Research about Alternative Splicing recently 楊佳熒

Transcription Start ATG (Met) TAA TAG TGA Translation Start Stop codon Intron 1Intron 2 5‘ 3‘ Exon 1 Exon 2 Exon 3 Acceptor splice site Donor splice site Intron 1Intron 2 Exon 1 Exon 2 Exon 3 AG GT AG GT mRNA Exon 1 Exon 2 Exon 3 3‘UTR 5‘UTR ORF Protein Features of a Mammalian Gene Gene start Gene end

Introduce NCBI (Nation Center for Biotechnology Information) refseq ----Genome Annotation

Known Gene Predicted Gene 6912

Alternative Splicing

Research about alternative splicing

NCBI (National Center of Biotechnology Information) TIGR (The Institute of Genomic Research) UniGene HGI(Human Gene Index) alignment Genome sequences

cDNA cDNA (complement DNA) EST (Expressed Sequence Tag) DB TIGR (The Institute of Genomic Research) NCBI (National Center of Biotechnology Information) Data Source HGI(Human Gene Index)UniGene

An alternative splicing example

Classification of alternative splicing

Two question 1.How many are the result of aberrant splicing or noise data ? 2.How many of these predicted splice variants are functional ?

A Comparative Method for Identification of Gene Structures and Alternatively Spliced Variants Trees-Juen Chuang, Feng-Chi Chen and Meng-Yuan Chou Bioinformatics Advance Access published June 24, 2004 Question 1: How many are the result of aberrant splicing or noise data ? Method 1 : 修補

Genome wide identification and classification of alternative splicing based on EST data S.Gupta, D.Zink, B.Korn, M.Vingron, S.A.Haas Bioinformatics Advance Access published April 29, 2004 Question 1: How many are the result of aberrant splicing or noise data ? Method 2 : 設定很嚴格的條件限制

Flow chart UniGene 1 assembly 2 GeneNest 3 Mapping to Genome(sim4) 4 SpliceNest

Four parameters 1.Alignment Quality Alignment quality is computed based on the sim4. 2.Signal Information (splice signal) (1) the presence of the consensus (GT-AG) splice signal (2) the presence of a non-consensus splice signal with perfect alignment in vicinity (+/-10 bases)

3.Common Boundaries Common boundaries observed among related exons of different transcripts provides further evidence for a splice junction. 4.Neighborhood Parameters overall splicing direction

How prevalent is functional alternative splicing in the human genome ? Rotem Sorek, Ron Shamir and Gil Ast TRENDS in Genetics Vol.20 No.2 February 2004 Question 2: How many of these predicted splice variants are functional ?

Method Finding exon-skipping (cassette exons) that are conserved between humans and mouse 1.Identification of mouse ESTs that contain the exon and the two flanking exons. 2.If the exon was not represented in mouse ESTs, the sequence of the human exon was searched against the intron by the skipping mouseEST on the mouse genome.

Conclude 1. We conclude that a signification portion of cassette exons evidence in EST database is not functional.

Idea 1. Discovery of novel splice forms and functional analysis of cancer- specific alternative splicing in human expressed sequences Qiang Xu and Christopher Lee Nucleic Acids Research, 2003, Vol.31 No.19

EGFR gene DWER

2. EST analysis online: WWW tools for detection of SNPs and alternative splice forms David Brett, Gerrit Lehmann, Jens Hanke, Stefan Gross, Jens Reich and Peer Bork Trends in Genetics, Volume 16, Issue 9, 1 September 2000,