RNA-RNA base pairing plays a critical role in the interactions between
pre-mRNAs and trans-acting factors during the processing of pre-mRNAs
(hnRNAs) into mRNAs, and it is likely that specific factors are requi
red to promote the annealing of RNAs. To identify particular nuclear c
omponents that have such activity, we fractionated HeLa nucleoplasm an
d assayed for activity which promoted the hybridization of a pre-mRNA
with an antisense RNA probe complementary to 60 nucleotides (nt) encom
passing the 3' splice site. At least nine major RNA annealing activiti
es were identified and, surprisingly, eight of these copurified partia
lly or to homogeneity with known hnRNP proteins. The activities of thr
ee of these proteins, hnRNP A1, C1 and U, were confirmed using purifie
d recombinant proteins. Moreover, we found that the RNA binding domain
alone of hnRNP C1/C2 had significant activity, indicating that this R
NA annealing may result, at least partly, from chaperone activity: a d
irect modulation of RNA conformation by hnRNP proteins. The finding th
at hnRNP proteins have strong RNA annealing activity indicates that th
ey can profoundly affect the interactions of pre-mRNAs with trans-acti
ng factors and suggests this to be an important function of hnRNP prot
eins in the processing of pre-mRNAs.