Pre-mRNA splicing is essential for proper gene expression in higher eukaryotic genomes, as the vast majority of genes contain introns that have to be accurately recognized and removed. Recent studies have revealed that >90% of the genes undergo alternative splicing, which is believed to contribute to the complexity of the proteome in different cell types and tissues in vertebrates and abundant evidence suggests that altered splicing causes a variety of human diseases. Despite extensive knowledge on the splicing mechanism based on biochemical dissection of model minigenes, we know little about how many genes are involved in the regulation of alternative splicing and where the functional RNA elements are embedded in the human genome. Built on our productive research in the current award period, we now propose a bold plan to systematically attack the critical gap of our knowledge about the regulation of alternative splicing. We will pursue three major lines of research by utilizing the latest and innovative genomics technologies. (1) We will use a new, automated platform recently developed in our lab to profile hundreds of conserved alternative splicing events against every annotated genes in the human genome. This unbiased approach will generate unprecedented information to uncover novel splicing regulators and deduce pathways in regulated splicing. (2) We will focus on RNA binding proteins involved in individual regulatory pathways to elucidate the molecular basis for regulated splicing by mapping their physical interactions with expressed RNA. For this purpose, we will construct a large panel of cell lines based on FLP-In 293 cells to express individual RNA binding proteins as a V5-tagged protein at the C- terminus, which will permit large-scale mapping of RNA-protein interactions by CLIP-seq (CrossLinking ImmunoPrecipitation followed by high throughput sequencing) under a similar and optimized set of conditions. (3) Our third goal is to use the information generated from the proposed mapping and functional studies to develop an integrated framework for de novo prediction of splicing regulation by using machine-learning and graphical models. This research has the potential to fundamentally change our view on splicing control and its contribution to human disease.

Public Health Relevance

This RNA genomics project aims to deduce the splicing code in the human genome by systematic determination of genes involved in regulated splicing, elucidation of regulatory pathways, and RNA-protein interactions. The proposed research will use the latest genomics technologies to reveal functional RNA elements in the human genome, which will provide the molecular basis for many RNA-related human diseases.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Feingold, Elise A
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University of California San Diego
Other Basic Sciences
Schools of Medicine
La Jolla
United States
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Roloff, Alexander; Nelles, David A; Thompson, Matthew P et al. (2018) Self-Transfecting Micellar RNA: Modulating Nanoparticle Cell Interactions via High Density Display of Small Molecule Ligands on Micelle Coronas. Bioconjug Chem 29:126-135
Zhang, Kai; Zhang, Xiaorong; Cai, Zhiqiang et al. (2018) A novel class of microRNA-recognition elements that function only within open reading frames. Nat Struct Mol Biol 25:1019-1027
Wheeler, Emily C; Van Nostrand, Eric L; Yeo, Gene W (2018) Advances and challenges in the detection of transcriptome-wide protein-RNA interactions. Wiley Interdiscip Rev RNA 9:
Krach, Florian; Batra, Ranjan; Wheeler, Emily C et al. (2018) Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS. Acta Neuropathol 136:405-423
Chen, Liang; Chen, Jia-Yu; Huang, Yi-Jou et al. (2018) The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations. Mol Cell 69:412-425.e6
Markmiller, Sebastian; Soltanieh, Sahar; Server, Kari L et al. (2018) Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. Cell 172:590-604.e13
Bao, Xichen; Guo, Xiangpeng; Yin, Menghui et al. (2018) Capturing the interactome of newly transcribed RNA. Nat Methods 15:213-220
Nussbacher, Julia K; Yeo, Gene W (2018) Systematic Discovery of RNA Binding Proteins that Regulate MicroRNA Levels. Mol Cell 69:1005-1016.e7
Hu, Jing; Qian, Hao; Xue, Yuanchao et al. (2018) PTB/nPTB: master regulators of neuronal fate in mammals. Biophys Rep 4:204-214
Van Nostrand, Eric L; Shishkin, Alexander A; Pratt, Gabriel A et al. (2017) Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions. Methods 126:29-37

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