A partially disordered region connects gene repression and activation functions of EZH2

Jiao, Lianying; Shubbar, Murtada; Yang, Xin; Zhang, Qi; Chen, Siming; Wu, Qiong; Chen, Zhe; Rizo, Josep; Liu, Xin

doi:10.1073/pnas.1914866117

Title: A partially disordered region connects gene repression and activation functions of EZH2

Journal Article · Mon Jul 06 00:00:00 EDT 2020 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1914866117· OSTI ID:1642238

^[1]; Shubbar, Murtada ^[1];

^[1];

^[1]; Chen, Siming ^[1]; Wu, Qiong ^[1]; Chen, Zhe ^[1]; Rizo, Josep ^[1]; Liu, Xin ^[1]

Univ. of Texas Southwestern Medical Center, Dallas, TX (United States)

Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressive Complex 2 (PRC2), which minimally requires two other subunits, EED and SUZ12, for enzymatic activity. EZH2 has been traditionally known to mediate histone H3K27 trimethylation, a hallmark of silent chromatin. Emerging evidence indicates that EZH2 also activates gene expression in cancer cells in a context distinct from canonical PRC2. The molecular mechanism underlying the functional conversion of EZH2 from a gene repressor to an activator is unclear. In this work, we show that EZH2 harbors a hidden, partially disordered transactivation domain (TAD) capable of interacting with components of active transcription machinery, mimicking archetypal acidic activators. The EZH2 TAD comprises the SRM (Stimulation-Responsive Motif) and SANT1 (SWI3, ADA2, N-CoR, and TFIIIB 1) regions that are normally involved in H3K27 methylation. The crystal structure of an EZH2–EED binary complex indicates that the EZH2 TAD mediates protein oligomerization in a noncanonical PRC2 context and is entirely sequestered. The EZH2 TAD can be unlocked by cancer-specific EZH2 phosphorylation events to undergo structural transitions that may enable subsequent transcriptional coactivator binding. The EZH2 TAD directly interacts with the transcriptional coactivator and histone acetyltransferase p300 and activates gene expression in a p300-dependent manner in cells. The corresponding TAD may also account for the gene activation function of EZH1, the paralog of EZH2. Distinct kinase signaling pathways that are known to abnormally convert EZH2 into a gene activator in cancer cells can now be understood in a common structural context of the EZH2 TAD.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Sponsoring Organization:: Welch Foundation; Cancer Prevention and Research Institute of Texas (CPRIT); Rita Allen Foundation; UT Southwestern Medical Center Endowed Scholar; American Heart Association (AHA); Cecil H. and Ida Green Center Training Program in Reproductive Biology Sciences Research; USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Institute of General Medical Sciences (NIGMS)

Grant/Contract Number:: I-1790; I-1304; R1119; GM114576; GM121662; GM136308; AC02-06CH11357; AC02-05CH11231; AC02-76SF00515; P30 GM124169-01, ALS-ENABLE

OSTI ID:: 1642238

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 117, Issue 29; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

Citation Metrics:

Cited by: 24 works

Citation information provided by
Web of Science

References (55)

EZH2 expands breast stem cells through activation of NOTCH1 signaling Gonzalez, M. E.; Moore, H. M.; Li, X. Proceedings of the National Academy of Sciences, Vol. 111, Issue 8 https://doi.org/10.1073/pnas.1308953111	journal	February 2014
Akt-Mediated Phosphorylation of EZH2 Suppresses Methylation of Lysine 27 in Histone H3 Cha, T. -L. Science, Vol. 310, Issue 5746 https://doi.org/10.1126/science.1118947	journal	October 2005
Refinement of Macromolecular Structures by the Maximum-Likelihood Method Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3 https://doi.org/10.1107/S0907444996012255	journal	May 1997
Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance Brooun, Alexei; Gajiwala, Ketan S.; Deng, Ya-Li Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11384	journal	April 2016
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator Kim, Jung; Lee, Yongik; Lu, Xiaodong Cell Reports, Vol. 25, Issue 10 https://doi.org/10.1016/j.celrep.2018.11.035	journal	December 2018
Estimation of protein secondary structure and error analysis from circular dichroism spectra van Stokkum, Ivo H. M.; Spoelder, Hans J. W.; Bloemendal, Michael Analytical Biochemistry, Vol. 191, Issue 1, p. 110-118 https://doi.org/10.1016/0003-2697(90)90396-Q	journal	November 1990
Synergistic activation of transcription by CBP and p53 Gu, Wei; Shi, Xiao-Lu; Roeder, Robert G. Nature, Vol. 387, Issue 6635 https://doi.org/10.1038/42972	journal	June 1997
PRIMUS: a Windows PC-based system for small-angle scattering data analysis Konarev, Petr V.; Volkov, Vladimir V.; Sokolova, Anna V. Journal of Applied Crystallography, Vol. 36, Issue 5, p. 1277-1282 https://doi.org/10.1107/S0021889803012779	journal	September 2003
Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions Xu, Jian; Shao, Zhen; Li, Dan Molecular Cell, Vol. 57, Issue 2 https://doi.org/10.1016/j.molcel.2014.12.009	journal	January 2015
Intrinsically disordered proteins in cellular signalling and regulation Wright, Peter E.; Dyson, H. Jane Nature Reviews Molecular Cell Biology, Vol. 16, Issue 1 https://doi.org/10.1038/nrm3920	journal	December 2014
Intrinsically unstructured proteins and their functions Dyson, H. Jane; Wright, Peter E. Nature Reviews Molecular Cell Biology, Vol. 6, Issue 3 https://doi.org/10.1038/nrm1589	journal	March 2005
Binding Interactions between Long Noncoding RNA HOTAIR and PRC2 Proteins Wu, Liang; Murat, Pierre; Matak-Vinkovic, Dijana Biochemistry, Vol. 52, Issue 52 https://doi.org/10.1021/bi401085h	journal	December 2013
Induced Helix in the VP16 Activation Domain upon Binding to a Human TAF Uesugi, M. Science, Vol. 277, Issue 5330 https://doi.org/10.1126/science.277.5330.1310	journal	August 1997
EZH2 overexpression in natural killer/T-cell lymphoma confers growth advantage independently of histone methyltransferase activity Yan, Junli; Ng, Siok-Bian; Tay, Jim Liang-Seah Blood, Vol. 121, Issue 22 https://doi.org/10.1182/blood-2012-08-450494	journal	May 2013
PAF and EZH2 Induce Wnt/β-Catenin Signaling Hyperactivation Jung, Hae-Yun; Jun, Sohee; Lee, Moonsup Molecular Cell, Vol. 52, Issue 2 https://doi.org/10.1016/j.molcel.2013.08.028	journal	October 2013
High-Precision Isothermal Titration Calorimetry with Automated Peak-Shape Analysis Keller, Sandro; Vargas, Carolyn; Zhao, Huaying Analytical Chemistry, Vol. 84, Issue 11 https://doi.org/10.1021/ac3007522	journal	June 2012
Dignam and Roeder Nuclear Extract Preparation Carey, M. F.; Peterson, C. L.; Smale, S. T. Cold Spring Harbor Protocols, Vol. 2009, Issue 12 https://doi.org/10.1101/pdb.prot5330	journal	December 2009
Phosphorylation of EZH2 Activates STAT3 Signaling via STAT3 Methylation and Promotes Tumorigenicity of Glioblastoma Stem-like Cells Kim, Eunhee; Kim, Misuk; Woo, Dong-Hun Cancer Cell, Vol. 23, Issue 6 https://doi.org/10.1016/j.ccr.2013.04.008	journal	June 2013
Ezh1 and Ezh2 Maintain Repressive Chromatin through Different Mechanisms Margueron, Raphael; Li, Guohong; Sarma, Kavitha Molecular Cell, Vol. 32, Issue 4 https://doi.org/10.1016/j.molcel.2008.11.004	journal	November 2008
Recognition of the disordered p53 transactivation domain by the transcriptional adapter zinc finger domains of CREB-binding protein Krois, Alexander S.; Ferreon, Josephine C.; Martinez-Yamout, Maria A. Proceedings of the National Academy of Sciences, Vol. 113, Issue 13 https://doi.org/10.1073/pnas.1602487113	journal	March 2016
Chemical shift dispersion and secondary structure prediction in unfolded and partly folded proteins Yao, Jian; Dyson, H. Jane; Wright, Peter E. FEBS Letters, Vol. 419, Issue 2-3 https://doi.org/10.1016/S0014-5793(97)01474-9	journal	December 1997
Conserved RNA-binding specificity of polycomb repressive complex 2 is achieved by dispersed amino acid patches in EZH2 Long, Yicheng; Bolanos, Ben; Gong, Lihu eLife, Vol. 6 https://doi.org/10.7554/eLife.31558	journal	November 2017
TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation Li, J.; Xi, Y.; Li, W. Oncogene, Vol. 36, Issue 21 https://doi.org/10.1038/onc.2016.453	journal	January 2017
Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours Lasko, Loren M.; Jakob, Clarissa G.; Edalji, Rohinton P. Nature, Vol. 550, Issue 7674 https://doi.org/10.1038/nature24028	journal	September 2017
Mutational analysis of a transcriptional activation region of the VP16 protein of herpes simplex virus [published erratum appears in Nucleic Acids Res 1998 Dec 1;26(23):537-8] Sullivan, S. Nucleic Acids Research, Vol. 26, Issue 19 https://doi.org/10.1093/nar/26.19.4487	journal	October 1998
Regulation of embryonic haematopoietic multipotency by EZH1 Vo, Linda T.; Kinney, Melissa A.; Liu, Xin Nature, Vol. 553, Issue 7689 https://doi.org/10.1038/nature25435	journal	January 2018
Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2 Jiao, L.; Liu, X. Science, Vol. 350, Issue 6258 https://doi.org/10.1126/science.aac4383	journal	October 2015
Estimation of Protein Secondary Structure from Circular Dichroism Spectra: Comparison of CONTIN, SELCON, and CDSSTR Methods with an Expanded Reference Set Sreerama, Narasimha; Woody, Robert W. Analytical Biochemistry, Vol. 287, Issue 2, p. 252-260 https://doi.org/10.1006/abio.2000.4880	journal	December 2000
Recruitment of p300/CBP in p53-Dependent Signal Pathways Avantaggiati, Maria Laura; Ogryzko, Vasily; Gardner, Kevin Cell, Vol. 89, Issue 7 https://doi.org/10.1016/S0092-8674(00)80304-9	journal	June 1997
Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: Application to adaptor protein complexes in cell signaling Houtman, Jon C. D.; Brown, Patrick H.; Bowden, Brent Protein Science, Vol. 16, Issue 1 https://doi.org/10.1110/ps.062558507	journal	January 2007
A model for transmission of the H3K27me3 epigenetic mark Hansen, Klaus H.; Bracken, Adrian P.; Pasini, Diego Nature Cell Biology, Vol. 10, Issue 11 https://doi.org/10.1038/ncb1787	journal	October 2008
EZH2 Oncogenic Activity in Castration-Resistant Prostate Cancer Cells Is Polycomb-Independent Xu, K.; Wu, Z. J.; Groner, A. C. Science, Vol. 338, Issue 6113 https://doi.org/10.1126/science.1227604	journal	December 2012
Integration of Estrogen and Wnt Signaling Circuits by the Polycomb Group Protein EZH2 in Breast Cancer Cells Shi, Bin; Liang, Jing; Yang, Xiaohan Molecular and Cellular Biology, Vol. 27, Issue 14 https://doi.org/10.1128/MCB.00162-07	journal	May 2007
Four domains of p300 each bind tightly to a sequence spanning both transactivation subdomains of p53 Teufel, D. P.; Freund, S. M.; Bycroft, M. Proceedings of the National Academy of Sciences, Vol. 104, Issue 17 https://doi.org/10.1073/pnas.0702010104	journal	April 2007
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source Classen, Scott; Hura, Greg L.; Holton, James M. Journal of Applied Crystallography, Vol. 46, Issue 1 https://doi.org/10.1107/S0021889812048698	journal	January 2013
RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2 Zhang, Qi; McKenzie, Nicholas J.; Warneford-Thomson, Robert Nature Structural & Molecular Biology, Vol. 26, Issue 3 https://doi.org/10.1038/s41594-019-0197-y	journal	March 2019
Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes Poepsel, Simon; Kasinath, Vignesh; Nogales, Eva Nature Structural & Molecular Biology, Vol. 25, Issue 2 https://doi.org/10.1038/s41594-018-0023-y	journal	January 2018
DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data Whitmore, L.; Wallace, B. A. Nucleic Acids Research, Vol. 32, Issue S2, p. W668-W673 https://doi.org/10.1093/nar/gkh371	journal	July 2004
Polycomb Protein Ezh1 Promotes RNA Polymerase II Elongation Mousavi, Kambiz; Zare, Hossein; Wang, A. Hongjun Molecular Cell, Vol. 45, Issue 2 https://doi.org/10.1016/j.molcel.2011.11.019	journal	January 2012
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Structural Basis of EZH2 Recognition by EED Han, Zhifu; Xing, Xinmiao; Hu, Min Structure, Vol. 15, Issue 10 https://doi.org/10.1016/j.str.2007.08.007	journal	October 2007
The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail Weaver, Tyler M.; Liu, Jiachen; Connelly, Katelyn E. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-018-37699-w	journal	January 2019
Estimation of globular protein secondary structure from circular dichroism Provencher, Stephen W.; Gloeckner, Juergen Biochemistry, Vol. 20, Issue 1, p. 33-37 https://doi.org/10.1021/bi00504a006	journal	January 1981
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
Genome Regulation by Polycomb and Trithorax: 70 Years and Counting Schuettengruber, Bernd; Bourbon, Henri-Marc; Di Croce, Luciano Cell, Vol. 171, Issue 1 https://doi.org/10.1016/j.cell.2017.08.002	journal	September 2017
EZH2 phosphorylation by JAK3 mediates a switch to noncanonical function in natural killer/T-cell lymphoma Yan, Junli; Li, Boheng; Lin, Baohong Blood, Vol. 128, Issue 7 https://doi.org/10.1182/blood-2016-01-690701	journal	August 2016
A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins Kikhney, Alexey G.; Svergun, Dmitri I. FEBS Letters, Vol. 589, Issue 19PartA https://doi.org/10.1016/j.febslet.2015.08.027	journal	August 2015
SUZ12 Is Required for Both the Histone Methyltransferase Activity and the Silencing Function of the EED-EZH2 Complex Cao, Ru; Zhang, Yi Molecular Cell, Vol. 15, Issue 1 https://doi.org/10.1016/j.molcel.2004.06.020	journal	July 2004
Structural basis of oncogenic histone H3K27M inhibition of human polycomb repressive complex 2 Justin, Neil; Zhang, Ying; Tarricone, Cataldo Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11316	journal	April 2016
Targeting EZH2 in cancer Kim, Kimberly H.; Roberts, Charles W. M. Nature Medicine, Vol. 22, Issue 2 https://doi.org/10.1038/nm.4036	journal	February 2016
Context-Specific Regulation of NF-κB Target Gene Expression by EZH2 in Breast Cancers Lee, Shuet Theng; Li, Zhimei; Wu, Zhenlong Molecular Cell, Vol. 43, Issue 5 https://doi.org/10.1016/j.molcel.2011.08.011	journal	September 2011
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Acetylation of Estrogen Receptor α by p300 at Lysines 266 and 268 Enhances the Deoxyribonucleic Acid Binding and Transactivation Activities of the Receptor Kim, Mi Young; Woo, Eileen M.; Chong, Yee Ting Esther Molecular Endocrinology, Vol. 20, Issue 7 https://doi.org/10.1210/me.2005-0531	journal	July 2006

Similar Records

An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors

Journal Article · Thu Jun 14 00:00:00 EDT 2018 · Scientific Reports · OSTI ID:1642238

Bratkowski, Matthew; Yang, Xin; Liu, Xin

Characterization of histone H3K27 modifications in the {beta}-globin locus

Journal Article · Fri Feb 11 00:00:00 EST 2011 · Biochemical and Biophysical Research Communications · OSTI ID:1642238

Kim, Yea Woon; Kim, AeRi

microRNA-124a suppresses PHF19 over-expression, EZH2 hyper-activation, and aberrant cell proliferation in human glioma

Journal Article · Sat Sep 15 00:00:00 EDT 2018 · Biochemical and Biophysical Research Communications · OSTI ID:1642238

Lu, Jian; Ji, Hongming; Tang, Huoquan; +1 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
EZH2
gene activation
transcriptional activation domain
phosphorylation
p300

Title: A partially disordered region connects gene repression and activation functions of EZH2

Citation Formats

References (55)

Similar Records

Related Subjects