A STATISTICAL MODEL FOR METHYLATION LEVEL INFERENCE USING BS-SEQ DATA M. BESSOUL, G. VIEJO | Université Pierre et Marie Curie | 2012 M A S T E R BIOINFORMATIQUE E T MODELISATION dimanche 17 juin 2012 

I. Background on DNA methylation II. Motivations III. BS-Seq IV. Data simulation V. Statistical model VI. MethSeq VII. Results VIII. Discussion CONTENT dimanche 17 juin 2012 

CH3 CH3 CH3 CH3 CH3 CH3 I. DNA METHYLATION DNMt ...the CH3 group binds to the C of a CpG dimanche 17 juin 2012 

DNA Polymerase AAAGATATAACGAGCATGCTAACCGTAATAAGCAGTCATGCA... DNA transcription Target gene Promoter region (CpG rich) I. DNA METHYLATION AND GENE SILENCING EFFECT. dimanche 17 juin 2012 

DNA Polymerase transcription AAAGATATAACGAGCATGCTAACCGTAATAAGCAGTCATGCA... DNA AAAGATATAACGAGCATGCTAACCGTAATAAGCAGTCATGCA... DNA transcription CH3 CH3 CH3 Target gene Promoter region (CpG rich) I. DNA METHYLATION AND GENE SILENCING EFFECT. dimanche 17 juin 2012 

II. MOTIVATIONS DNA Methylated region 0 1 dimanche 17 juin 2012 

III. BS-SEQ G C C C T A m m G C T C T A Sodium bisulfite + PCR G C T C T A BISULFITE SEQUENCING dimanche 17 juin 2012 

III. BS-SEQ G C C C T A m m G C T C T A G T A T T T Sodium bisulfite + PCR G C T C T A Alignment BS Sequence over C-less reference BISULFITE SEQUENCING Bisulfite sequence C-less sequence dimanche 17 juin 2012 

III. BS-SEQ ALIGNMENT G C T C T A G T A T T T dimanche 17 juin 2012 

III. BS-SEQ ALIGNMENT C-less seq reads G C T C T A G T A T T T dimanche 17 juin 2012 

III. BS-SEQ ALIGNMENT C-less seq reads G C T C T A G T A T T T What do we get ? For every C position : •Number of overlapping reads : •Number of mismatches : yreads yc dimanche 17 juin 2012 

IV. DATA SIMULATION GENOME (.fasta file) Real profile (5mC positions) Short reads Random methylation simulation Bisulfite transformation Bowtie alignment SAM file Parsing BS-Seq data (coverage + mismatches at C positions) Sequencing C-less index Comparison .py script .py script .py script Alignment and parsing Data simulation dimanche 17 juin 2012