Transcript - Cal State LA - Instructional Web Server

Methylation Patterns in
Homo sapiens
Brian Watson
Under the supervision of Dr.
Steven Smith at City of Hope
Introduction
• Methylation occurs
at different stages
• Usually it is
performed by
DNMT1,3a,3b
• Favors CpG sites
• CpG islands are
found upstream
from about 40% of
the genes
Taras’ hypothesis
• Taras Schevchek suggested the
concentration of CWG sites are higher
upstream from the gene.
CpG and Non-CpG
methylation
M•EcoRII
M•SssI
adds
adds
a methyl
a methyl
group
group
to to
C(m)G
C(m)CWGG
M•SssI
M•EcoRII
M•EcoRII
M•SssI
CH3
*
*
CH3 *
5’ CCCAGGCGTCGCTTCCGCG 3’
GGGTCCGCAGCGAAGGCGC
Dr. Smith’s labs previous work
• Does M•EcoRII cause the cell to
change gene expression?
•It appeared that although Non-CpG methylation occurred through M•EcoRII,
it didn’t change gene expression.
NO
My part
CCTACCAGGAGTCGTTAGNTTAGATG……TAAATCGTGCGTTGCCAGG
The color blue
greenrepresents
black
represents
representsCG
the
CGsites
EcoRII
the gene
sites
1 EcoRII(CCAGG) upstream, 1 EcoRII(CCAGG) downstream
1 SssI(CG) upstream, 2 SssI(CG)downstream
AHHH Python
• UCSC genome browser
The computer counts much faster than I do.
Create my own file.
Adjust the counts to take into account new distances.
Results upstream vs
downstream
*CpG
•CWGIslands
sites appear
seemed
to to
beaffect
of equal
the distribution
distribution
•upstream vs downstream
Upon dividing the upstream results with the
downstream results we expect the values of
the CG cites to be higher around the CG islands
*
We expect the number of Non-CG sites to be a lot
higher through the upstream region as well.
*
Results comparison gene
vs genome
Y axis is (frequency of sequence around the gene-frequency of sequence in
the genome) / frequency of the genome
Summary of conclusions
• Equal distribution of Non-CG sites
upstream vs downstream
• Higher frequency of CG sites around
genes than genome wide distribution
• Not a significantly higher frequency
of Non-CG sites around genes
Where do we go from
here.
Look for a change in gene expression
at genes with higher levels than
expected of CG and non-CG sites.
Acknowledgements
City of Hope
Dr. Steven Smith
Dr. Kristofer Munson
Dr. Jarrod Clark
Dr. Taras Schevchuck
SoCalBSI
National Institute of Health(NIH)
National Science Foundation(NSF)