novel stress-induced condensates of the negative elongation factor (NELF) as the nuclear counterparts of cytosolic stress granules. This provides a new perspective on transcription repression orchestrated by phase separation. Suboptimal growth conditions that reduce viability or fitness inflict stresses on cells. Ubiquitous stresses, including heat shock, oxidative stimulation, and toxins, put cells at risk, and rapid adaptation is crucial for cell survival. To this end, cells have evolved sophisticated adaptation mechanisms to produce accurate dynamic outcomes in response to stresses, the most significant of which is the reprogramming of transcription (Joutsen and Sistonen, 2019Joutsen J. Sistonen L. Tailoring of proteostasis networks with heat shock factors.Cold Spring Harb. Perspect. Biol. 2019; 11: a034066Crossref PubMed Scopus (34) Google Scholar). Stress-derived gene expression variations are often accompanied by alterations in intracellular homeostasis, enzyme kinetic activities, cytoskeletal organization, cell-cycle progression, and cellular metabolism (Nadeau and Landry, 2007Nadeau S.I. Landry J. Mechanisms of activation and regulation of the heat shock-sensitive signaling pathways.in: Csermely P. Vígh L. Molecular aspects of the stress response: chaperones, membranes and networks. Springer, 2007: 100-113Crossref Scopus (53) Google Scholar). Adaptive changes in transcription vary in response to different stresses, but they usually include repression of housekeeping genes and induction of cytoprotective genes (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 (86) Google Scholar). The former is achieved, at least in part, at the level of promoter-proximal pausing of RNA polymerase (Pol) II. Along with the opening of chromatin structure, Pol II and general transcription factors (TFs) function as the pre-initiation complex upstream of the transcription start sites (TSSs). Upon transcription of the initial 20–60 nucleotides, Pol II is paused by negative elongation factor (NELF) and DRB sensitivity-inducing factor (DSIF) (Lee et al., 2008Lee C. Li X. Hechmer A. Eisen M. Biggin M.D. Venters B.J. Jiang C. Li J. Pugh B.F. Gilmour D.S. NELF and GAGA factor are linked to promoter-proximal pausing at many genes in Drosophila.Mol. Cell. Biol. 2008; 28: 3290-3300Crossref PubMed Scopus (161) Google Scholar). Under normal conditions, the positive transcription elongation factor (P-TEFb) complex phosphorylates the C-terminal domain (CTD) of Pol II, NELF, and DSIF, resulting in the dissociation of NELF from the chromatin while DSIF switches to a positive elongation factor that promotes the transcriptional elongation by Pol II (Bugai et al., 2019Bugai A. Quaresma A.J.C. Friedel C.C. Lenasi T. Düster R. Sibley C.R. Fujinaga K. Kukanja P. Hennig T. Blasius M. P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress.Mol. Cell. 2019; 74: 254-267.e210Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar). Under stressful conditions, Pol II is tightly associated with the components that retain it in a paused state, which leads to its increased accumulation in the TSS and its clearance from gene bodies. Specifically, the enhanced binding of NELF to the promoters of repressed genes under heat shock results in the exit of Pol II from gene bodies (Aprile-Garcia et al., 2019Aprile-Garcia F. Tomar P. Hummel B. Khavaran A. Sawarkar R. Nascent-protein ubiquitination is required for heat shock-induced gene downregulation in human cells.Nat. Struct. Mol. Biol. 2019; 26: 137-146Crossref PubMed Scopus (17) Google Scholar). Taken together, previous studies show how the dynamic gene expression alterations that occur in response to stress are primarily dependent on the pause-release state of Pol II (Aprile-Garcia et al., 2019Aprile-Garcia F. Tomar P. Hummel B. Khavaran A. Sawarkar R. Nascent-protein ubiquitination is required for heat shock-induced gene downregulation in human cells.Nat. Struct. Mol. Biol. 2019; 26: 137-146Crossref PubMed Scopus (17) Google Scholar). Accumulating evidence suggests that NELF, as one of the key regulators during promoter-proximal pausing, resides at downregulated gene promoters during the stress response. Nonetheless, the detailed molecular mechanisms of stress-induced repression are still poorly understood. In this case, Rawat et al., 2021Rawat P. Boehning M. Hummel B. Aprile-Garcia F. Pandit A.S. Eisenhardt N. Khavaran A. Niskanen E. Vos S.M. Palvimo J.J. et al.Stress-induced nuclear condensation of NELF drives transcriptional downregulation.Mol. Cell. 2021; (this issue): 1013-1026Abstract Full Text Full Text PDF Scopus (12) Google Scholar have laid out the evidence for a novel mechanism for coping with stress. While doing so, the authors neatly rationalized the previous observations. Specifically, NELF undergoes phase separation to form condensates in stressed cells. Upon stress onset, condensation facilitates enhanced recruitment of NELF to promoters for transcriptional downregulation. The phase separation is regulated by stress-triggered SUMOylation and dephosphorylation of NELF. With careful dissection, the authors showed that the intrinsically disordered region (IDR) in NELFA, one of four subunits of NELF, is necessary for NELF condensation. Importantly, by a strategy of deleting the endogenous IDR and grafting with heterologous ones, it was nearly unambiguously demonstrated that the phase separation property of NELF is required for its transcriptional repression activity. Although not adequately addressed in the study, it seems likely that the SUMO interaction motif (SIM) in NELF may be involved in multivalent SIM-SUMO interactions between modular domains, which would facilitate phase separation of NELF under stress conditions. Also, importantly, NELF condensation is required for cellular viability under stressful conditions. Rawat et al., 2021Rawat P. Boehning M. Hummel B. Aprile-Garcia F. Pandit A.S. Eisenhardt N. Khavaran A. Niskanen E. Vos S.M. Palvimo J.J. et al.Stress-induced nuclear condensation of NELF drives transcriptional downregulation.Mol. Cell. 2021; (this issue): 1013-1026Abstract Full Text Full Text PDF Scopus (12) Google Scholar suggest that the nuclear NELF condensates can be considered as counterparts of cytosolic stress granules. NELF condensates achieve decreased Pol II elongation and hence transcriptional downregulation of housekeeping genes. More work is needed for a more comprehensive investigation of the functional importance of NELF condensation. Along this line, many important questions remain to be addressed. NELF-E is an RNA-binding protein essential for NELF complex function. What is the role of RNA in regulating NELF condensation? What percentage of downregulated genes in stressed cells are targeted by NELF condensation? In other words, is NELF condensation a global stress-responsive transcription repression mechanism, or does it facilitate transcriptional reprogramming in response to specific types of stress? Are any other nuclear condensation events involved in transcriptional reprogramming under stress? In conclusion, Rawat et al., 2021Rawat P. Boehning M. Hummel B. Aprile-Garcia F. Pandit A.S. Eisenhardt N. Khavaran A. Niskanen E. Vos S.M. Palvimo J.J. et al.Stress-induced nuclear condensation of NELF drives transcriptional downregulation.Mol. Cell. 2021; (this issue): 1013-1026Abstract Full Text Full Text PDF Scopus (12) Google Scholar took an inventive approach to delineate how stress leads to the sophisticated control of NELF on downregulated gene promoters. Their work provides a novel framework for studying and characterizing the cellular stress response beyond cytosolic stress granules. Accumulating evidence demonstrates that biomolecular condensates are bona fide macromolecular factories that can trigger gene transcription, buffer gene expression noise, or establish genome compartmentalization. A number of transcription condensates are induced by environmental factors like temperature, osmotic stress, and hypoxic shock, represented by EARLY FLOWERING 3 (ELF3) (Jung et al., 2020Jung J.-H. Barbosa A.D. Hutin S. Kumita J.R. Gao M. Derwort D. Silva C.S. Lai X. Pierre E. Geng F. et al.A prion-like domain in ELF3 functions as a thermosensor in Arabidopsis.Nature. 2020; 585: 256-260Crossref PubMed Scopus (78) Google Scholar), Yes-associated protein (YAP) (Cai et al., 2019Cai D. Feliciano D. Dong P. Flores E. Gruebele M. Porat-Shliom N. Sukenik S. Liu Z. Lippincott-Schwartz J. Phase separation of YAP reorganizes genome topology for long-term YAP target gene expression.Nat. Cell Biol. 2019; 21: 1578-1589Crossref PubMed Scopus (89) Google Scholar), and Tetrachlorodibenzo-p-dioxin (TCDD)-inducible poly(ADP-ribose) polymerase (TiPARP) (Zhang et al., 2020Zhang L. Cao J. Dong L. Lin H. TiPARP forms nuclear condensates to degrade HIF-1a and suppress tumorigenesis.Proc. Natl. Acad. Sci. USA. 2020; 117: 13447-13456Crossref PubMed Scopus (18) Google Scholar), respectively (Figure 1). Regulated biomolecular phase separation and condensate formation are likely widely used as cellular mechanisms due to their ability to respond quickly and adapt to fluctuating environments. More examples are expected in the near future. Furthermore, since phase separation of chromatin-binding proteins facilitates long-distance interactions between different regions of the genome, which leads to the formation of chromatin subcompartments, this work is intriguing and timely given the research enthusiasm surrounding genome-wide and stress-specific transcriptional programming in response to different types of stresses. Integrating knowledge about phase separation with transcriptional regulation will be an exciting area for future investigation. This work was supported by grants from the National Key Research and Development Program ( 2019YFA0508403 to P.L.) and the National Natural Science Foundation of China ( 31871443 to P.L.). The authors declare no competing interests. P.L. is a member of the advisory board of Molecular Cell. Stress-induced nuclear condensation of NELF drives transcriptional downregulationRawat et al.Molecular CellFebruary 5, 2021In BriefRawat et al. discovered stress-induced condensation of the transcriptional regulator NELF in human cells, recapitulated by phase separation of recombinant NELF in vitro. NELF condensation is governed by its disordered tentacles and stress-contingent changes in NELF phosphorylation and SUMOylation. NELF condensation facilitates stress-mediated transcriptional downregulation, supporting cell survival upon stress. Full-Text PDF Open Access