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Methylation Patterns in Homo sapiens

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.

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Methylation Patterns in Homo sapiens

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  1. Methylation Patterns in Homo sapiens Brian Watson Under the supervision of Dr. Steven Smith at City of Hope

  2. 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

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

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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. * *

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

  10. 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

  11. 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.

  12. 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)

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