Rapid degradation of DHX36 revealing its transcriptional role by interacting with G-quadruplex

Abstract

Accumulating evidence indicates that G-quadruplexes (G4s) are involved in transcriptional regulation. Previous studies have demonstrated that DHX36 preferentially resolves G4s, suggesting its potential impact on gene transcription mediated by these structures. However, systematic validation is required to establish a link between DHX36 activity and its roles in transcriptional regulation. In this study, we investigate the role of DHX36 in transcription. First, we employ the cleavage under targets and tagmentation (CUT&Tag), an efficient method for mapping protein– DNA interactions, to identify the binding sites in the chromatin of MCF-7 cells. Subsequently, we use the auxin-inducible degron (AID) protein degradation system and improved nascent RNA sequencing method acrylonitrile-mediated uridine-tocytidine conversion sequencing (AMUC-seq) to pinpoint genes directly regulated by DHX36. Our results reveal a significant enrichment of G4 structures at DHX36 target sites, predominantly located in active genomic regions. In vitro assays further demonstrate DHX36’s interaction with G4 sequences from three specific oncogenes. These findings underscore the potential role of DHX36 in modulating gene transcription through G4 structures.

Keywords

G-quadruplex / nascent RNA / protein degradation / transcription

References

[1] V. S. Chambers, G. Marsico, J. M. Boutell, M. Di Antonio, G. P. Smith, S. Balasubramanian, Nat. Biotechnol. 2015, 33, 877.

[2] G. Marsico, V. S. Chambers, A. B. Sahakyan, P. McCauley, J. M. Boutell, M. Di Antonio, S. Balasubramanian, Nucleic Acids Res. 2019, 47, 3862.

[3] C. K. Kwok, G. Marsico, A. B. Sahakyan, V. S. Chambers, S. Balasubramanian, Nat. Methods 2016, 13, 841.

[4] R. Hansel-Hertsch, D. Beraldi, S. V. Lensing, G. Marsico, K. Zyner, A. Parry, M. Di Antonio, J. Pike, H. Kimura, M. Narita, D. Tannahill, S. Balasubramanian, Nat. Genet. 2016, 48, 1267.

[5] C. H. Li, H. H. Wang, Z. N. Yin, P. P. Fang, R. J. Xiao, Y. Xiang, W. Wang, Q. Z. Li, B. L. Huang, J. Huang, K. Liang, Genome Res. 2021, 31, 1546.

[6] Y. L. Wu, K. Shin-ya, R. M. Brosh, Mol. Cell. Biol. 2008, 28, 4116.

[7] A. De Magis, S. G. Manzo, M. Russo, J. Marinello, R. Morigi, O. Sordet, G. Capranico, Proc. Nat. Acad. Sci. U.S.A. 2019, 116, 816.

[8] A. Siddiqui-Jain, C. L. Grand, D. J. Bearss, L. H. Hurley, Proc. Nat. Acad. Sci. U.S.A. 2002, 99, 11593.

[9] B. P. Belotserkovskii, J. H. S. Shin, P. C. Hanawalt, Nucleic Acids Res. 2017, 45, 6589.

[10] R. Shahid, A. Bugaut, S. Balasubramanian, Biochemistry 2010, 49, 8300.

[11] H. Liu, Y. N. Lu, T. Paul, G. Periz, M. T. Banco, A. R. Ferre-D’Amare, J. D. Rothstein, L. R. Hayes, S. Myong, J. Wang, J. Am. Chem. Soc. 2021, 143, 7368.

[12] J. Seenisamy, E. M. Rezler, T. J. Powell, D. Tye, V. Gokhale, C. S. Joshi, A. Siddiqui-Jain, L. H. Hurley, J. Am. Chem. Soc. 2004, 126, 8702.

[13] T. S. Dexheimer, D. Sun, L. H. Hurley, J. Am. Chem. Soc. 2006, 128, 5404.

[14] Y. Qin, E. M. Rezler, V. Gokhale, D. Sun, L. H. Hurley, Nucleic Acids Res. 2007, 35, 7698.

[15] C. Marchetti, K. G. Zyner, S. A. Ohnmacht, M. Robson, S. M. Haider, J. P. Morton, G. Marsico, T. Vo, S. Laughlin-Toth, A. A. Ahmed, G. Di Vita, I. Pazitna, M. Gunaratnam, R. J. Besser, A. C. G. Andrade, S. Diocou, J. A. Pike, D. Tannahill, R. B. Pedley, T. R. J. Evans, W. D. Wilson, S. Balasubramanian, S. Neidle, J. Med. Chem. 2018, 61, 2500.

[16] J. Robinson, F. Raguseo, S. P. Nuccio, D. Liano, M. Di Antonio Nucleic Acids Res. 2021, 49, 8419.

[17] P. Mohaghegh, J. K. Karow, R. M. Brosh, V. A. Bohr, I. D. Hickson, Nucleic Acids Res. 2001, 29, 2843.

[18] S. D. Creacy, E. D. Routh, F. Iwamoto, Y. Nagamine, S. A. Akman, J. P. Vaughn, J. Biol. Chem. 2008, 283, 34626.

[19] L. T. Gray, A. C. Vallur, J. Eddy, N. Maizels, Nat. Chem. Biol. 2014, 10, 313.

[20] M. C. Chen, R. Tippana, N. A. Demeshkina, P. Murat, S. Balasubramanian, S. Myong, A. R. Ferre-D’Amare, Nature 2018, 558, 465.

[21] W. W. Huang, P. J. Smaldino, Q. Zhang, L. D. Miller, P. Cao, K. Stadelman, M. M. Wan, B. Giri, M. Lei, Y. Nagamine, J. P. Vaughn, S. A. Akman, G. Sui, Nucleic Acids Res. 2012, 40, 1033.

[22] E. P. Booy, R. Howard, O. Marushchak, E. O. Ariyo, M. Meier, S. K. Novakowski, S. R. Deo, E. Dzananovic, J. Stetefeld, S. A. McKenna, Nucleic Acids Res. 2014, 42, 3346.

[23] A. V. Lee, S. Oesterreich, N. E. Davidson, J. Natl. Cancer Inst. 2015, 107, djv073.

[24] H. S Kaya-Okur, S. J. Wu, C. A. Codomo, E. S. Pledger, T. D. Bryson, J. G. Henikoff, K. Ahmad, S. Henikoff, Nat. Commun. 2019, 10, 1930.

[25] R. Hansel-Hertsch, J. Spiegel, G. Marsico, D. Tannahill, S. Balasubramanian, Nat. Protoc. 2018, 13, 551.

[26] W. W. I Hui, A. Simeone, K. G. Zyner, D. Tannahill, S. Balasubramanian, Sci. Rep. 2021, 11, 23641.

[27] S. Li, X. Prasanna, V. T. Salo, I. Vattulainen, E. Ikonen, Nat. Methods 2019, 16, 866.

[28] Y. Chen, F. Wu, Z. Chen, Z. He, Q. Wei, W. Zeng, K. Chen, F. Xiao, Y. Yuan, X. Weng, Y. Zhou, X. Zhou, Adv. Sci. 2020, 7, 1900997.

[29] S. L. Berger, Nature 2007, 447, 407.

[30] C. C. Tian, J. Q. Zhou, X. R. Li, Y. Gao, Q. Wen, X. Kang, N. Wang, Y. Yao, J. H. Jiang, G. B. Song, T. Zhang, S. Hu, J. Liao, C. Yu, Z. Wang, X. Liu, X. Pei, K. Chan, Z. Liu, H. Gan, Nat. Commun. 2023, 14, 3429.

[31] F. Ramirez, D. P. Ryan, B. Gruning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dundar, T. Manke, Nucleic Acids Res. 2016, 44, W160.

[32] A. Bedrat, L. Lacroix, J. L. Mergny, Nucleic Acids Res. 2016, 44, 1746.

[33] K. Lyu, S. B. Chen, E. Y. C. Chow, H. Z. Zhao, J. H. Yuan, M. Cai, J. H. Shi, T. F. Chan, J. H. Tan, C. K. Kwok, Angew. Chem. Int. Ed. 2022, 61, e202203553.

[34] S. Balasubramanian, L. H. Hurley, S. Neidle Nat. Rev. Drug Discov. 2011, 10, 261.

[35] K. Zhang, T. Zhang, Y. Zhang, J. Yuan, X. Tang, C. Zhang, Q. Yin, Y. Zhang, M.-H. Tong, J. Mol. Cell Biol. 2022, 14, mjac069.

[36] J. W. Nie, M. Y. Jiang, X. T. Zhang, H. Tang, H. W. Jin, X. Y. Huang, B. Y. Yuan, C. X. Zhang, J. C. Lai, Y. Nagamine, D. Pan, W. Wang, Z. Yang, Cell Rep. 2015, 13, 723.

[37] Y. X. Cui, Z. L. Li, J. X. Cao, J. Lane, E. Birkin, X. F. Dong, L. J. Zhang, W. G. Jiang, Front. Oncol. 2021, 11, 655757.

[38] Y. D. Zeng, T. Qin, V. Flamini, C. Tan, X. K. Zhang, Y. Z. Cong, E. Birkin, W. G. Jiang, H. R. Yao, Y. X. Cui, Am. J. Cancer Res. 2020, 10, 4211.

[39] K. Matsumura, Y. Kawasaki, M. Miyamoto, Y. Kamoshida, J. Nakamura, L. Negishi, S. Suda, T. Akiyama, Oncogene 2017, 36, 1191.

[40] G. I Aldana-Masangkay, K. M. Sakamoto, J. Biomed. Biotechnol. 2011, 2011, 875824.

[41] G. Zurlo, X. Liu, M. Takada, C. Fan, J. M. Simon, T. S. Ptacek, J. Rodriguez, A. von Kriegsheim, J. Liu, J. W. Locasale, A. Robinson, J. Zhang, J. M. Holler, B. Kim, M. Zikánová, J. Bierau, L. Xie, X. Chen, M. Li, C. M. Perou, Q. Zhang, Nat. Commun. 2019, 10, 5177.

[42] B. Langmead, S. L. Salzberg, Nat. Methods 2012, 9, 357.

[43] Q. H. Li, J. B. Brown, H. Y. Huang, P. J. Bickel, Ann. Appl. Stat. 2011, 5, 1752.

[44] K. W. Zheng, J. Y. Zhang, Y. D. He, J. Y. Gong, C. J. Wen, J. N. Chen, Y. H. Hao, Y. Zhao, Z. Tan, Nucleic Acids Res. 2020, 48, 11706.

[45] C. Lo Giudice, M. A. Tangaro, G. Pesole, E. Picardi, Nat. Protoc. 2020, 15, 1098.

[46] A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski, S. Jha, P. Batut, M. Chaisson, T. R. Gingeras, Bioinformatics 2013, 29, 15.

[47] S. Anders, P. T. Pyl, W. Huber, Bioinformatics 2015, 31, 166.

[48] B. T. Sherman, M. Hao, J. Qiu, X. L. Jiao, M. W. Baseler, H. C. Lane, T. Imamichi, W. Z. Chang, Nucleic Acids Res. 2022, 50, W216.

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2024 The Author(s). Aggregate published by SCUT, AIEI, and John Wiley & Sons Australia, Ltd.