The process of alternative splicing (AS) is a powerful mechanism for generating mRNA diversity from protein coding genes. Alternative mRNA isoforms from the same gene can differ subtly from each other or have radical alterations in their sequence composition. Remarkably, very little is known about whether or not this diverse pool of mRNA is converted to protein. One intriguing clue for solving this problem comes from our previous studies suggesting that the process of alternative splicing influences the translational efficiency of the resultant mRNA isoforms. In this proposal, we use both genome-wide and molecular approaches to untangle the intricate mechanisms coupling post-transcriptional gene expression. To accomplish this goal we propose the following specific aims: (1) Determine the prevalence and impact of AS-TC in human gene regulation. In this aim we will quantify mRNA isoforms with respect to the translating polyribosomes in 15 different ENCODE cell lines and two different primate stem cell model systems using our recently developed Frac-Seq methodology. These experiments will reveal the scope of AS-TC regulatory events and determine if this is a conserved mechanism for spatial or temporal regulation of gene expression. (2) Using the Serine and Arginine-rich protein SRSF1 as a model, we will elucidate the roles and targets of shuttling RNA binding proteins in coupling of post- transcriptional gene regulation. In this aim we will map the binding sites of SRSF1 or non-shuttling mutants in different subcellular fractions using CLIP-Seq;Determine the dependency of AS-TC on SRSF1 using Frac-Seq;Discover novel trans-acting AS-TC factors using RNA affinity chromatography. The results of this work will define a new paradigm for the function(s) of shuttling proteins such as SRSF1 in the coordination of post- transcriptional gene expression. (3) Determine the molecular mechanisms regulating isoform-specific mRNA translation. In this aim we will elucidate the full repertoire of RNA elements and structures that regulate polyribosome association using FragSeq and QUEPASA then determine biochemically how sequence elements involved in AS-TC modulate mechanisms of translation initiation and elongation. By determining how AS-TC elements regulate mRNA translation we will be able to refute or support the central hypothesis of this proposal, that alternative splicing generates isoforms with different translational efficiency. If sequences associated with differential polyribosome association do not directly control translation initiation or elongation, then we will con- sider our alternative hypothesis: that a significant fraction of mRNA isoform diversity arises from noisy splicing which are then excluded from polyribosomes by some unknown mRNA surveillance pathway. Solving this important problem will not only reveal how cis-elements influence translational yield, but will also define mechanistic links between the processes of alternative splicing and mRNA translation. In the long-term, our research program will facilitate new opportunities for RNA-based diagnostics and therapies that will be applicable to a wide array of human diseases.

Public Health Relevance

The transfer of protein coding information from our genome to the protein synthesis machinery occurs through a messenger RNA (mRNA) intermediate. Defective mRNA processing contributes to many human diseases including cancer, spinal muscular atrophy, cystic fibrosis and diabetes in complex ways that are poorly understood. This project will improve human health through the identification of regulatory sequences and mechanisms controlling two of the most important aspects RNA processing, alternative pre-mRNA splicing and mRNA translation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Bender, Michael T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Santa Cruz
Other Domestic Higher Education
Santa Cruz
United States
Zip Code
Howard, Jonathan M; Lin, Hai; Wallace, Andrew J et al. (2018) HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo. Genome Res 28:689-698
Rice, Edward S; Kohno, Satomi; John, John St et al. (2017) Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res 27:686-696
Penalva, Luiz O; Sanford, Jeremy R (2017) From mechanisms to therapy: RNA processing's impact on human genetics. Hum Genet 136:1013-1014
Martinez-Nunez, Rocio T; Sanford, Jeremy R (2016) Studying Isoform-Specific mRNA Recruitment to Polyribosomes with Frac-seq. Methods Mol Biol 1358:99-108
Ennajdaoui, Hanane; Howard, Jonathan M; Sterne-Weiler, Timothy et al. (2016) IGF2BP3 Modulates the Interaction of Invasion-Associated Transcripts with RISC. Cell Rep 15:1876-83
Palanichamy, Jayanth Kumar; Tran, Tiffany M; Howard, Jonathan M et al. (2016) RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. J Clin Invest 126:1495-511
Howard, Jonathan M; Sanford, Jeremy R (2015) The RNAissance family: SR proteins as multifaceted regulators of gene expression. Wiley Interdiscip Rev RNA 6:93-110
Hansen, Heidi Theil; Rasmussen, Simon Horskjær; Adolph, Sidsel Kramshøj et al. (2015) Drosophila Imp iCLIP identifies an RNA assemblage coordinating F-actin formation. Genome Biol 16:123
Roberts, Jacqueline M; Ennajdaoui, Hanane; Edmondson, Carina et al. (2014) Splicing factor TRA2B is required for neural progenitor survival. J Comp Neurol 522:372-92