Solution Structure of the HIV-1 Intron Splicing Silencer and its Interactions with the UP1 Domain of hnRNP A1 [Gene Regulation]

November 25th, 2015 by Jain, N., Morgan, C. E., Rife, B. D., Salemi, M., Tolbert, B. S.

Splicing patterns in HIV-1 are maintained through cis regulatory elements that recruit antagonistic host RNA binding proteins. The activity of the 3 prime acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b) and an exonic splicing enhancer (ESE3). Since HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate the UP1 domain of hnRNP A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA binding protein.