Characterization of the HeLa cell 35 kDa Alu-element binding protein

Human Alu-elements are short interspersed DNA sequences that comprise approximately 5% of the human genome. The physiological role of Alu-elements are unknown, although they are proposed to be involved in DNA replication, transcriptional regulation and nuclear transport of signal recognition particle RNA. Proteins that bind to Alu-element and Alu RNA have been identified in human cells. In HeLa cells, two proteins of 120 kDa and 35 kDa specifically bind to Alu-elements. We find that the 35 kDa protein is localized exclusively to the nucleus, while the 120 kDa protein is distributed between nucleus and cytoplasm. The 35 kDa protein is regulated by phosphorylation. Upon dephosphorylation, its DNA binding activity is significantly enhanced. Contrary to the recent identification of the smaller Alu-element binding protein as annexin II, we find that annexin II is not an Alu-element binding protein. Using a variety of techniques, we demonstrate that the 35 kDa Alu-element binding protein is distinct from annexin II.