research about alternative splicing recently 楊佳熒

Research about Alternative Splicing recently

楊佳熒

Transcription Start

ATG (Met) TAATAGTGA

Translation Start Stop codon

Intron 1 Intron 25‘ 3‘Exon 1 Exon 2 Exon 3

Acceptor splice site

Donor splice site

Intron 1 Intron 2Exon 1 Exon 2 Exon 3AGGT AGGT

mRNA Exon 1 Exon 2 Exon 33‘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 Gene20660

Predicted Gene6912

<ex>

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-s

pecific alternative splicing in human expressed sequences

Qiang Xu and Christopher LeeNucleic 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,