title: The 28S-18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor.
abstract: In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from approximately 11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an approximately 55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A' pre-rRNA processing sites within the 5' external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5' ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C. fasciculata and Trypanosoma brucei involves 3'-terminal addition of three A residues that are not present in the corresponding DNA sequences.
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada.
authors.forename: M N
authors.initials: MN
authors.lastname: Schnare
authors.forename: J C
authors.initials: JC
authors.lastname: Collings
authors.forename: D F
authors.initials: DF
authors.lastname: Spencer
authors.forename: M W
authors.initials: MW
authors.lastname: Gray
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D017124:Conserved Sequence; D016831:Crithidia fasciculata / Q000235:genetics* / Q000378:metabolism; D016054:DNA, Protozoan / Q000235:genetics* / Q000378:metabolism; D004275:DNA, Ribosomal / Q000235:genetics* / Q000378:metabolism; D018740:Genetic Heterogeneity; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D012335:RNA, Ribosomal / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid; D015183:Restriction Mapping; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014346:Trypanosoma brucei brucei / Q000235:genetics
chemical_list: D016054:DNA, Protozoan; D004275:DNA, Ribosomal; D012322:RNA Precursors; D012335:RNA, Ribosomal; D020537:RNA, Small Nucleolar; C117378:RNA, U3 small nucleolar