Proteins that recognize unique features of U7 snRNA and may substitute for Gemin5 in the assembly of U7-specific Sm ring.

U7 snRNA is a 60-nucleotide component of U7 snRNP, a multi-subunit endonuclease that cleaves precursors of metazoan replication-dependent histone mRNAs at the 3' end, hence generating mature histone mRNAs. The Sm site in U7 snRNA differs from the Sm site in spliceosomal snRNAs and promotes the assembly of a unique Sm ring of the U7 snRNP containing Lsm10 and Lsm11 instead of the spliceosomal SmD1 and SmD2 proteins. The assembly of the spliceosomal Sm ring depends on the SMN complex, with one of its nine subunits, Gemin5, recognizing the spliceosomal-type Sm site. While the assembly of the U7-specific Sm ring also requires the SMN complex, the identity of the protein that recognizes the unusual Sm site of U7 snRNA resulting in the incorporation of Lsm10 and Lsm11 has not been determined. Here, we looked for proteins that interact with U7 snRNA. Among U7 snRNA binders, mass spectrometry identified Polypyrimidine Tract-Binding Protein 1 (PTBP1) and Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 (IGF2BP3). The binding of these two proteins to U7 snRNA depends on its unique Sm site and on the upstream CUCUUU motif that base pairs with histone pre-mRNAs and defines substrate specificity of U7 snRNP. Among proteins bound to U7 snRNA, we also identified hnRNP A1. We show that hnRNP A1 interacts with the SMN protein of the SMN complex, a likely prerequisite for the protein that substitutes for Gemin5 in the assembly of U7-specific Sm ring. Finally, our studies also suggest a mechanism that explains why Gemin5 does not bind the Sm site of U7 snRNA.