Gene regulation: My lab seeks to uncover mechanisms and pathways underlying post-transcriptional control, mediated by the interaction between RNA binding proteins and cis-regulatory elements. We utilize large-scale biochemical and genomics assays coupled with high-throughput sequencing to study the molecular mechanisms of and biological impact underlying alternative splicing, polyadenylation, transport, translation, RNA turnover and microRNA biology. We are the world’s leader in developing the molecular and cellular resources and robust technologies required for truly large-scale studies of hundreds of RNA binding proteins and their RNA targets.
RNA-targeting CRISPR/Cas: My lab published the first demonstration of targeting RNA in live cells using the CRISPR/Cas9 technology in 2016 and we are pursuing multiple avenues of applications ranging from therapeutic intervention of neuromuscular diseases to single cell RNA imaging.
Neurological diseases: My lab studies the molecular basis of mental disorders such as autism spectrum disorders and neurodegenerative diseases (ALS) using in vitro stem cell models and in vivo mice models.
Virus-host interactions: My lab reveals new insights into how DNA and RNA viruses affect the host transcriptome.
Single cell technologies and analysis: My lab develops new molecular capture methods and machine-learning approaches to single cell RNA-seq/DNA analysis and visualization tools.
- Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo E-C, Krach F, Yang D, Sen A, Fulzele A, Wozniak J, Gonzalez DJ, Kankel MW, Gao F-B, Bennet EJ, Lecuyer E, Yeo GW. Context-dependent and disease-specific diversity in protein interactions within Stress Granules. Cell, 2018. PMID:29373831
- Batra R, Nelles DA, Pirie E, Blue SM, Marina RJ, Wang H, Chaim IA, Thomas JD, Zhang N, Nguyen V, Aigner S, Markmiller S, Xia G, Corbett KD, Swanson MS, Yeo GW. Elimination of toxic microsatellite repeat expansion RNA by RNA-targeting Cas9. Cell, 2017. PMID:28803727. (Recommended by Faculty 1000).
- Song Y, Botvinnik OB, Lovci MT, Kakaradov B, Liu P, Xu JL, Yeo GW. Single-cell alternative splicing analysis with Expedition reveals splicing dynamics during neuron differentiation. Molecular Cell, 2017. PMID:28673540
- Martinez FJ, Pratt GA, Van Nostrand EL, Batra R, Huelga SC, Kapeli K, Freese P, Chun SJ, Ling K, Gelboin-Burkhart C, Fijany L, Wang H, Nussbacher JK, Broski, SM, Kim HJ, Lardelli R, Sundararaman B, Donohue JP, Javaherian A, Lykke-Andersen J, Finkbeiner S, Bennett F, Ares M, Burge CB, Taylor JP, Rigo F, Yeo GW. Protein-RNA networks regulated by normal and ALS-associated mutant HNRNPA2B1 in the nervous system. Neuron, 2016. PMID:27773581
- Nelles DA, Fang M, O’Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW. Programmable RNA tracking in Live Cells with CRISPR/Cas9, Cell, 2016. Corresponding. PMID: 26997482. (Recommended by Faculty 1000, Top 100 stories in 2016 in Discover magazine, Dec 2016).
- Van Nostrand EL, Pratt GA, Shishkin AA, Gelboin-Burkhart C, Fang M, Sundararaman B, Blue SM, Nguyen TB, Surka C, Elkins K, Stanton R, Rigo F, Guttman M, Yeo GW. Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites, Nature Methods, 2016. Corresponding. PMID: 27018577. (Recommended by Faculty 1000).
- Sundararaman B, Zhan L, Blue S, Stanton R, Elkins K, Olson S, Wei X, Van Nostrand EL, Huelga SC, Smalec BM, Wang X, Hong EL, Davidson JM, Lecuyer E, Graveley BR, Yeo GW. Resources for the comprehensive discovery of functional RNA elements, Molecular Cell, 2016. Corresponding. PMID: 26990993. (Recommended by Faculty 1000).
- Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark T, Gehman LT, Hoon S, Massirer K, Pratt GA, Black DL, Gray J, Conboy JG, Yeo GW. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nature Structural and Molecular Biology, 2013. PMID: 24213538. Corresponding. (Highlighted in Editor’s Choice in Science). (Recommended by Faculty 1000).