Poster abstracts
Poster number 63 submitted by Niyati Jain
Rules of RNA Specificity of hnRNP A1 Revealed by Global and Quantitative Analysis of its Affinity Distribution
Niyati Jain (Department of Chemistry, Case Western Reserve University, Cleveland, OH), Hsuan-Chun Lin (Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH), Christopher E. Morgan (Department of Chemistry, Case Western Reserve University, Cleveland, OH), Michael E. Harris (Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH), Blanton S. Tolbert (Department of Chemistry, Case Western Reserve University, Cleveland, OH)
Abstract:
The selectivity of many RNA binding proteins (RBPs) is more complex than
specific versus non-specific. Heterogeneous nuclear ribonucleoprotein A1
(hnRNP A1) is a multipurpose RBP involved in normal and pathologic RNA
metabolism. Transcriptome-wide mapping and in vitro evolution identify
consensus motifs; however, such data do not reveal how surrounding RNA
sequence and structural context modulate affinity. We determined the affinity of
hnRNP A1 for all possible sequence variants (n=16,384) of the HIV ESS3 7-nt
apical loop. Analysis of the affinity distribution identifies the optimal motif 5’-
YAG-3’ and shows how its copy number, position in the loop and loop structure
modulate affinity. We show that specificity is determined by association rate
constants, and that variants lacking the minimal sequence motif bind competitively with consensus RNA.
Thus, the results reveal general rules of specificity of hnRNP A1 and provide a quantitative framework for understanding
how it discriminates between alternative competing RNA ligands in vivo.
Keywords: RNA binding proteins, hnRNP A1