Messenger RNA processing sites in Trypanosoma brucei.
In Kinetoplastids, protein-coding genes are transcribed polycistronically by RNA polymerase II. Individual mature mRNAs are generated from polycistronic precursors by 5' trans splicing of a 39-nt capped leader RNA and 3' polyadenylation. It was previously known that trans splicing generally occurs at an AG dinucleotide downstream of a polypyrimidine tract, and that polyadenylation is coupled to downstream trans splicing. The few polyadenylation sites that had been examined were 100-400 nt upstream of the polypyrimidine tract which marked the adjacent trans splice site. We wished to define the sequence requirements for trypanosome mRNA processing more tightly and to generate a predictive algorithm. By scanning all available Trypanosoma brucei cDNAs for splicing and polyadenylation sites, we found that trans splicing generally occurs at the first AG following a polypyrimidine tract of 8-25 nt, giving rise to 5'-UTRs of a median length of 68 nt. We also found that in general, polyadenylation occurs at a position with one or more A residues located between 80 and 140 nt from the downstream polypyrimidine tract. These data were used to calibrate free parameters in a grammar model with distance constraints, enabling prediction of polyadenylation and trans splice sites for most protein-coding genes in the trypanosome genome. The data from the genome analysis and the program are available from: .
Benz
Corinna
C
Zentrum für Molekulare Biologie, Im Neuenheimer Feld 282, D69120 Heidelberg, Germany.
Nilsson
Daniel
D
Andersson
Björn
B
Clayton
Christine
C
Guilbride
D Lys
DL
D020121:5' Untranslated Regions / Q000096:biosynthesis; D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D003198:Computer Simulation; D017124:Conserved Sequence; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D026723:Polyadenylation; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000378:metabolism*; D016053:RNA, Protozoan / Q000235:genetics / Q000378:metabolism*; D020040:Trans-Splicing; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000378:metabolism
D020121:5' Untranslated Regions; D012322:RNA Precursors; D012333:RNA, Messenger; D016053:RNA, Protozoan; D012321:DNA-Directed RNA Polymerases