COURSE OF BIOINFORMATICS�A.A. 2014-2015

�How to analyse and predict

(alternative) splicing and its regulation

Is the splicing mechanism clear?

http://vcell.ndsu.nodak.edu/animations/

Is the splicing mechanism clear?

http://www.phschool.com/science/biology_place/

Is the splicing mechanism clear?

http://www.geneinfinity.org/sp/sp_coding.html

from: Burset et al., NAR (2000)

Is alternative splicing clear?

from: Cartegni et al., Nature Review Genetics (2002)

Why to study (alternative) splicing?

•  More than 90% of human genes are differentially spliced

•  Alternative splicing is a mayor source of genetic variation (about 30k genes encoding for 100-200k proteins)

•  Many genetic disorder are caused by mutations affecting the splicing machinery (ex. Spinal Muscular Atrophy, SMA)

•  Many alterations of the splicing process have been described in Cancer (ex. BRCA1)

Is my gene affected by alternative splicing event(s)?

We will use the human BRCA1 gene

How many splicing variants are described in:

NCBI_Gene

UCSC Genome browser

fastDBthe Friendly Alternative Splicing and Transcripts database

BRCA1 in NCBI_Gene

2013  

BRCA1 in UCSC Genome browser

???  

GRCh37UCSC genes, RefSeq GenesAlt Event, SIB Alt-Splicing

2013  

BRCA1 in fastDBh

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mouse Brca1 in fastDB

mouse Brca1 in UCSC

2013  

BRCA1 in UCSC Genome browser

???Is this an alternative skipped/included exon or it is an artifact?

Which are the evidences supporting it?What about splice junctions??

GRCh37UCSC genes, RefSeq GenesHuman mRNA, Spliced EST

Regulation of alternative splicing

http://www.h-invitational.jp/h-dbas/as_mechanism.jsp

Can we predict putative binding sites for SR/hnRNP in our alternative exon?

ESEFINDER http://rulai.cshl.edu/cgi-bin/tools/ESE3/

esefinder.cgi

SFmap http://sfmap.technion.ac.il/

ESRsearch

http://esrsearch.tau.ac.il

BRCA1 in UCSC Genome browser

Recover the sequence of the putative exon

GRCh37UCSC genes, RefSeq GenesHuman mRNA, Spliced EST

ESEFINDER  

Alternative Exon

ESEFINDER  

Alternative Exon Intronic Sequence

SFmap_Alternative Exon  

SFmap_Intronic Sequence  

ESRsearch  

BIBLIOGRAPHY

Burset M, Seledtsov IA, Solovyev VV.Analysis of canonical and non-canonical splice sites in mammalian genomes.Nucleic Acids Res. 2000 Nov 1;28(21):4364-75.

Cartegni L, Chew SL, Krainer AR.Listening to silence and understanding nonsense: exonic mutations that affect splicing.Nat Rev Genet. 2002 Apr;3(4):285-98.

Smith, P. J., Zhang, C., Wang, J. Chew, S. L., Zhang, M. Q. and Krainer, A. R.An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum. Mol. Genet. 15(16): 2490-2508.

Paz I., Akerman M., Dror I., Kosti I. and Mandel-Gutfreund Y.SFmap: a web server for motif analysis and prediction of splicing factor binding sites.�Nucleic Acids Res. 2010 38:W281-W285.