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Abstract
An RNA-dependent association of Ku antigen with nuclear DNA helicase II (NDH II),
alternatively named RNA helicase A (RHA), was found in nuclear extracts of HeLa cells
by immunoprecipitation and by gel filtration chromatography. Both Ku antigen and NDH
II were associated with hnRNP complexes. Two-dimensional gel electrophoresis showed
that Ku antigen was most abundantly associated with hnRNP C, K, J, H and F, but apparently
not with others, such as hnRNP A1. Unexpectedly, DNA-dependent protein kinase (DNA-PK),
which comprises Ku antigen as the DNA binding subunit, phosphorylated hnRNP proteins
in an RNA-dependent manner. DNA-PK also phosphorylated recombinant NDH II in the presence
of RNA. RNA binding assays displayed a preference of DNA-PK for poly(rG), but not
for poly(rA), poly(rC) or poly(rU). This RNA binding affinity of DNA-PK can be ascribed
to its Ku86 subunit. Consistently, poly(rG) most strongly stimulated the DNA-PK-catalyzed
phosphorylation of NDH II. RNA interference studies revealed that a suppressed expression
of NDH II altered the nuclear distribution of hnRNP C, while silencing DNA-PK changed
the subnuclear distribution of NDH II and hnRNP C. These results support the view
that DNA-PK can also function as an RNA-dependent protein kinase to regulate some
aspects of RNA metabolism, such as RNA processing and transport.