Christopher Burge

Christopher Burge

CSB Program Director; Professor of Biology and Biological Engineering; 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.





Sarah Wylie



Assistant Phone


  • 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.


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

Key Publications

  1. 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
  2. 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
  3. Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Wang, ET, Cody, NA, Jog, S, Biancolella, M, Wang, TT, Treacy, DJ, Luo, S, Schroth, GP, Housman, DE, Reddy, S et al.. 2012. Cell 150, 710-24.
    doi: 10.1016/j.cell.2012.06.041PMID:22901804
  4. Alternative isoform regulation in human tissue transcriptomes. Wang, ET, Sandberg, R, Luo, S, Khrebtukova, I, Zhang, L, Mayr, C, Kingsmore, SF, Schroth, GP, Burge, CB. 2008. Nature 456, 470-6.
    doi: 10.1038/nature07509PMID:18978772
  5. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Sandberg, R, Neilson, JR, Sarma, A, Sharp, PA, Burge, CB. 2008. Science 320, 1643-7.
    doi: 10.1126/science.1155390PMID:18566288

Recent Publications

  1. Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells. Kröger, C, Afeyan, A, Mraz, J, Eaton, EN, Reinhardt, F, Khodor, YL, Thiru, P, Bierie, B, Ye, X, Burge, CB et al.. 2019. Proc. Natl. Acad. Sci. U.S.A. 116, 7353-7362.
    doi: 10.1073/pnas.1812876116PMID:30910979
  2. Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes. Rohani, N, Hao, L, Alexis, MS, Joughin, BA, Krismer, K, Moufarrej, MN, Soltis, AR, Lauffenburger, DA, Yaffe, MB, Burge, CB et al.. 2019. Cancer Res. 79, 1952-1966.
    doi: 10.1158/0008-5472.CAN-18-1604PMID:30755444
  3. Widespread Accumulation of Ribosome-Associated Isolated 3' UTRs in Neuronal Cell Populations of the Aging Brain. Sudmant, PH, Lee, H, Dominguez, D, Heiman, M, Burge, CB. 2018. Cell Rep 25, 2447-2456.e4.
    doi: 10.1016/j.celrep.2018.10.094PMID:30485811
  4. Numerous recursive sites contribute to accuracy of splicing in long introns in flies. Pai, AA, Paggi, JM, Yan, P, Adelman, K, Burge, CB. 2018. PLoS Genet. 14, e1007588.
    doi: 10.1371/journal.pgen.1007588PMID:30148878
  5. The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. Pai, AA, Henriques, T, McCue, K, Burkholder, A, Adelman, K, Burge, CB. 2017. Elife 6, .
    doi: 10.7554/eLife.32537PMID:29280736
  6. A Requirement for Mena, an Actin Regulator, in Local mRNA Translation in Developing Neurons. Vidaki, M, Drees, F, Saxena, T, Lanslots, E, Taliaferro, MJ, Tatarakis, A, Burge, CB, Wang, ET, Gertler, FB. 2017. Neuron 95, 608-622.e5.
    doi: 10.1016/j.neuron.2017.06.048PMID:28735747
  7. RNA Sequence Context Effects Measured In Vitro Predict In Vivo Protein Binding and Regulation. Taliaferro, JM, Lambert, NJ, Sudmant, PH, Dominguez, D, Merkin, JJ, Alexis, MS, Bazile, C, Burge, CB. 2016. Mol. Cell 64, 294-306.
    doi: 10.1016/j.molcel.2016.08.035PMID:27720642
  8. Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection. Pai, AA, Baharian, G, Pagé Sabourin, A, Brinkworth, JF, Nédélec, Y, Foley, JW, Grenier, JC, Siddle, KJ, Dumaine, A, Yotova, V et al.. 2016. PLoS Genet. 12, e1006338.
    doi: 10.1371/journal.pgen.1006338PMID:27690314
  9. Identification of new branch points and unconventional introns in Saccharomyces cerevisiae. Gould, GM, Paggi, JM, Guo, Y, Phizicky, DV, Zinshteyn, B, Wang, ET, Gilbert, WV, Gifford, DK, Burge, CB. 2016. RNA 22, 1522-34.
    doi: 10.1261/rna.057216.116PMID:27473169
  10. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Conway, AE, Van Nostrand, EL, Pratt, GA, Aigner, S, Wilbert, ML, Sundararaman, B, Freese, P, Lambert, NJ, Sathe, S, Liang, TY et al.. 2016. Cell Rep 15, 666-679.
    doi: 10.1016/j.celrep.2016.03.052PMID:27068461
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