Unveiling E2F4, TEAD1 and AP-1 as regulatory transcription factors of the replicative senescence program by multi-omics analysis

doi:10.1007/s13238-021-00894-z

Protein Cell

2022, Vol. 13

Issue (10) : 742-759 https://doi.org/10.1007/s13238-021-00894-z

RESEARCH ARTICLE

Unveiling E2F4, TEAD1 and AP-1 as regulatory transcription factors of the replicative senescence program by multi-omics analysis

Yuting Wang¹, Liping Liu¹, Yifan Song², Xiaojie Yu², Hongkui Deng^1,^2,³(

)

¹. School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
². The MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
³. State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China

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Abstract

Senescence, a stable state of growth arrest, affects many physiological and pathophysiological processes, especially aging. Previous work has indicated that transcription factors (TFs) play a role in regulating senescence. However, a systematic study of regulatory TFs during replicative senescence (RS) using multi-omics analysis is still lacking. Here, we generated time-resolved RNA-seq, reduced representation bisulfite sequencing (RRBS) and ATAC-seq datasets during RS of mouse skin fibroblasts, which demonstrated that an enhanced inflammatory response and reduced proliferative capacity were the main characteristics of RS in both the transcriptome and epigenome. Through integrative analysis and genetic manipulations, we found that transcription factors E2F4, TEAD1 and AP-1 are key regulators of RS. Overexpression of E2f4 improved cellular proliferative capacity, attenuated SA-β-Gal activity and changed RS-associated differentially methylated sites (DMSs). Moreover, knockdown of Tead1 attenuated SA-β-Gal activity and partially altered the RS-associated transcriptome. In addition, knock-down of Atf3, one member of AP-1 superfamily TFs, reduced Cdkn2a (p16) expression in pre-senescent fibroblasts. Taken together, the results of this study identified transcription factors regulating the senescence program through multi-omics analysis, providing potential therapeutic targets for anti-aging.

Keywords transcription factor senescence multi-omics

Corresponding Author(s): Hongkui Deng

About author:

Tongcan Cui and Yizhe Hou contributed equally to this work.

Online First Date: 01 March 2022 Issue Date: 16 August 2022

Cite this article:

Yuting Wang,Liping Liu,Yifan Song, et al. Unveiling E2F4, TEAD1 and AP-1 as regulatory transcription factors of the replicative senescence program by multi-omics analysis[J]. Protein Cell, 2022, 13(10): 742-759.

URL:

https://academic.hep.com.cn/pac/EN/10.1007/s13238-021-00894-z
https://academic.hep.com.cn/pac/EN/Y2022/V13/I10/742

1	RA Avelar, JG Ortega, R Tacutu, EJ Tyler, D Bennett, P Binetti, A Budovsky, K Chatsirisupachai, E Johnson, A Murray et al (2020) A multidimensional systems biology analysis of cellular senescence in aging and disease. Genome Biol 21: 91 https://doi.org/10.1186/s13059-020-01990-9
2	DJ Baker, BG Childs, M Durik, ME Wijers, CJ Sieben, J Zhong, RA Saltness, KB Jeganathan, GC Verzosa, A Pezeshki et al (2016) Naturally occurring p16(Ink4a)-positive cells shorten healthy lifespan. Nature 530: 184- 189 https://doi.org/10.1038/nature16932
3	I Berest, C Arnold, A Reyes-Palomares, G Palla, KD Rasmussen, H Giles, PM Bruch, W Huber, S Dietrich, K Helin et al (2020) Quantification of differential transcription factor activity and multiomics-based classification into activators and repressors:diffTF. Cell Rep 29: 3147- 3159.e3112 https://doi.org/10.1016/j.celrep.2019.10.106
4	JD Buenrostro, B Wu, HY Chang, WJ Greenleaf (2015) ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 109: 21.29.21- 21.29.29 https://doi.org/10.1002/0471142727.mb2129s109
5	Y Cai, H Zhou, Y Zhu, Q Sun, Y Ji, A Xue, Y Wang, W Chen, X Yu, L Wang et al (2020) Elimination of senescent cells by β-galactosidase-targeted prodrug attenuates inflammation and restores physical function in aged mice. Cell Res 30: 574- 589 https://doi.org/10.1038/s41422-020-0314-9
6	M Chan, H Yuan, I Soifer, TM Maile, RY Wang, A Ireland, J O’Brien, L Chan, T Vijay et al (2021) Revisiting the hayflick limit: insights from an integrated analysis of changing transcripts, proteins, metabolites and chromatin. bioRxiv.
7	G Collin, A Huna, M Warnier, JM Flaman, D Bernard (2018) Transcriptional repression of DNA repair genes is a hallmark and a cause of cellular senescence. Cell Death Dis 9: 259 https://doi.org/10.1038/s41419-018-0300-z
8	AR Colombo, HK Elias, G Ramsingh (2018) Senescence induction universally activates transposable element expression. Cell Cycle 17: 1846- 1857 https://doi.org/10.1080/15384101.2018.1502576
9	JP Coppé, CK Patil, F Rodier, Y Sun, DP Muñoz, J Goldstein, PS Nelson, PY Desprez, J Campisi (2008) Senescence-associated secretory phenotypes reveal cell-nonautonomous functions of oncogenic RAS and the p53 tumor suppressor. PLoS Biol 6: 2853- 2868
10	MR Corces, AE Trevino, EG Hamilton, PG Greenside, NA Sinnott-Armstrong, S Vesuna, AT Satpathy, AJ Rubin, KS Montine, B Wu et al (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14: 959- 962 https://doi.org/10.1038/nmeth.4396
11	M De Cecco, T Ito, AP Petrashen, AE Elias, NJ Skvir, SW Criscione, A Caligiana, G Brocculi, EM Adney, JD Boeke et al (2019) L1 drives IFN in senescent cells and promotes age-associated inflammation. Nature 566: 73- 78 https://doi.org/10.1038/s41586-018-0784-9
12	M Eren, AE Boe, EA Klyachko, DE Vaughan (2014) Role of plasminogen activator inhibitor-1 in senescence and aging. Semin Thromb Hemost 40: 645- 651 https://doi.org/10.1055/s-0034-1387883
13	H Feng, KN Conneely, H Wu (2014) A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res 42: e69 https://doi.org/10.1093/nar/gku154
14	H Garneau, MC Paquin, JC Carrier, N Rivard (2009) E2F4 expression is required for cell cycle progression of normal intestinal crypt cells and colorectal cancer cells. J Cell Physiol 221: 350- 358 https://doi.org/10.1002/jcp.21859
15	Y Guan, C Zhang, G Lyu, X Huang, X Zhang, T Zhuang, L Jia, L Zhang, C Zhang, C Li et al (2020) Senescence-activated enhancer landscape orchestrates the senescence-associated secretory phenotype in murine fibroblasts. Nucleic Acids Res 48: 10909- 10923 https://doi.org/10.1093/nar/gkaa858
16	S Hänzelmann, F Beier, EG Gusmao, CM Koch, S Hummel, I Charapitsa, S Joussen, V Benes, TH Brümmendorf, G Reid et al (2015) Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites. Clin Epigenet 7: 19 https://doi.org/10.1186/s13148-015-0057-5
17	A Hernandez-Segura, J Nehme, M Demaria (2018) Hallmarks of cellular senescence. Trends Cell Biol 28: 436- 453 https://doi.org/10.1016/j.tcb.2018.02.001
18	I Hernando-Herraez, B Evano, T Stubbs, PH Commere, M Jan Bonder, S Clark, S Andrews, S Tajbakhsh, W Reik (2019) Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells. Nat Commun 10: 4361 https://doi.org/10.1038/s41467-019-12293-4
19	J Hsu, J Sage (2016) Novel functions for the transcription factor E2F4 in development and disease. Cell Cycle 15: 3183- 3190 https://doi.org/10.1080/15384101.2016.1234551
20	J Hsu, J Arand, A Chaikovsky, NA Mooney, J Demeter, CM Brison, R Oliverio, H Vogel, SM Rubin, PK Jackson et al (2019) E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family. Nat Commun 10: 2939 https://doi.org/10.1038/s41467-019-10901-x
21	PO Humbert, C Rogers, S Ganiatsas, RL Landsberg, JM Trimarchi, S Dandapani, C Brugnara, S Erdman, M Schrenzel, RT Bronson et al (2000) E2F4 is essential for normal erythrocyte maturation and neonatal viability. Mol Cell 6: 281- 291 https://doi.org/10.1016/S1097-2765(00)00029-0
22	M Iwafuchi-Doi, KS Zaret (2014) Pioneer transcription factors in cell reprogramming. Genes Dev 28: 2679- 2692 https://doi.org/10.1101/gad.253443.114
23	Z Ji, L He, A Regev, K Struhl (2019) Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers. Proc Natl Acad Sci USA 116: 9453- 9462 https://doi.org/10.1073/pnas.1821068116
24	J Joung, S Konermann, JS Gootenberg, OO Abudayyeh, RJ Platt, MD Brigham, NE Sanjana, F Zhang (2017) Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc 12: 828- 863 https://doi.org/10.1038/nprot.2017.016
25	KJ Kurppa, Y Liu, C To, T Zhang, M Fan, A Vajdi, EH Knelson, Y Xie, K Lim, P Cejas et al (2020) Treatment-induced tumor dormancy through YAP-mediated transcriptional reprogramming of the apoptotic pathway. Cancer Cell 37: 104- 122 https://doi.org/10.1016/j.ccell.2019.12.006
26	Z Li, MH Schulz, T Look, M Begemann, M Zenke, IG Costa (2019) Identification of transcription factor binding sites using ATACseq. Genome Biol 20: 45 https://doi.org/10.1186/s13059-019-1642-2
27	K Maehara, K Yamakoshi, N Ohtani, Y Kubo, A Takahashi, S Arase, N Jones, E Hara (2005) Reduction of total E2F/DP activity induces senescence-like cell cycle arrest in cancer cells lacking functional pRB and p53. J Cell Biol 168: 553- 560 https://doi.org/10.1083/jcb.200411093
28	S Marquard, S Thomann, SME Weiler, M Bissinger, T Lutz, C Sticht, M Tóth, C de la Torre, N Gretz, BK Straub et al (2020) Yesassociated protein (YAP) induces a secretome phenotype and transcriptionally regulates plasminogen activator Inhibitor-1 (PAI-1) expression in hepatocarcinogenesis. Cell Commun Signal 18: 166 https://doi.org/10.1186/s12964-020-00634-6
29	P Marti, C Stein, T Blumer, Y Abraham, MT Dill, M Pikiolek, V Orsini, G Jurisic, P Megel, Z Makowska et al (2015) YAP promotes proliferation, chemoresistance, and angiogenesis in human cholangiocarcinoma through TEAD transcription factors. Hepatology 62: 1497- 1510 https://doi.org/10.1002/hep.27992
30	RI Martínez-Zamudio, PF Roux, J de Freitas, L Robinson, G Doré, B Sun, D Belenki, M Milanovic, U Herbig, CA Schmitt et al (2020) AP-1 imprints a reversible transcriptional programme of senescent cells. Nat Cell Biol 22: 842- 855 https://doi.org/10.1038/s41556-020-0529-5
31	C Minteer, M Morselli, M Meer, J Cao, S Lang, M Pellegrini, Q Yan, M Levine (2020) A DNAmRep epigenetic fingerprint for determining cellular replication age. bioRxiv
32	DM Nelson, T McBryan, JC Jeyapalan, JM Sedivy, PD Adams (2014) A comparison of oncogene-induced senescence and replicative senescence: implications for tumor suppression and aging. Age 36: 9637 https://doi.org/10.1007/s11357-014-9637-0
33	L Potocki, E Kuna, K Filip, B Kasprzyk, A Lewinska, M Wnuk (2019) Activation of transposable elements and genetic instability during long-term culture of the human fungal pathogen Candida albicans. Biogerontology 20: 457- 474 https://doi.org/10.1007/s10522-019-09809-2
34	M Purcell, A Kruger, MA Tainsky (2014) Gene expression profiling of replicative and induced senescence. Cell Cycle 13: 3927- 3937 https://doi.org/10.4161/15384101.2014.973327
35	K Qu, LC Zaba, AT Satpathy, PG Giresi, R Li, Y Jin, R Armstrong, C Jin, N Schmitt, Z Rahbar et al (2017) Chromatin accessibility landscape of cutaneous T cell lymphoma and dynamic response to HDAC inhibitors. Cancer Cell 32: 27- 41 https://doi.org/10.1016/j.ccell.2017.05.008
36	R Sanokawa-Akakura, S Akakura, EA Ostrakhovitch, S Tabibzadeh (2019) Replicative senescence is distinguishable from DNA damage-induced senescence by increased methylation of promoter of rDNA and reduced expression of rRNA. Mech Ageing Dev 183: 111149 https://doi.org/10.1016/j.mad.2019.111149
37	E Shaulian, M Karin (2002) AP-1 as a regulator of cell life and death. Nat Cell Biol 4: E131- 136 https://doi.org/10.1038/ncb0502-e131
38	RI Sherwood, T Hashimoto, CW O’Donnell, S Lewis, AA Barkal, JP van Hoff, V Karun, T Jaakkola, DK Gifford (2014) Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nat Biotechnol 32: 171- 178 https://doi.org/10.1038/nbt.2798
39	F Spitz, EE Furlong (2012) Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13: 613- 626 https://doi.org/10.1038/nrg3207
40	Ö Uluçkan, J Guinea-Viniegra, M Jimenez, EF Wagner (2015) Signalling in inflammatory skin disease by AP-1 (Fos/Jun). Clin Exp Rheumatol 33: S44- 49
41	JM van Deursen (2014) The role of senescent cells in ageing. Nature 509: 439- 446 https://doi.org/10.1038/nature13193
42	DE Vaughan, R Rai, SS Khan, M Eren, AK Ghosh (2017) Plasminogen activator inhibitor-1 is a marker and a mediator of senescence. Arterioscler Thromb Vasc Biol 37: 1446- 1452 https://doi.org/10.1161/ATVBAHA.117.309451
43	W Wagner, S Bork, P Horn, D Krunic, T Walenda, A Diehlmann, V Benes, J Blake, FX Huber, V Eckstein et al (2009) Aging and replicative senescence have related effects on human stem and progenitor cells. PLoS ONE 4: e5846 https://doi.org/10.1371/journal.pone.0005846
44	W Wagner, E Fernandez-Rebollo, J Frobel (2016) DNA-methylation changes in replicative senescence and aging: two sides of the same coin? Epigenomics 8: 1- 3 https://doi.org/10.2217/epi.15.100
45	J Wang, C Zibetti, P Shang, SR Sripathi, P Zhang, M Cano, T Hoang, S Xia, H Ji, SL Merbs et al (2018) ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration. Nat Commun 9: 1364 https://doi.org/10.1038/s41467-018-03856-y
46	ES Wong, BM Schmitt, A Kazachenka, D Thybert, A Redmond, F Connor, TF Rayner, C Feig, AC Ferguson-Smith, JC Marioni et al (2017) Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution. Nat Commun 8: 1092 https://doi.org/10.1038/s41467-017-01037-x
47	M Xu, T Pirtskhalava, JN Farr, BM Weigand, AK Palmer, MM Weivoda, CL Inman, MB Ogrodnik, CM Hachfeld, DG Fraser et al (2018) Senolytics improve physical function and increase lifespan in old age. Nat Med 24: 1246- 1256 https://doi.org/10.1038/s41591-018-0092-9
48	FX Yu, B Zhao, KL Guan (2015) Hippo pathway in organ size control, tissue homeostasis, and cancer. Cell 163: 811- 828 https://doi.org/10.1016/j.cell.2015.10.044
49	C Zhang, X Zhang, L Huang, X Huang, XL Tian, L Zhang, W Tao (2021) ATF3 drives senescence by reconstructing accessible chromatin profiles. Aging Cell 20: e13315 https://doi.org/10.1111/acel.13315

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