"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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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!