1. Mohamad Ali Najia Summer Fellow, Bioinformatics and Integrative Genomics Program Harvard-MIT Division of Health Sciences and Technology Department of Cancer Biology, Dana-Farber Cancer Institute Harvard Medical School Allele-Specific DNA Methylation and Monoallelically Expressed Genes

2. Monoallelic Expression Serizawa et al. 2000 MonoallelicBiallelic X ~10% of all autosomal genes present monoallelic expression Gimelbrant et al. 2007 Biological Mechanism(s): Unknown Temporal onset? Cell types affected? Regulatory mechanisms? Biological Importance M P DNA Methylation Challenge Previous detection approaches  noisy

3. Mechanistic Insights into Autosomal MAE Hypothesis: Monoallelically expressed genes present an allele- specific difference in DNA methylation in clonal cell populations Does allele-specific DNA methylation correspond to allele-specific expression? X Clone 1 M P X Clone 2 M P Clone 3 M P

4. Multiplex Padlock Probes Reference Allele Alternative Allele A T C C C C C T T T A G G G G A A C Zhang et al. 2009 Lymphoblast clones C  T Bisulfite Conversion Amplification Padlock Probes T Differential Methylation Score Alternative Allele Bias Reference Allele Bias 0+1

5. Padlock Probe Method Validation A B C D E F

6. Enriched Allele-Specific Methylation A B * * * * C * = p << 0.0001 Annotate SNP Neighborhood

7. Allelic Bias Categorization Opposite Bias Same Bias Clone 1 Clone 2 R A R A No Bias

8. Clone-Specific MAE and Allele-Specific Methylation * = p << 0.0001 AB * * * * All CpGsUpstream CpGs

9. ConclusionsConclusions Padlock probe technology can detect allele-specific methylation associated with X chromosome inactivation Allele-specific methylation is enriched with allele- specific gene expression on autosomes Genes that show clone-specific monoallelic expression are highly enriched with clone and allele specific methylation

10. Future Work MAE Gene Maternal Paternal MAE Gene Maternal Paternal Clone 1Clone 2 Gene Expression Does clone and allele specific DNA methylation correlate with the level of gene expression?

11. AcknowledgementsAcknowledgements Gimelbrant Lab: Alexander Gimelbrant, PhD (PI) Virginia Savova, PhD Anwesha Nag, PhD Sébastien Vigneau, PhD Jason Alvarez Sponsors/Funding Sources: National Institutes of Health National Science Foundation i2b2 National Center for Biocomputing Harvard-MIT Division of Health Sciences and Technology (HST) Massachusetts Institute of Technology Harvard Medical School Dana-Farber Cancer Institute Harvard-MIT HST Summer Institute: Susanne Churchill, PhD Sonal Jhaveri, PhD Barbara Mawn

12. Generation of Functionally Diverse Cells X Chromosome Inactivation Imprinting Autosomal Monoallelic Expression Maternal Paternal Balazsi et al. 2011

13. Targeted SNPs and CpG Dinucleotides Zhang et al. 2009 Individual 1Individual 2