Zeevik Melamed & Dror Hollander Gil Ast Lab Sackler Medical School 03-05-2011 RNA Splicing, UCSC...
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Zeevik Melamed & Dror Hollander Gil Ast Lab Sackler Medical School 03-05-2011 UCSC Genome Browser & Galaxy
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Transcript of Zeevik Melamed & Dror Hollander Gil Ast Lab Sackler Medical School 03-05-2011 RNA Splicing, UCSC...
Zeevik Melamed & Dror HollanderGil Ast LabSackler Medical School
03-05-2011
RNA Splicing,UCSC Genome Browser & Galaxy
Lectures Overview
Introduction to RNA splicing UCSC genome browser & Galaxy Hands-on session
RNA Splicing
Outline of the 1st part
Background - Determining gene
architecture
Alternative splicing (AS)
Regulation of AS
Detection of splicing events
AS and disease
A Genomic View
exon 1 exon 2
3’ splice site
5’ splice site Polypyrimidine tract
C\T {15-20}
Branch site
A
Pre-mRNAmature-mRNA
intron
The Splicing Process
Outline of the 1st part
Background - Determining gene
architecture
Alternative splicing (AS)
Regulation of AS
Detection of splicing events
AS and disease
Gene number
Arabidopsis thaliana25,500~
Drosophila melanogaster~13,600
C. elegans 19,000~
Rice (Oryza sativa) ~50,000
Mouse~24,000
Homo Sapiens~24,000
Alternative Splicing
Exon 19Exon 20
Exon 21Intron 19
Intron 20
pre-mRNA
Splicing isoform 1 Splicing isoform 2
Exon 19Exon 20
Exon 20
Exon 21
mRNA
Exon 19 Exon 21
Sources of Biological complexity
With a limited number of genes
Post-trancriptional modifications:
Alternative splicing
Contradicts the central dogma of molecular biology:
One gene – one protein
Alternative Splicing Events
Outline of the 1st part
Background - Determining gene
architecture
Alternative splicing (AS)
Regulation of AS
Detection of splicing events
AS and disease
Hollander et al. 2010
Regulation of Alternative Splicing
Trans-acting regulatory proteins
PTBPTBP1, a splicing factor known to repress alternatively spliced exons in non-neuronal tissues
Expression of PTB and nPTB is Expression of PTB and nPTB is anti-correlated across human tissuesanti-correlated across human tissues
Ratio to reference pool
nPTB is enriched in CNS tissues PTB is depleted.
nPTB
PTB
Brain tissues
Outline of the 1st part
Background - Determining gene
architecture
Alternative splicing (AS)
Regulation of AS
Detection of splicing events
AS and disease
Detection of splicing events
Outline of the 1st part
Background - Determining gene
architecture
Alternative splicing (AS)
Regulation of AS
Detection of splicing events
AS and disease
FD – Familial Dysautonomia
Riley-Day Syndrome
Familial dysautonomia (FD) is an autosomal recessive congenital neuropathy that occurs almost exclusively in the Ashkenazi Jewish (AJ) population.
Carrier frequency of 1:31 in AJ population and 1:18 in those of Polish descent.
Abnormal development and survival of the sensory and autonomic nervous system with progressive depletion of sensory and autonomic neurons.
FD symptoms include gastrointestinal and cardiovascular dysfunction, vomiting crises, pain and temperature insensitivity, and recurrent pneumonia
50% of patients die before the age of 40 years .
FD mutationIVS +6T>C in >99.3% of disease-causing alleles which results in the skipping of exon 20 and consequently generates a frameshift , which yields a stop codon in the reading frame of exon 21.
