Polypyrimidine Tract-Binding Protein 1 and hnRNP A1 recognize unique features of the Sm site in U7 snRNA

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 containing Lsm10 and Lsm11 instead of SmD1 and SmD2 found in the spliceosomal snRNPs. The assembly of the spliceosomal Sm ring depends on the SMN complex, with one of its nine subunits, Gemin5, recognizing the spliceosomal Sm site. While the assembly of the U7-specific Sm ring also requires the SMN complex, the unusual Sm site of U7 snRNA is not recognized by Gemin5, and the identity of its counterpart that performs this function in biogenesis of U7 snRNP, has not been determined. Here, we looked for proteins that bind U7 snRNA but not to its mutant altered within the Sm site. We identified Polypyrimidine Tract-Binding Protein 1 (PTBP1) as the main protein that meets this specificity. Binding of PTBP1 to U7 snRNA also depends on the upstream CUCUUU motif that base pairs with histone pre-mRNAs and defines substrate specificity of U7 snRNP. Thus, PTBP1 simultaneously recognizes two functionally essential and highly conserved sites within U7 snRNA. In addition to PTBP1, U7 snRNA interacts with hnRNP A1, which recognizes a different part of the U7-specific Sm site. Interestingly, the two proteins can form with U7 snRNA a larger complex, which also contains SMN protein, a subunit of the SMN complex. Altogether, these results raise the possibility that PTBP1 and hnRNP A1 act collectively to substitute for Gemin5 in the assembly of U7-specific Sm ring.