Methylation patterns in homo sapiens
Download
1 / 12

Methylation Patterns in Homo sapiens - PowerPoint PPT Presentation


  • 128 Views
  • Updated On :

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Methylation Patterns in Homo sapiens' - torie


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
Methylation patterns in homo sapiens

Methylation Patterns in Homo sapiens

Brian Watson

Under the supervision of Dr. Steven Smith at City of Hope


Introduction
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’ hypothesis

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


Cpg and non cpg methylation
CpG and Non-CpG methylation

CCCAGGCGTCGCTTCCGCG

GGGTCCGCAGCGAAGGCGC

M•EcoRII adds a methyl group to C(m)CWGG

M•SssI adds a methyl group to C(m)G

M•EcoRII

M•SssI

M•SssI

M•EcoRII

* * CH3 *

CH3

5’ CCCAGGCGTCGCTTCCGCG 3’

CCCAGGCGTCGCTTCCGCG

CCCAGGCGTCGCTTCCGCG

GGGTCCGCAGCGAAGGCGC


Methylation patterns in homo sapiens

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
My part

CCTACCAGGAGTCGTTAGNTTAGATG……TAAATCGTGCGTTGCCAGG

CCTACCAGGAGTCGTTAGNTTAGATG……TAAATCGTGCGTTGCCAGG

The color green represents CG the gene

CCTACCAGGAGTCGTTAGNTTAGATG……TAAATCGTGCGTTGCCAGG

The color black represents the EcoRII sites

CCTACCAGGAGTCGTTAGNTTAGATG……TAAATCGTGCGTTGCCAGG

The color blue represents CG sites

1 EcoRII(CCAGG) upstream, 1 EcoRII(CCAGG) downstream

1 SssI(CG) upstream, 2 SssI(CG)downstream


Ahhh python
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
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.

*

*


Results comparison gene vs genome
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
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
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
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)