Re: Alternative Splicing

On 1 Dec 2005 10:20:02 -0800, Colum <columdowney@xxxxxxxxx> wrote:

> Hey, thanks guys, all this info is really helping...wasnt too pleased
> to hear Gil Ast's Scientific American publication being slammed by
> Larry as it was the first paper my project supervisor handed me when we
> first got together to chat about Alternative Splicing...should i bother
> with it at all???haha

Go to the ECgene database for the human HSPA5 gene. Here's the link ....

http://genome.ewha.ac.kr/cgi-bin/ECquery.cgi?organism=human&query=HSPA5

According to this database entry the HSPA5 gene encodes 18 transcript
variants producing 8 distinct proteins. This is completely wrong. The
HSPA5 gene is highly conserved and there's zero chance that humans
have evolved to produce 7 different functional protein variants. Here's
the annotated EntrezGene entry for this gene in the human genome
database.

http://www.ncbi.nlm.nih.gov/entrez/
query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=3309

Note that NCBI has rejected all alternative splice variants. They know
that the EST data is an artifact for this well-characterized gene.

Go back and look at the pattern of so-called "alternatively-spliced"
products that's shown on the ECgene website. Keep that image in mind.

It's hard to find papers that challenge the current fad but here's a short
list of articles that promote alternative splicing. As you read the papers
keep thinking about the phoney HSPA5 pattern. Ask yourself whether the
results being reported are any different that the results on the ECgene
website.

Look for critical analysis of the data and discussions of possible
artifacts in the EST database. Look for references to those well-
characterized genes where the predicted alternative splicing has been
rejected by genome annotators. Be very suspicious if you don't find any
mention of those problems in the pepers you read. The absence of
skepticism is one of the characteristics of very bad science. This
is mostly bad science.

Most of the authors of the following papers have an agenda. They are
looking for ways to explain the complexity of humans in light of the fact
that we have "only" 25,000 genes. They can't adjust to the fact that
we may not be that much more complex than a fruit fly or a turnip.
They think that alternative splicing gives them a way out but if you
read the Maniatis and Tasic paper very carefully you'll see that even
that assumption is flawed.

Molecular biologists don't understand evolution. That's one of the reasons
why such bad science gets into the literature.


Bonaldo, M.F., Lennon, G., and Soares, M.B. (1996) Normalization and
subtraction: two approaches to facilitate gene discovery.
Genome Res. 6:791-806.

Boue, S., Letunic, I., and Bork, P. (2003) Alternative splicing and
evolution. Bioessays 25:1031-4.

Brett, D., Pospisil, H., Valcarcel, J., Reich, J., and Bork, P. (2002)
Alternative splicing and genome complexity. Nat. Genet. 30:29-30.

Cartegni, L., Chew, S.L., and Krainer, A.R. (2002) Listening to silence
and understanding nonsense: exonic mutations that affect splicing.
Nat. Rev. 3:285-98.

Ewing. B. and Green, P. (2000) Analysis of expressed sequence tags
indicates 35,000 human genes. Nat. Genet. 25:232-234.

Graveley, B.R. (2001) Alternative splicing: increasing diversity in the
proteomic world. Trends Genet. 17:100-7.

Gupta, S., Zink, D., Korn, B., Vingron, M., and Haas, S.A. (2004)
Strengths and weaknesses of EST-based prediction of tissue-specific
alternative splicing. BMC Genomics 28:72.

Gupta, S., Zink, D., Korn, B., Vingron, M., and Haas, S.A..(2004b)
Genome wide identification and classification of alternative splicing
based on EST data. Bioinformatics 20:2579-85.

Kreahling, J. and Graveley, B.R. (2004) The origins and implications of
Aluternative splicing. Trends Genet. 20:1-4.

Kriventseva, E.V., Koch, I., Apweiler, R., Vingron, M., Bork, P.,
Gelfand, M.S., and Sunyaev, S. (2003) Increase of functional diversity
by alternative splicing. Trends Genet 19:124-8.

Larsson, T.P., Murray, C.G., Hill, T., Fredriksson, R., and Schioth, H.B.
(2005) Comparison of the current RefSeq, Ensembl and EST databases for
counting genes and gene discovery. FEBS Lett. 579:690-8.

Lavorgna, G., Dahary, D., Lehner, B., Sorek, R., Sanderson, C.M., and
Casari, G. (2004) In search of antisense. Trends Biochem. Sci. 29:88-94.

Lee, C,, Atanelov, L,, Modrek, B., and Xing, Y. (2003) ASAP: the
Alternative Splicing Annotation Project. Nucl. Acids Res. 2003 31:101-5.

Lee, Y., Tsai, J., Sunkara, S., Karamycheva, S., Pertea, G., Sultana, R.,
Antonescu, V., Chan, A., Cheung, F., and Quackenbush, J. (2005) The TIGR
Gene Indices: clustering and assembling EST and known genes and integration
with eukaryotic genomes. Nucl. Acids Res. 33:D71-4.

Maniatis, T.and Tasic, B. (2002) Alternative pre-mRNA splicing and proteome
expansion in metazoans. Nature 418:236-43.

Modrek, B, and Lee, C. (2002) A genomic view of alternative splicing.
Nat. Genet. 30:13-9.

Murray, C. G., Larsson, T.P., Hill, T., Bjorklind, R., Fredriksson, R., and
Schioth, H.B. (2005) Evaluation of EST-data using the genome assembly.
Biochem. Biophys. Res. Commun. 331:1566-76.

Nekrutenko, A. (2004) Reconciling the numbers: ESTs versus protein-coding
genes. Mol. Biol. Evol. 21:1278-82.

Nekrutenko, A., Chung, W.Y., Li, W.H. (2003) An evolutionary approach
reveals a high protein-coding capacity of the human genome.
Trends Genet. 19:306-10.

Resch, A., Xing, Y., Alekseyenko, A., Modrek, B., and Lee, C. (2004)
Evidence for a subpopulation of conserved alternative splicing events
under selection pressure for protein reading frame preservation.
Nucl. Acids Res. 32:1261-9.

Resch, A., Xing, Y., Modrek, B., Gorlick, M., Riley, R., and Lee, C. (2004)
Assessing the impact of alternative splicing on domain interactions in
the human proteome. J. Proteome Res. 3:76-83.

Scheetz, T.E., Trivedi, N., Roberts, C.A., Kucaba, T., Berger, B., Robinson,
N.L., Birkett, C.L., Gavin, A.J., O'Leary, B., Braun, T.A., Bonaldo,
M.F., Robinson, J.P., Sheffield, V.C., Soares, M.B., and Casavant, T.L.
(2003) ESTprep: preprocessing cDNA sequence reads.
Bioinformatics 19:1318-24.

Schuler, G.D. (1997) Pieces of the puzzle: expressed sequence tags and the
catalog of human genes. J. Mol. Med. 75:694-8.

Smith, C.W.J. and Valcárcel, J. (2000) Alternative pre-mRNA splicing: the
logic of combinatorial control. Trends Biochem. Sci. 25:381-8.

Sorek, R. and Safer, H.M. (2003) A novel algorithm for computational
identification of contaminated EST libraries. Nucl. Acids Res. 31:1067-74.

Sorek, R., Shamir, R., and Ast, G. (2004) How prevalent is functional
alternative splicing in the human genome? Trends Genet. 20:68-71.

Yeo, G.W., Van Nostrand, E., Holste, D., Poggio, T., and Burge, C.B. (2005)
Identification and analysis of alternative splicing events conserved in
human and mouse. Proc. Natl. Acad. Sci. (USA) 102:2850-5.

Yeo, G., Holste, D., Kreimanm G., and Burge, C.B. (2004) Variation in
alternative splicing across human tissues. Genome Biol. 5:R74.

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Larry Moran





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