High-affinity chromodomains engineered for improved detection of histone methylation and enhanced CRISPR-based gene repression
Veggiani, G.; Villaseñor, R.; Martyn, G. D.; Tang, J. Q.; Krone, W. M.; Gu, J.; Chen, C.; Waters, M. L.; Pearce, K. H.; Baubec, T.; Sidhu, S. S.
(2022) Nature Communications, volume 13, issue 1
(Article)
Abstract
Histone methylation is an important post-translational modification that plays a crucial role in regulating cellular functions, and its dysregulation is implicated in cancer and developmental defects. Therefore, systematic characterization of histone methylation is necessary to elucidate complex biological processes, identify biomarkers, and ultimately, enable drug discovery. Studying histone methylation relies
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on the use of antibodies, but these suffer from lot-to-lot variation, are costly, and cannot be used in live cells. Chromatin-modification reader domains are potential affinity reagents for methylated histones, but their application is limited by their modest affinities. We used phage display to identify key residues that greatly enhance the affinities of Cbx chromodomains for methylated histone marks and develop a general strategy for enhancing the affinity of chromodomains of the human Cbx protein family. Our strategy allows us to develop powerful probes for genome-wide binding analysis and live-cell imaging. Furthermore, we use optimized chromodomains to develop extremely potent CRISPR-based repressors for tailored gene silencing. Our results highlight the power of engineered chromodomains for analyzing protein interaction networks involving chromatin and represent a modular platform for efficient gene silencing.
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Keywords: Antibodies, Binding, Dna, Domains, Generation, H3, Nonhistone protein methylation, Phage-display, Proteomic analysis, Specificity, General, General Physics and Astronomy, General Chemistry, General Biochemistry,Genetics and Molecular Biology
ISSN: 2041-1723
Publisher: Nature Publishing Group
Note: Funding Information: We thank Dr Ario de Marco (University of Nova Gorica) for Erv1p and DsbC plasmids. We are also grateful to Mr. Nick Jarvik (University of Toronto) for assistance with BLI measurements. The authors wish to thank Dr. Greg Wasney and Mr. James Magnus Jorgensen (The Hospital for Sick Children’s Structural & Biophysical Core Facility) for assistance with FP assays, and Dr. Reza Saberianfar (University of Toronto) for technical help with Incucyte. We wish to thank Dr. Mikko Taipale and Dr. Nader Alerasool (University of Toronto) for HEK293T pSV40–EGFP cells, pLX303 and pLCKO lentiviral vectors. In addition, the authors are grateful to Dr. Ning Yang and Dr. Mart Ustav Jr. for useful discussions and comments on the manuscript. Finally, the authors thank the Functional Genomics Centre Zurich (FGCZ), S3IT Zurich, the Center for Microscopy and Image Analysis, and Cytometry Facility at University of Zurich for their support. JQT is a recipient of the CIHR-CGS-M. Funding was provided by the Ontario Research Fund grant ORF-RE09-027 (S.S.S). R.V. acknowledges support from the Forschungskredit of the University of Zurich, grant no. [FK-21-060], and the Deutsche Forschungsgemeinschaft [468577222]. T.B. acknowledges support from the European Research Council (865094 - ChromatinLEGO - ERC-2019-COG), and the EMBO Young Investigator program. Funding Information: We thank Dr Ario de Marco (University of Nova Gorica) for Erv1p and DsbC plasmids. We are also grateful to Mr. Nick Jarvik (University of Toronto) for assistance with BLI measurements. The authors wish to thank Dr. Greg Wasney and Mr. James Magnus Jorgensen (The Hospital for Sick Children’s Structural & Biophysical Core Facility) for assistance with FP assays, and Dr. Reza Saberianfar (University of Toronto) for technical help with Incucyte. We wish to thank Dr. Mikko Taipale and Dr. Nader Alerasool (University of Toronto) for HEK293T pSV40–EGFP cells, pLX303 and pLCKO lentiviral vectors. In addition, the authors are grateful to Dr. Ning Yang and Dr. Mart Ustav Jr. for useful discussions and comments on the manuscript. Finally, the authors thank the Functional Genomics Centre Zurich (FGCZ), S3IT Zurich, the Center for Microscopy and Image Analysis, and Cytometry Facility at University of Zurich for their support. JQT is a recipient of the CIHR-CGS-M. Funding was provided by the Ontario Research Fund grant ORF-RE09-027 (S.S.S). R.V. acknowledges support from the Forschungskredit of the University of Zurich, grant no. [FK-21-060], and the Deutsche Forschungsgemeinschaft [468577222]. T.B. acknowledges support from the European Research Council (865094 - ChromatinLEGO - ERC-2019-COG), and the EMBO Young Investigator program. Publisher Copyright: © 2022, The Author(s).
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