RNA binding proteins (RBPs) interact with functional RNA elements embedded within pre- and mature messenger RNA to form messenger ribonucleoprotein (mRNP) complexes. These interactions result in the faithful execution of RNA processing events such as pre-mRNA alternative splicing, RNA stability and translational control. Aberrant alterations in the interactions between the RBPs and their RNA elements ultimately lead to behavioral abnormalities and neurological developmental defects, which can often manifest as fatal diseases such as Spinal Muscular Atrophy and Amyotrophic Lateral Sclerosis or life-long debilitating behavioral abnormalities such as Prader-Willi/Angelman Syndromes, Schizophrenia and Autism Spectrum Disorder. These findings underscore the importance of investigating the roles of these RBPs in the brain. In particular, our project is aimed at systematically, using genome-wide biochemical and bioinformatic assays, identifying the functional RNA elements that are recognized by RBPs in mouse brain and human neurons. We will develop a novel resource of human pluripotent stem cells stably expressing tagged RBPs that can be differentiated into human neurons. This will enable the identification of RNA binding sites of 50 RBPs in human neural RNAs in a uniform and systematic manner using cutting-edge genomic approaches such as cross-linking and immunoprecipitation followed by high-throughput sequencing (CLIP- seq). To reveal the splicing, stability, and translational changes that are dependent on direct binding of these RBPs we will perform high-throughput sequencing of mRNAs (RNA-seq) and ribosome-protected fragments (RPFs). Finally, we will leverage our computational expertise to build predictive models using this genome-wide, multi-scale, mRNP code in the brain.

Public Health Relevance

Over the last decade, defects in RNA binding proteins (RBPs) themselves or the interactions between RNA binding sites of RBPs have become recognized as increasingly responsible for neurological disease and mental disorders. This proposal seeks to establish the interactions among selected RBPs and their functional RNA elements in mammalian neurons. This will be a crucial first step in elucidating the RNA networks regulated by these RBPs in the brain.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Research Project (R01)
Project #
Application #
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Mamounas, Laura
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Diego
Other Basic Sciences
Schools of Medicine
La Jolla
United States
Zip Code
Washburn, Michael C; Kakaradov, Boyko; Sundararaman, Balaji et al. (2014) The dsRBP and inactive editor ADR-1 utilizes dsRNA binding to regulate A-to-I RNA editing across the C. elegans transcriptome. Cell Rep 6:599-607
Siddiqi, Saima; Foo, Jia Nee; Vu, Anthony et al. (2014) A novel splice-site mutation in ALS2 establishes the diagnosis of juvenile amyotrophic lateral sclerosis in a family with early onset anarthria and generalized dystonias. PLoS One 9:e113258
Arsenio, Janilyn; Kakaradov, Boyko; Metz, Patrick J et al. (2014) Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses. Nat Immunol 15:365-72
Rush, Anthony M; Nelles, David A; Blum, Angela P et al. (2014) Intracellular mRNA regulation with self-assembled locked nucleic acid polymer nanoparticles. J Am Chem Soc 136:7615-8
Belzile, Jean-Philippe; Stark, Thomas J; Yeo, Gene W et al. (2014) Human cytomegalovirus infection of human embryonic stem cell-derived primitive neural stem cells is restricted at several steps but leads to the persistence of viral DNA. J Virol 88:4021-39
Van Wynsberghe, Priscilla M; Finnegan, Emily F; Stark, Thomas et al. (2014) The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans. Dev Biol 390:126-35
Lovci, Michael T; Ghanem, Dana; Marr, Henry et al. (2013) Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol 20:1434-42
Lagier-Tourenne, Clotilde; Baughn, Michael; Rigo, Frank et al. (2013) Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for ALS and frontotemporal degeneration. Proc Natl Acad Sci U S A 110:E4530-9
Marchetto, Maria C N; Narvaiza, Inigo; Denli, Ahmet M et al. (2013) Differential L1 regulation in pluripotent stem cells of humans and apes. Nature 503:525-9
Verma, Sunil K; Deshmukh, Vaibhav; Liu, Patrick et al. (2013) Reactivation of fetal splicing programs in diabetic hearts is mediated by protein kinase C signaling. J Biol Chem 288:35372-86

Showing the most recent 10 out of 13 publications