In vitro reconstitution of yeast splicing with U4 snRNA reveals multiple roles for the 3′ stem–loop

Proteins confer asymmetric accessibility to U4's 3′ stem–loop in untreated splicing extract. (A) Secondary structure of the U4 3′ stem–loop showing the binding sites of oligonucleotides targeting the 5′ and 3′ sides (black and gray lines, respectively). (B) The U4 3′ stem–loop is only degraded in the presence of proteins. Denaturing Northern blot probed for U4, showing U4 size in the absence (lanes 1,5) or presence (lanes 2–4,6–8) of oligonucleotide targeting the 5′ or 3′ side of the 3′ stem–loop, or the Sm site. Lanes 1–4 are in the presence of proteins, while lanes 5–8 are in the absence of proteins.