Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution

Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA seq...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 114; no. 9; pp. 2206 - 2211
Main Authors Jain, Niyati, Lin, Hsuan-Chun, Morgan, Christopher E., Harris, Michael E., Tolbert, Blanton S.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 28.02.2017
Subjects
Binding sites
Biological Sciences
Lentivirus
Ligands
Physical Sciences
Quantitative analysis
Retroviridae
Ribonucleic acid
RNA
Transcription factors
thermodynamics
RNA structure
protein–RNA specificity
binding kinetics
hnRNP A1
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Summary:Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding 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 exon splicing silencer 3 (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. For a subset of ESS3 variants, 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.
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Edited by Michael F. Summers, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD, and approved January 13, 2017 (received for review October 1, 2016)
1N.J. and H.-C.L. contributed equally to this work.
Author contributions: M.E.H. and B.S.T. designed research; N.J., H.-C.L., and C.E.M. performed research; N.J., H.-C.L., C.E.M., M.E.H., and B.S.T. analyzed data; and M.E.H. and B.S.T. wrote the paper.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1616371114