Splicing is a complex mechanism that generates mature mRNA from pre-mRNA and which is essential for a correct gene expression. It involves many factors – nearly 400, if we consider alternative splicing as well – and it is tightly controlled. A new paper published in Molecular Cell by Juan Valcárcel, head of the Regulation of Alternative pre-mRNA Splicing group at the CRG, and colleagues has now identified an heterogeneous nuclear ribonucleoprotein (hnRNP) that helps in the recognition of the 3′ splice site.
The essential pre-mRNA splicing factor U2AF guides the early stages of splice site choice by recognizing a polypyrimidine (Py) tract consensus sequence near the 3′ splice site. The U2AF 65 KDa subunit binds to the Py tract while its 35 KDa subunit binds the invariant AG dinucleotide at the intron 3′ end.
Since Py tracts are relatively poorly conserved in higher eukaryotes, how does U2AF find the right ones?
By using in vitro and in vivo depletion, as well as reconstitution assays using purified components, the authors have identified hnRNP A1 as an RNA binding protein that allows U2AF to discriminate between pyrimidine-rich RNA sequences followed or not by a 3′ splice site AG.
Valcárcel and colleagues have demonstrated using biochemical assays and NMR that hnRNP A1 forms a ternary complex with the U2AF heterodimer on AG-containing/uridine-rich RNAs, while it displaces U2AF from non-AG-containing/uridine-rich RNAs.
Tavanez JP, Madl T, Kooshapur H, Sattler M, Valcárcel J
hnRNP A1 Proofreads 3′ Splice Site Recognition by U2AF.
Mol Cell. 2012 Feb 10;45(3):314-29