title: A common core structure for U3 small nucleolar RNAs.
abstract: U3 nucleolar small RNA (snRNA) is involved in early processing of the primary rRNA transcript. A secondary structure model for the unusually small Trypanosoma brucei U3 snRNA was deduced by chemical modification and enzymatic cleavage of U3 snRNA in deproteinized and ribonucleoprotein (RNP) forms. Comprehensive alignment of U3 snRNAs from vertebrate, plant, fungal and protozoan species clearly delineated conserved and divergent features. The 5' domain of the T. brucei U3 snRNA appears to form one small, flexible 5' stem loop structure followed by a long single-stranded region; this model is a variation on 5' domain structures proposed for other U3 snRNAs which do not conform to a single model. The 3' domain of T. brucei U3 snRNA contains four single-stranded sequences conserved between U3 snRNAs. Of these, structural probing determined that the configurations of GAU region and box B and C sequences are altered by protein interactions in U3 snRNP. Conspicuously, the 3' domains of trypanosomal U3 snRNAs lack stem loops II and III, indicating that these structures are not required for conserved U3 snRNA functions.
authors.affiliation: Intercampus Program in Molecular Parasitology, School of Pharmacy, University of California, San Francisco 94143-1204.
authors.forename: T
authors.initials: T
authors.lastname: Hartshorne
authors.forename: N
authors.initials: N
authors.lastname: Agabian
mesh_terms: D000818:Animals; D001483:Base Sequence; D004722:Endoribonucleases / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012342:RNA, Small Nuclear / Q000737:chemistry*; D006163:Ribonuclease T1 / Q000378:metabolism; D012259:Ribonuclease, Pancreatic / Q000378:metabolism; D017411:Ribonucleoproteins, Small Nuclear / Q000737:chemistry; D012689:Sequence Homology, Nucleic Acid; D014346:Trypanosoma brucei brucei / Q000235:genetics*
chemical_list: D012342:RNA, Small Nuclear; D017411:Ribonucleoproteins, Small Nuclear; D004722:Endoribonucleases; C032825:ribonuclease V(1); D006163:Ribonuclease T1; D012259:Ribonuclease, Pancreatic