The Ribosomal Protein Binding Site in Saccharomyces cerevisiae ...
"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae"
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of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae" Michal Wolff Advisors: Prof. Martin Kupiec (TAU) DR. Ron Unger
description
"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae". Michal Wolff Advisors: Prof. Martin Kupiec (TAU) DR. Ron Unger. Why? -there is something special about them. Number of intron containing genes = 242 - PowerPoint PPT Presentation
Transcript of "Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae"
"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in
Saccharomyces cerevisiae"
Michal WolffAdvisors:Prof. Martin Kupiec (TAU)DR. Ron Unger
Why? -there is something special about them
Number of intron containing genes = 242 Number of ribosomal protein intron containing
genes = 105 = 43% Number of ribosomal protein genes = 140 Ribosomal protein gene introns in the yeast are
larger On average the ribosomal intron length is 405
while the non-ribosomal is 151
Why ?Intron size bias by gene class
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Intron size (bp)
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ribosomal gene introns
non-ribosomal geneintrons
What? - The sequence
homology, consensus, all the intron, areas in the intron, nucleotides.
What? - Secondary structure
Where? - Ares lab Yeast Intron Database
Gene/ORF Name: YMR230W
Description: Small ribosomal subunit protein S10B (rat S10).
Number of introns: 1
Ares Intron Name YMR230W_13_732413_733140_INTRON_53_462
Comments
Length Info (in nt) 410; to Branch base (lariat length) 371
Location relative to orf (nt) start 53; stop 462
Features GUAUGU UUACUAACAAGG AAUAG
Sequence
>YMR230W_13_732417_732466_PREGUUGAUGCCAAAGCAAGAAAGAAACAAAAUUCACCAAUACUUGUUUCAAG>YMR230W_13_732413_733140_INTRON_53_462GUAUGUUUGCAUUUUUUAGGUGAAAUAUGCAGUGAUAUGCUCCGAAAUGGAUAGCAAAGAUGAUAAAUGAAAAUACAAUUAAAUUGAACUUGAAUAUCAUUAAAAGUGGUAGAAAACCGAUUGUUUCAAAAAGAUCUUUGUGGACAAGUACGGCAGUGCAUGAAUCCGAAAGAAAAGUGCAACCUAAGCAGAAUUCCAUUAUUUCACGCGUCCAUUUUUAUAAUGUUUGAACUUUUGAGUCCUUAUAGAAAUGCUAAUAUUAUGAUCAAAGCGAUUAUAUCAUUUACUUUACAGUUUCCGGAGUUUCCGUAUUAUUGCAAAAGGACCACAAACAAUUGAAAUCAUGAUAUCGUAAGAAAUAUUAUUACUAACAAGGAAGAUCAUUGAAUUACGAUCGCAUAUCGAAAUAG>YMR230W_13_732875_732924_POSTAAGGUGUUGUCGUCGCUAAGAAGGAUUUCAACCAAGCUAAGCACGAAGAA
How? – Perl & Bioinformatics Tools
Perl - originally designed for text processing
EMBOSS – sequence alignment mfold – secondary structure BLAST – all against all
How? – Data Analysis
Microsoft Excelchartssortgraphsχ² - expected – non-ribosomal behavior
Results – upstream the intronglutamine
CAA
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nucleotides upstream of the intron
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upstream ribosomal intron
upstream non-ribosomal introns
Results – downstream the intronlysine
AAG
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nucleotides downstream of intron
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downstream ribosomal introns
downstreamstream non-ribosomalintrons
Results – in the intron
Hexamers - The biggest difference (30-40%) is in the AU rich sequences for the ribosomal sequences.
Octamer - The ribosomal introns had more poly U octamers then the non-ribosomal ones.
Results - in the intron
10-20 nucleotides upstream from the 3’ end the ribosomal introns have a high probability to contain a polyU sequence.
The area between the branchpoint and the 3’ splice site is around 30 bases long.
UUU,AUU,UUA
Results - in the intronUUU
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area in intron
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ribosomal - upstream 3' end
non-ribosomal - upstream 3' end
Results – in the branchpoint-3’
distribution of nucleotides in the branchpoint-3' end area
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nucleotide
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e ribosomal introns
non-ribosomal introns
ribosomal introns 29.80% 12.38% 8.67% 49.15%
non-ribosomal introns 30.53% 16.49% 13.96% 39.02%
A C G U
Results – in the branchpoint-3’
common subsequences A-polyUpolyUpolyU-A
U subsequence with a mutation – In the area – more in the ribosomal introns In the whole intron – more in the non-
ribosomal
Results – in the branchpoint-3’U sequences with one mutation in the intron
and the branchpoint - 3' site area
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sequence length(bp)
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ribosomal introns branchpoint-3' site
non-ribosomal introns branchpoint-3' site
ribosomal introns
non-ribosomal introns
Conclusion
The branchpoint-3’ splice site area might be homologues – all against all blast.
The difference between ribosomal and non-ribosomal may be connected with a polyU sequence.
The ribosomal gene introns and the non-ribosomal gene introns are not similar.
Thanks for listening!
