Christopher Burge

Christopher Burge

CSB Program Director; Uncas (1923) and Helen Whitaker Professor; Extramural Member of KIICR; Associate Member of the Broad Institute

Christopher Burge applies a combination of experimental and computational approaches to understand the regulatory codes underlying pre-mRNA splicing and other types of post-transcriptional gene regulation.

617-258-5997

Phone

68-271

Office

cburge@mit.edu

Email

Building 68 - Koch Biology Building

Location

Lab Website
Jessica Klees

Assistant

Education

  • PhD, 1997, Stanford University
  • BS, 1990, Biological Sciences, Stanford University

Research Summary

We aim to understand the code for RNA splicing: how the precise locations of introns and splice sites are identified in primary transcripts and how its specificity changes in different cell types. Toward this end, we are mapping the RNA-binding affinity spectra of dozens of human RNA-binding proteins and integrating this information with in vivo binding and activity data.  We are also studying the functions of 3’ untranslated regions, including their roles in mRNA localization and microRNA regulation. The lab uses a combination of computational and experimental approaches to address these questions.

Awards

  • Schering-Plough Research Institute Award (ASBMB), 2007
  • Overton Prize for Computational Biology (ISCB), 2001

Key Publications

  1. A large-scale binding and functional map of human RNA-binding proteins. Van Nostrand, EL, Freese, P, Pratt, GA, Wang, X, Wei, X, Xiao, R, Blue, SM, Chen, JY, Cody, NAL, Dominguez, D et al.. 2020. Nature 583, 711-719.
    doi: 10.1038/s41586-020-2077-3PMID:32728246
  2. Exon-Mediated Activation of Transcription Starts. Fiszbein, A, Krick, KS, Begg, BE, Burge, CB. 2019. Cell 179, 1551-1565.e17.
    doi: 10.1016/j.cell.2019.11.002PMID:31787377
  3. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins. Dominguez, D, Freese, P, Alexis, MS, Su, A, Hochman, M, Palden, T, Bazile, C, Lambert, NJ, Van Nostrand, EL, Pratt, GA et al.. 2018. Mol Cell 70, 854-867.e9.
    doi: 10.1016/j.molcel.2018.05.001PMID:29883606
  4. Distal Alternative Last Exons Localize mRNAs to Neural Projections. Taliaferro, JM, Vidaki, M, Oliveira, R, Olson, S, Zhan, L, Saxena, T, Wang, ET, Graveley, BR, Gertler, FB, Swanson, MS et al.. 2016. Mol Cell 61, 821-33.
    doi: 10.1016/j.molcel.2016.01.020PMID:26907613
  5. Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Merkin, J, Russell, C, Chen, P, Burge, CB. 2012. Science 338, 1593-9.
    doi: 10.1126/science.1228186PMID:23258891

Recent Publications

  1. Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease. Martin-Geary, AC, Blakes, AJM, Dawes, R, Findlay, SD, Lord, J, Dong, S, Walker, S, Talbot-Martin, J, Wieder, N, D'Souza, EN et al.. 2025. Genome Med 17, 40.
    doi: 10.1186/s13073-025-01464-2PMID:40229884
  2. Sequence-dependent and -independent effects of intron-mediated enhancement learned from thousands of random introns. Kowal, EJK, Sakai, Y, McGurk, MP, Pasetsky, ZJ, Burge, CB. 2025. Nucleic Acids Res 53, .
    doi: 10.1093/nar/gkaf097PMID:39995040
  3. LUC7 proteins define two major classes of 5' splice sites in animals and plants. Kenny, CJ, McGurk, MP, Schüler, S, Cordero, A, Laubinger, S, Burge, CB. 2025. Nat Commun 16, 1574.
    doi: 10.1038/s41467-025-56577-4PMID:39979239
  4. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. Harris, SE, Alexis, MS, Giri, G, Cavazos, FF Jr, Hu, Y, Murn, J, Aleman, MM, Burge, CB, Dominguez, D. 2024. Nat Commun 15, 8400.
    doi: 10.1038/s41467-024-52231-7PMID:39333159
  5. Molecular and cellular context influences SCN8A variant function. Vanoye, CG, Abramova, TV, DeKeyser, JM, Ghabra, NF, Oudin, MJ, Burge, CB, Helbig, I, Thompson, CH, George, AL Jr. 2024. JCI Insight 9, .
    doi: 10.1172/jci.insight.177530PMID:38771640
  6. An interpretable model of pre-mRNA splicing for animal and plant genes. McCue, K, Burge, CB. 2024. Sci Adv 10, eadn1547.
    doi: 10.1126/sciadv.adn1547PMID:38718117
  7. Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro. Harris, SE, Alexis, MS, Giri, G, Cavazos, FF, Murn, J, Aleman, MM, Burge, CB, Dominguez, D. 2024. bioRxiv , .
    doi: 10.1101/2024.01.29.577729PMID:38352439
  8. Regulatory features aid interpretation of 3'UTR variants. Romo, L, Findlay, SD, Burge, CB. 2024. Am J Hum Genet 111, 350-363.
    doi: 10.1016/j.ajhg.2023.12.017PMID:38237594
  9. Improved modeling of RNA-binding protein motifs in an interpretable neural model of RNA splicing. Gupta, K, Yang, C, McCue, K, Bastani, O, Sharp, PA, Burge, CB, Solar-Lezama, A. 2024. Genome Biol 25, 23.
    doi: 10.1186/s13059-023-03162-xPMID:38229106
  10. Quantifying negative selection in human 3' UTRs uncovers constrained targets of RNA-binding proteins. Findlay, SD, Romo, L, Burge, CB. 2024. Nat Commun 15, 85.
    doi: 10.1038/s41467-023-44456-9PMID:38168060
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