Methylation Patterns in Homo sapiens

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Methylation Patterns in Homo sapiens

• Brian Watson
• Under the supervision of Dr. Steven Smith at City
  of Hope

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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

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Taras hypothesis

• Taras Schevchek suggested the concentration of
  CWG sites are higher upstream from the gene.

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CpG and Non-CpG methylation
MEcoRII adds a methyl group to C(m)CWGG
MSssI adds a methyl group to C(m)G
MEcoRII
MSssI
MSssI
MEcoRII
CH3
CH3

• CCCAGGCGTCGCTTCCGCG
• GGGTCCGCAGCGAAGGCGC

CCCAGGCGTCGCTTCCGCG
CCCAGGCGTCGCTTCCGCG GGGTCCGCAGCGAAGGCGC
5 CCCAGGCGTCGCTTCCGCG 3
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Dr. Smiths labs previous work

• Does MEcoRII cause the cell to change gene
  expression?

• It appeared that although Non-CpG methylation
  occurred through MEcoRII,
• it didnt change gene expression.

NO
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My part
CCTACCAGGAGTCGTTAGNTTAGATGTAAATCGTGCGTTGCCAGG
CCTACCAGGAGTCGTTAGNTTAGATGTAAATCGTGCGTTGCCAGG T
he color green represents CG the gene
CCTACCAGGAGTCGTTAGNTTAGATGTAAATCGTGCGTTGCCAGG T
he color black represents the EcoRII sites
CCTACCAGGAGTCGTTAGNTTAGATGTAAATCGTGCGTTGCCAGG T
he color blue represents CG sites
1 EcoRII(CCAGG) upstream, 1 EcoRII(CCAGG)
downstream
1 SssI(CG) upstream, 2 SssI(CG)downstream
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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.
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Results upstream vs downstream
CpG Islands seemed to affect the distribution

• CWG sites appear to be of equal 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.


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Results comparison gene vs genome
Y axis is (frequency of sequence around the
gene-frequency of sequence in the genome) /
frequency of the genome
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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

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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.
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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)