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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project--Cooperative Agreements (U01)
Project #
5U01GM094653-03
Application #
8307867
Study Section
Special Emphasis Panel (ZGM1-CBB-0 (BC))
Program Officer
Preusch, Peter C
Project Start
2010-09-30
Project End
2015-06-30
Budget Start
2012-07-01
Budget End
2013-06-30
Support Year
3
Fiscal Year
2012
Total Cost
$1,062,857
Indirect Cost
$503,164
Name
Scripps Research Institute
Department
Type
DUNS #
781613492
City
La Jolla
State
CA
Country
United States
Zip Code
92037
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