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Dr. Fu's lab


Research Overview

The Fu laboratory is interested in molecular and cell biology of RNA metabolism and regulation in higher eukaryotic cells. Current research interests in the Fu lab include the regulation of alternative splicing, functional RNA elements in mammalian genomes, transcription/splicing coupling, nuclear architecture, and cellular reprogramming.

 

Research Interest

  1. Regulation of gene expression by SR proteins
  2. We have long-term interests in the SR family of splicing factors and regulators (Fu and Maniatis, 1990; Fu, 1995). These RNA binding proteins are responsible for committing newly transcribed pre-mRNA into the splicing pathway (Fu, 1993) and are extensively involved in the regulation of alternative splicing in development (Xu et al., 2005). Besides their traditional functions in regulated splicing, specific SR proteins, particularly SC35 (now re-named as SRSF2), also facilitate transcriptional elongation (Lin et al., 2008). More recently, we show that SRSF2 mediates the release of paused RNA polymerase from gene promoters by regulating translocation of a Pol II CTD kinase (pTEFb) from a non-coding RNA (7SK) complex to promoter-associated nascent RNA (Ji et al., 2013). These findings highlight fundamental functions of SR proteins in integrating several key gene expression processes in mammalian cells (Zhong et al., 2009). We are now pursuing multiple projects to dissect the function of SR proteins in gene expression and determine their contributions to key developmental and disease processes.

  3. Functional genomics of RNA binding proteins
  4. We have been using functional genomics approaches, particularly next generation sequencing, to elucidate functional RNA elements in higher eukaryotic genomes. Using Crosslinking Immunoprecipitation coupled with deep sequencing (CLIP-seq), we have been mapping genome-wide interactions of specific RNA binding proteins with transcribed RNAs in mammalian genomes to determine their functions and elucidate new regulatory principles (Xue et al., 2009; Pandit et al., 2013). We have developed the RNA-mediated oligo Annealing, Selection, and Ligation (RASL) strategy for large-scale analysis of gene expression and alternative splicing (Yeakley et al., 2002). Coupling RASL with deep sequencing (RASL-seq), we have established an automated platform for chemical screenings (Li et al., 2012). We are using these high throughput technologies to dissect regulatory networks through genome-wide knockdown and overexpression screenings.

  5. Signaling splicing regulation by SR protein-specific kinases
  6. Our lab has identified and extensively characterized the SRPK family of kinases specific for SR proteins and RS domain-containing proteins (Gui et al., 1994; Zhou and Fu, 2013). This family of kinases uses an unusual mechanism to catalyze processive phosphorylation reactions on their substrates. We show that the activities of SRPKs are subjected to regulation by molecular chaperones in the cytoplasm (Zhong et al., 2008). More recently, we demonstrate that these splicing kinases are direct downstream targets for activated Akt and are responsible for transducing growth signals to regulate alternative splicing in the nucleus (Zhou et al., 2012). We are pursuing these splicing kinases as convergent points for different signaling events and their vital roles in cell proliferation and tumorigenesis.

  7. Regulatory RNA and RNA binding proteins in cellular reprogramming
  8. Numerous non-coding RNAs are expressed from mammalian genomes. We provide evidence for the inducted expression of enhancer-derived RNA (called eRNA) and their association with regulated gene expression during cellular reprogramming (Wang et al., 2011). As different regulatory RNAs likely function via specific RNA binding proteins, we are deciphering new regulatory paradigms by characterizing key RNA binding proteins during cellular reprogramming. We recently show that a nuclear matrix protein (called hnRNP U/SAF-A) interacts with diverse non-coding RNAs to regulate intracellular trafficking and function of RNA-protein complexes (Xiao et al., 2012). This opens new doors in understanding non-coding RNA functions in regulated gene expression. We have recently discovered that regulated expression of an RNA binding protein (PTB) is sufficient to induce large-scale reprogramming of gene expression, resulting in phenotypic conversion of fully differentiated cells into functional neurons (Xue et al., 2013). These findings generate a new research direction in our lab to develop novel strategies for neuronal induction in differentiated cells and explore their applications in neurodegenerative diseases.

     

Selective publications

  • Fu, X-D, Maniatis, T. (1990). Factor required for mammalian spliceosome assembly is localized to discrete regions in the nucleus. Nature, 343:437--441 [PubMed]
  • Fu, X-D (1993). Specific commitment of different pre-mRNAs to splicing by single SR proteins. Nature, 365:82--85 [PubMed]
  • Gui, J.F., Lane, W.S., Fu, X-D (1994). A serine kinase regulates intracellular localization of splicing factors in the cell cycle. Nature, 369:678--682 [PubMed]
  • Fu, X-D (1995). The superfamily of arginine/serine-rich splicing factors. RNA, 1:663--680 [PubMed]
  • Yeakley, J.M., Fan, J-B, Doucet, D., Luo, L., Wickham, E., Ye, Z., Chee, M.S., Fu, X-D (2002). Profiling alternative splicing on fiber-optic arrays. Nat Biotechnol, 20:353--358 [PubMed]
  • Xu, X., Yang, D., Ding, J-H, Wang, W., Chu, P-H, Dalton, N.D., Wang, H-Y, Bermingham, J.R., Ye, Z., Liu, F., Rosenfeld, M.G., Manley, J.L., Ross, J., Chen, J., Xiao, R-P, Cheng, H., Fu, X-D (2005). ASF/SF2-regulated CaMKIIdelta alternative splicing temporally reprograms excitation-contraction coupling in cardiac muscle. Cell, 120:59--72 [PubMed]
  • Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S., Fu, X-D (2008). The splicing factor SC35 has an active role in transcriptional elongation. Nat Struct Mol Biol, 15:819--826 [PubMed]
  • Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y-S, Zhang, C., Yeo, G., Black, D.L., Sun, H., Fu, X-D*, Zhang, Y.* (2009). Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell, 36:996--1006 (*co-corresponding authors) [PubMed]
  • Zhong, X-Y, Ding, J-H, Adams, J.A., Ghosh, G., Fu, X-D (2009). Regulation of SR protein phosphorylation and alternative splicing by modulating kinetic interactions of SRPK1 with molecular chaperones. Genes Dev, 23:482--495 [PubMed]
  • Zhong, X-Y, Wang, P., Han, J., Rosenfeld, M.G., Fu, X-D (2009). SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Mol Cell, 35:1--10 [PubMed]
  • Wang, D., Garcia-Bassets, I., Benner, C., Li, W., Su, X., Zhou, Y., Qiu, J., Liu, W., Kaikkonen, M.U., Ohgi, K.A., Glass, C.K., Rosenfeld, M.G., Fu, X-D (2011). Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature, 474:390--394 [PubMed]
  • Li, H., Zhou, H., Wang, D., Qiu, J., Zhou, Y., Li, X., Rosenfeld, M.G., Ding, S., Fu, X-D (2012). Versatile pathway-centric approach based on high-throughput sequencing to anticancer drug discovery. Proc Natl Acad Sci U S A, 109:4609--4614 [PubMed]
  • Xiao, R., Tang, P., Yang, B., Huang, J., Zhou, Y., Shao, C., Li, H., Sun, H., Zhang, Y., Fu, X-D (2012). Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation. Mol Cell, 45:656--668 [PubMed]
  • Zhou, Z., Qiu, J., Liu, W., Zhou, Y., Plocinik, R.M., Li, H., Hu, Q., Ghosh, G., Adams, J.A., Rosenfeld, M.G., Fu, X-D (2012). The Akt-SRPK-SR axis constitutes a major pathway in transducing EGF signaling to regulate alternative splicing in the nucleus. Mol Cell, 47:422--433 [PubMed]
  • Xue, Y., Ouyang, K., Huang, J., Zhou, Y., Ouyang, H., Li, H., Wang, G., Wu, Q., Wei, C., Bi, Y., Jiang, L., Cai, Z., Sun, H., Zhang, K., Zhang, Y., Chen, J., Fu, X-D (2013). Direct conversion of fibroblasts to neurons by reprogramming PTB-regulated microRNA circuits. Cell, 152:82--96 [PubMed]
  • Pandit, S., Zhou, Y., Shiue, L., Coutinho-Mansfield, G., Li, H., Qiu, J., Huang, J., Yeo, G.W., Ares, J.M., Fu, X-D (2013). Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell, 50:223--235 [PubMed]
  • Ji, X., Zhou, Y., Pandit, S., Huang, J., Li, H., Lin, C.Y., Xiao, R., Burge, C.B., Fu, X-D (2013). SR proteins collaborate with 7SK and promoter-associated nascent RNA to release paused polymerase. Cell, 153:855--868 [PubMed]
  • Zhou, Z., Fu, X-D (2013). Regulation of splicing by SR proteins and SR protein-specific kinases. Chromosoma, 122:191--207 [PubMed]

   © 2013. Fu lab at the University of California in San Diego