EXPERIMENTAL PROTOCOLS
Our laboratory team provides help and support with optimization for researchers who would like to use our approach to identify direct RNA-protein interactions. For detailed protocols for RNA antisense purification with mass spectrometry (RAP-MS), please click the links below.
Protocols for UV-crosslinked RNA-protein purification and identification
The most updated version and optimization details for human cancer cells are available in the following article:
Trang N, Su T, Hall S, et al. Streamlined Purification of RNA-Protein Complexes Using UV Cross-Linking and RNA Antisense Purification. Methods Mol Biol. 2023;2666:213-229. doi:10.1007/978-1-0716-3191-1_16
Protocols for UV-crosslinked RNA-protein purification and identification
The most updated version and optimization details for human cancer cells are available in the following article:
Trang N, Su T, Hall S, et al. Streamlined Purification of RNA-Protein Complexes Using UV Cross-Linking and RNA Antisense Purification. Methods Mol Biol. 2023;2666:213-229. doi:10.1007/978-1-0716-3191-1_16
| trang_2023_mimb.pdf |
This previous version of RAP-MS is from 2018, and contains details for purification of RNA-protein complexes from mouse embryonic stem cells:
| mchugh2018_rap-ms_mimb.pdf |
RESEARCH AND EDUCATION SUPPORT
Our laboratory team strives to make science approachable, understandable, and welcoming for all who want to participate. We value transparency, data sharing, and open access to scientific findings. Our affiliation with UC San Diego enables our work with a broad range of students and scientists, enhancing our commitment to advancing education and research: chemistryandbiochemistry.ucsd.edu/
PUBLICATIONS
Balaji A., Button A.C., Hall S.D., Zhu J., Ellis L., Lavorando E., Ashley E.L., Johnson R., Sarikhani E., Jahed Z., and McHugh C.A. 2025. The levels of the long non-coding RNA MALAT1 affect cell viability and modulate TDP-43 binding to mRNA in the nucleus. Journal of Biological Chemistry 301:108207.
Hall S.D., Tran K., Zhu J., Su T., and McHugh C.A. 2025. DUBR non-coding RNA regulates gene expression by affecting AP-1 enhancer accessibility. Functional & Integrative Genomics 25: 68.
Button A.C., Hall S.D., Ashley E.L, and McHugh C.A. 2024. Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA. RNA Journal 30:240-255.
Sarikhani E., Patel V., Li Z., Meganathan D.P., Rahmani K., Sadr L., Hosseini R., Visda D., Shukla S., Naghsh‐Nilchi H., Balaji A., McMahon G., Chen S., Schöneberg J., McHugh C.A., Shi L., and Jahed Z. 2024. Engineered Nanotopographies Induce Transient Openings in the Nuclear Membrane. Advanced Functional Materials 35: 2410035.
Su T., Kong L., Cheung D., Zhu J., Chou V., Camden N., Huang C., and McHugh C.A. 2023. GRAS1 non-coding RNA protects against DNA damage and cell death by binding NKAP. bioRxiv 2023.06.20.545783; doi: https://doi.org/10.1101/2023.06.20.545783
Trang N., Su. T., Hall S., Boutros N., Kong B., Huang C. and McHugh, C.A. 2023. Streamlined purification of RNA-protein complexes using UV crosslinking and RNA antisense purification. Methods in Molecular Biology: RNA-Protein Interactions and Complexes. 213-229.
Burnett C.A., Wong, A.T., Vasquez, C.A., McHugh, C.A., Yeo, G.W., and Komor, A.C. 2022. Examination of the Cell Cycle Dependence of Cytosine and Adenine Base Editors. Frontiers in Genome Editing 4: 932718.
McHugh C.A. and Guttman M. 2018. RAP-MS: A method to identify proteins that interact directly with a specific RNA molecule in cells. In Methods in Molecular Biology: RNA Detection – Methods and Protocols.
McHugh C.A., Chen C.K., Chow A., Surka C.F., Tran C., McDonel P., Pandya-Jones A., Blanco M., Burghard C., Moradian A., Sweredoski M.J., Shishkin A.A., Su J., Lander E.S., Hess S., Plath K., and Guttman M. 2015. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521: 232-236.
McHugh C.A., Fontana J., Nemecek D., Cheng N., Aksyuk A.A., Heymann J.B., Winkler D.C., Lam A.S., Wall J.S., Steven A.C., and Hoiczyk E. 2014. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO Journal 33: 1896-1911.
McHugh C.A., Russell P., and Guttman M. 2014. Methods for comprehensive experimental identification of RNA-protein interactions. Genome Biology 15: 203-212.
Koch M.K., McHugh C.A., and Hoiczyk E. 2011. BacM, an N-terminally processed bactofilin of Myxococcus xanthus, is crucial for proper cell shape. Molecular Microbiology 80: 1031-1051.
Hoiczyk E., Ring M.W., McHugh C.A., Schwär G., Bode E., Krug D., Altmeyer M.O., Lu J.Z., and Bode H.B. 2009. Lipid body formation plays a central role in cell fate determination during developmental differentiation of Myxococcus xanthus. Molecular Microbiology 74: 497-517.
Dinglasan R.R., Devenport M., Florens L., Johnson J.R., McHugh C.A., Donnelly-Doman M., Carucci D.J., Yates J.R., and Jacobs-Lorena M. 2009. The Anopheles gambiae adult midgut peritrophic matrix proteome. Insect Biochemistry and Molecular Biology 39: 125-134.
Carra J.H., McHugh C.A., Mulligan S., Machiesky L.M., Soares A.S., and Millard C.B. 2007. Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site. BMC Structural Biology 7: 72.
Sergueev K., McHugh C.A., and Hoiczyk E. 2006. Type III secretion systems: Bacterial injection devices for microbe-host interactions. In J. M. Shipley (ed), Microbiology Monographs. Vol. 2: Complex intracellular structures in prokaryotes. Springer, Heidelberg; pp. 339-347.
McHugh C.A., Tammariello R.F., Millard C.B., and Carra J.H. 2004. Improved stability of a protein vaccine through elimination of a partially unfolded state. Protein Science 13: 2736-43.
TEACHING
Course information for enrolled students is available through UCSD Canvas
CHEM 109
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CHEM 164
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CHEM 264
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