A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

Xiaoya Zhang; Abhisek Bhattacharya; Chunxiang Pu; Yan Dai; Jia Liu; Lang Rao; Chaoguang Tian

doi:10.1016/j.jgg.2024.05.010

A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

doi: 10.1016/j.jgg.2024.05.010

a. National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
b. School of Pharmacy, Jilin University, Changchun, Jilin 130012, China;
c. Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA

基金项目:

This study was funded by the Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project (TSBICIP-CXRC-048).

详细信息

通讯作者:
Lang Rao,E-mail:raolang@tib.cas.cn

Chaoguang Tian,E-mail:tian_cg@tib.cas.cn

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- 文章访问数: 10
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出版历程
- 收稿日期: 2024-03-04
- 录用日期: 2024-05-31
- 修回日期: 2024-05-29
- 网络出版日期: 2025-06-05
- 刊出日期: 2024-06-06

A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

a. National Technology Innovation Center of Synthetic Biology, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China;
b. School of Pharmacy, Jilin University, Changchun, Jilin 130012, China;
c. Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA

Funds:

This study was funded by the Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project (TSBICIP-CXRC-048).

摘要

摘要:
Histone citrullination, an important post-translational modification mediated by peptidyl arginine deiminases, is essential for many physiological processes and epigenetic regulation. However, the causal relationship between histone citrullination and specific gene regulation remains unresolved. In this study, we develop a programmable epigenetic editor by fusing the peptidyl arginine deiminase (PAD) PPAD from Porphyromonas gingivalis with dCas9. With the assistance of gRNA, PPAD-dCas9 can recruit PPADs to specific genomic loci, enabling direct manipulation of the epigenetic landscape and regulation of gene expression. Our citrullination editor allows for the site-specific manipulation of histone H3R2,8,17 and H3R26 at target human gene loci, resulting in the activation or suppression of different genes in a locus-specific manner. Moreover, the epigenetic effects of the citrullination editor are specific and sustained. This epigenetic editor offers an accurate and efficient tool for exploring gene regulation of histone citrullination.
- Histone /
- Citrullination /
- Epigenetic editor /
- Peptidyl arginine deiminase /
- dCas9
Abstract:
Histone citrullination, an important post-translational modification mediated by peptidyl arginine deiminases, is essential for many physiological processes and epigenetic regulation. However, the causal relationship between histone citrullination and specific gene regulation remains unresolved. In this study, we develop a programmable epigenetic editor by fusing the peptidyl arginine deiminase (PAD) PPAD from Porphyromonas gingivalis with dCas9. With the assistance of gRNA, PPAD-dCas9 can recruit PPADs to specific genomic loci, enabling direct manipulation of the epigenetic landscape and regulation of gene expression. Our citrullination editor allows for the site-specific manipulation of histone H3R2,8,17 and H3R26 at target human gene loci, resulting in the activation or suppression of different genes in a locus-specific manner. Moreover, the epigenetic effects of the citrullination editor are specific and sustained. This epigenetic editor offers an accurate and efficient tool for exploring gene regulation of histone citrullination.
- Histone /
- Citrullination /
- Epigenetic editor /
- Peptidyl arginine deiminase /
- dCas9

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参考文献(42)

Aquino-Jarquin, G., 2019. CRISPR-Cas14 is now part of the artillery for gene editing and molecular diagnostic. Nanomedicine 18, 428-431.

Arita, K., Hashimoto, H., Shimizu, T., Nakashima, K., Yamada, M., Sato, M., 2004. Structural basis for Ca²⁺-induced activation of human PAD4. Nat. Struct. Mol. Biol. 11, 777-783.

Berger, S.L., 2007. The complex language of chromatin regulation during transcription. Nature 447, 407-412.

Chen, T., Chen, X., Zhang, S., Zhu, J., Tang, B., Wang, A., Dong, L., Zhang, Z., Yu, C., Sun, Y., et al., 2021. The Genome Sequence Archive Family: toward explosive data growth and diverse data types. Genomics Proteomics Bioinformatics 19, 578-583.

Christensen, A.O., Li, G., Young, C.H., Snow, B., Khan, S.A., DeVore, S.B., Edwards, S., Bouma, G.J., Navratil, A.M., Cherrington, B.D., et al., 2022. Peptidylarginine deiminase enzymes and citrullinated proteins in female reproductive physiology and associated diseases. Biol. Reprod. 107, 1395-1410.

Curis, E., Nicolis, I., Moinard, C., Osowska, S., Zerrouk, N., Benazeth, S., Cynober, L., 2005. Almost all about citrulline in mammals. Amino Acids 29, 177-205.

East-Seletsky, A., O'Connell, M.R., Knight, S.C., Burstein, D., Cate, J.H., Tjian, R., Doudna, J.A., 2016. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature 538, 270-273.

Figueredo, C.M., Sete, M.R., Carlos, J.C., Lira, R., Jr., Bostrom, E., Sztajnbok, F., 2018. Presence of anti-Porphyromonas gingivalis-peptidylarginine deiminase antibodies in serum from juvenile systemic lupus erythematosus patients. Acta. Reumatol. Port. 43, 239-240.

Fuhrmann, J., Clancy, K.W., Thompson, P.R., 2015. Chemical biology of protein arginine modifications in epigenetic regulation. Chem. Rev. 115, 5413-5461.

Gao, L., Cox, D.B.T., Yan, W.X., Manteiga, J.C., Schneider, M.W., Yamano, T., Nishimasu, H., Nureki, O., Crosetto, N., Zhang, F., 2017. Engineered Cpf1 variants with altered PAM specificities. Nat. Biotechnol. 35, 789-792.

Goulas, T., Mizgalska, D., Garcia-Ferrer, I., Kantyka, T., Guevara, T., Szmigielski, B., Sroka, A., Millan, C., Uson, I., Veillard, F., et al., 2015. Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase. Sci. Rep. 5, 11969.

Guertin, M.J., Zhang, X., Anguish, L., Kim, S., Varticovski, L., Lis, J.T., Hager, G.L., Coonrod, S.A., 2014. Targeted H3R26 deimination specifically facilitates estrogen receptor binding by modifying nucleosome structure. PLoS Genet. 10, e1004613.

Gyorgy, B., Toth, E., Tarcsa, E., Falus, A., Buzas, E.I., 2006. Citrullination: a posttranslational modification in health and disease. Int. J. Biochem. Cell Biol. 38, 1662-1677.

Hamam, H.J., Palaniyar, N., 2019. Post-translational modifications in NETosis and NETs-mediated diseases. Biomolecules 9, 369.

Hilton, I.B., D'Ippolito, A.M., Vockley, C.M., Thakore, P.I., Crawford, G.E., Reddy, T.E., Gersbach, C.A., 2015. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33, 510-517.

Horibata, S., Coonrod, S.A., Cherrington, B.D., 2012. Role for peptidylarginine deiminase enzymes in disease and female reproduction. J. Reprod. Dev. 58, 274-282.

Huang, H., Sabari, B.R., Garcia, B.A., Allis, C.D., Zhao, Y., 2014. SnapShot: histone modifications. Cell 159, 458.-458.

Konermann, S., Brigham, M.D., Trevino, A.E., Joung, J., Abudayyeh, O.O., Barcena, C., Hsu, P.D., Habib, N., Gootenberg, J.S., Nishimasu, H., et al., 2015. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588.

Konig, M.F., Paracha, A.S., Moni, M., Bingham, C.O., 3rd, Andrade, F., 2015. Defining the role of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) in rheumatoid arthritis through the study of PPAD biology. Ann. Rheum. Dis. 74, 2054-2061.

Kouzarides, T., 2007. Chromatin modifications and their function. Cell 128, 693-705.

Liu, Y.L., Lee, C.Y., Huang, Y.N., Chen, H.Y., Liu, G.Y., Hung, H.C., 2017. Probing the roles of calcium-binding sites during the folding of human peptidylarginine deiminase 4. Sci. Rep. 7, 2429.

Ma, A.C., Chen, Y., Blackburn, P.R., Ekker, S.C., 2016. TALEN-mediated mutagenesis and genome editing. Methods Mol. Biol. 1451, 17-30.

Maeder, M.L., Linder, S.J., Reyon, D., Angstman, J.F., Fu, Y., Sander, J.D., Joung, J.K., 2013. Robust, synergistic regulation of human gene expression using TALE activators. Nat. Methods 10, 243-245.

Mali, P., Yang, L., Esvelt, K.M., Aach, J., Guell, M., DiCarlo, J.E., Norville, J.E., Church, G.M., 2013. RNA-guided human genome engineering via Cas9. Science 339, 823-826.

McNee, G., Eales, K.L., Wei, W., Williams, D.S., Barkhuizen, A., Bartlett, D.B., Essex, S., Anandram, S., Filer, A., Moss, P.A., et al., 2017. Citrullination of histone H3 drives IL-6 production by bone marrow mesenchymal stem cells in MGUS and multiple myeloma. Leukemia 31, 373-381.

Members, C.-N., Partners, 2024. Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2024. Nucleic Acids Res. 52, D18-D32.

Nakamura, M., Gao, Y., Dominguez, A.A., Qi, L.S., 2021. CRISPR technologies for precise epigenome editing. Nat. Cell Biol. 23, 11-22.

Perez-Pinera, P., Kocak, D.D., Vockley, C.M., Adler, A.F., Kabadi, A.M., Polstein, L.R., Thakore, P.I., Glass, K.A., Ousterout, D.G., Leong, K.W., et al., 2013a. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat. Methods 10, 973-976.

Perez-Pinera, P., Ousterout, D.G., Brunger, J.M., Farin, A.M., Glass, K.A., Guilak, F., Crawford, G.E., Hartemink, A.J., Gersbach, C.A., 2013b. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat. Methods 10, 239-242.

Pironti, G., Gastaldello, S., Rassier, D.E., Lanner, J.T., Carlstrom, M., Lund, L.H., Westerblad, H., Yamada, T., Andersson, D.C., 2022. Citrullination is linked to reduced Ca2+ sensitivity in hearts of a murine model of rheumatoid arthritis. Acta. Physiol. (Oxf) 236, e13869.

Segal, D.J., Meckler, J.F., 2013. Genome engineering at the dawn of the golden age. Annu. Rev. Genomics Hum. Genet. 14, 135-158.

Slade, D.J., Fang, P., Dreyton, C.J., Zhang, Y., Fuhrmann, J., Rempel, D., Bax, B.D., Coonrod, S.A., Lewis, H.D., Guo, M., et al., 2015. Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design. ACS Chem. Biol. 10, 1043-1053.

Thirugnanasambandham, I., Radhakrishnan, A., Kuppusamy, G., Kumar Singh, S., Dua, K., 2022. Peptidylarginine deiminase-4: Medico-formulative strategy towards management of rheumatoid arthritis. Biochem. Pharmacol. 200, 115040.

Vossenaar, E.R., Zendman, A.J., van Venrooij, W.J., Pruijn, G.J., 2003. PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease. Bioessays 25, 1106-1118.

Wang, L., Song, G., Zhang, X., Feng, T., Pan, J., Chen, W., Yang, M., Bai, X., Pang, Y., Yu, J., et al., 2017. PADI2-mediated citrullination promotes prostate cancer progression. Cancer Res. 77, 5755-5768.

Wang, S., Wang, Y., 2013. Peptidylarginine deiminases in citrullination, gene regulation, health and pathogenesis. Biochim. Biophys. Acta. 1829, 1126-1135.

Wang, Y., Chen, R., Gan, Y., Ying, S., 2021. The roles of PAD2- and PAD4-mediated protein citrullination catalysis in cancers. Int. J. Cancer 148, 267-276.

Wu, X., Scott, D.A., Kriz, A.J., Chiu, A.C., Hsu, P.D., Dadon, D.B., Cheng, A.W., Trevino, A.E., Konermann, S., Chen, S., et al., 2014. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 32, 670-676.

Xu, X., Chemparathy, A., Zeng, L., Kempton, H.R., Shang, S., Nakamura, M., Qi, L.S., 2021. Engineered miniature CRISPR-Cas system for mammalian genome regulation and editing. Mol. Cell 81, 4333-4345.

Yu, K., Proost, P., 2022. Insights into peptidylarginine deiminase expression and citrullination pathways. Trends Cell Biol. 32, 746-761.

Zalatan, J.G., Lee, M.E., Almeida, R., Gilbert, L.A., Whitehead, E.H., La Russa, M., Tsai, J.C., Weissman, J.S., Dueber, J.E., Qi, L.S., et al., 2015. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339-350.

Zhao, W., Xu, Y., Wang, Y., Gao, D., King, J., Xu, Y., Liang, F.S., 2021. Investigating crosstalk between H3K27 acetylation and H3K4 trimethylation in CRISPR/dCas-based epigenome editing and gene activation. Sci. Rep. 11, 15912.

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A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

doi: 10.1016/j.jgg.2024.05.010

通讯作者:
Lang Rao,E-mail:raolang@tib.cas.cn

Chaoguang Tian,E-mail:tian_cg@tib.cas.cn

计量

A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

计量

目录

留言板

A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

doi: 10.1016/j.jgg.2024.05.010

通讯作者: Lang Rao,E-mail:raolang@tib.cas.cn Chaoguang Tian,E-mail:tian_cg@tib.cas.cn

计量

出版历程

A programmable CRISPR/dCas9-based epigenetic editing system enabling loci-targeted histone citrullination and precise transcription regulation

计量

出版历程

目录

通讯作者:
Lang Rao,E-mail:raolang@tib.cas.cn

Chaoguang Tian,E-mail:tian_cg@tib.cas.cn