This proposal outlines a plan to combine genomic data analysis, biochemistry, structural biology, and functional characterization to understand the role of ribonucleoprotein complexes in regulating T-cell activation. Expression data were mined to identify a set of RNA-binding proteins that were either differentially expressed or alternatively spliced, upon T-cell activation. These RNA-binding proteins constitute the input into a structural genomics effort, representing the first of three structural target streams. Protein interacting partners for these RNA-binding proteins have been identified from the Human Interactome Database, and the formation of specific protein-protein complexes will be confirmed both in T-cells and in vitro. The resulting set of protein-protein complexes will be input into a structural genomics effort as the second target stream. The RNA targets for the RNA-binding proteins will be identified using high throughput sequencing and crosslinking (HITS-CLIP), and confirmed in T-cells and in vitro. The resulting set of RNA-protein complexes will be input into a structural genomics effort as the third target stream. For the proteins, protein-protein complexes, and RNA-protein complexes that emerge from the structural genomics effort, functional validation will be carried out in T-cells to determine the role of these specific components in T-cell activation. This work should provide significant new insights into the structure of ribonucleoprotein complexes in general, as well as insights into how these complexes are involved in posttranscriptional gene regulation.
|Whisenant, Thomas C (2017) Gene expression profiling of U2AF2 dependent RNA-protein interactions during CD4 + T cell activation. Genom Data 11:77-80|
|Stepanyuk, Galina A; Serrano, Pedro; Peralta, Eigen et al. (2016) UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta Crystallogr D Struct Biol 72:497-511|
|Whisenant, Thomas C; Peralta, Eigen R; Aarreberg, Lauren D et al. (2015) The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells. PLoS One 10:e0144409|
|Head, Steven R; Komori, H Kiyomi; LaMere, Sarah A et al. (2014) Library construction for next-generation sequencing: overviews and challenges. Biotechniques 56:61-4, 66, 68, passim|
|Podshivalova, Katie; Salomon, Daniel R (2013) MicroRNA regulation of T-lymphocyte immunity: modulation of molecular networks responsible for T-cell activation, differentiation, and development. Crit Rev Immunol 33:435-76|