300599 UE Praktikum Bioinformatik
3 stündiges Blockpraktikum. Ziel ist die selbstständige
Durchführung eines kleinen bioinformatischen Forschungsprojekts
Ort: Computer-Praktikumsraum des Inst. f. Theoret. Chemie,
Rennweg 95b, 1030 Wien EINGANG: Dr. Bohrg. 7, großes
Gebäude im Hof.
Thema 2010/11:
Genannotation durch Promotorsuche
Background
Protein coding genes are usually identified on the basis of the
codon bias characteristic for ORFs. An alternative that does not
rely on features of coding sequences is to search for the promotor
sequences of the transcript. in this course we will concentrate
on Pol III transcripts which feature especially distinct promotor
motifs.
One difficulty of the approach is that promotor motifs tend to
vary considerably from species to species. It is therefore necessary
to identify promotor motifs in each species (or at least for different
phylogenetic subgroups) by inspecting the upstream regions of known
Pol III genes such as U6 snRNAs etc.
Introductory Slides
RNAs know to be Pol III transcripts with external promoters
- 7SK snRNA
- tRNA-Sec
- Y RNAs
- U6 snRNAs
- RNA component of RNAseP
- RNA component of RNAseMRP
Literature
Literature search at: http://www.ncbi.nlm.nih.gov/pubmed/
- An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene.
- Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies.
- Staf, a promiscuous activator for enhanced transcription by RNA polymerases II and III.
- Functional redundancy of promoter elements ensures efficient transcription of the human 7SK gene in vivo.
- Gene encoding human Ro-associated autoantigen Y5 RNA.
- Structural organization of Staf-DNA complexes.
- Flexible zinc finger requirement for binding of the transcriptional activator staf to U6 small nuclear RNA and tRNA(Sec) promoters.
- Characterization of snRNA and snRNA-type genes in the pufferfish Fugu rubripes.
- Zebrafish U6 small nuclear RNA gene promoters contain a SPH element in an unusual location.
Data bases
Ensembl http://www.ensembl.org/index.html
UCSC Genome browser http://genome.ucsc.edu/
BLAST @ NCBI http://blast.ncbi.nlm.nih.gov/Blast.cgi
Programs
Jalview - multiple alignment editor http://www.jalview.org
Seaview - multiple alignment editor http://pbil.univ-lyon1.fr/software/seaview.html