Mohamad Ali NajiaSummer Fellow, Bioinformatics and Integrative Genomics Program

Harvard-MIT Division of Health Sciences and Technology

Department of Cancer Biology, Dana-Farber Cancer InstituteHarvard Medical School

Allele-Specific DNA Methylation and Monoallelically Expressed Genes

Monoallelic Expression

Serizawa et al. 2000

Monoallelic Biallelic

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

MP

DNA Methylation Challenge Previous detection approaches noisy

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?

XClone 1 M

P

XClone 2 M

P

Clone 3 MP

Multiplex Padlock Probes

Reference Allele

Alternative Allele

AT

C

C

C

C

C

T

T

T

A

GGGG

AA

C

Zhang et al. 2009

Lymphoblast clones

C TBisulfite Conversion

Amplification

Padlock Probes

T

Differential Methylation Score

-1

Alternative Allele Bias Reference Allele Bias

0 +1

𝑠𝑐𝑜𝑟𝑒=(𝐶𝑟−𝐶𝑎)

∑𝐶

Padlock Probe Method Validation

A

B

C

D

E

F

Enriched Allele-Specific MethylationA

B

*

*

**

C

* = p << 0.0001

Annotate SNP Neighborhood

Allelic Bias CategorizationOpposite Bias Same Bias

Clone 1

Clone 2

RA

RA

No Bias

Clone-Specific MAE and Allele-Specific Methylation

* = p << 0.0001

A B

*

*

*

*

All CpGs Upstream CpGs

Conclusions

• 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

Future Work

MAE Gene

MAE Gene

Maternal

Paternal

MAE Gene

MAE Gene

Maternal

Paternal

Clone 1 Clone 2

Gene Expression

Does clone and allele specific DNA methylation correlate with the level of gene expression?

Acknowledgements

Gimelbrant Lab:Alexander Gimelbrant, PhD (PI)Virginia Savova, PhDAnwesha Nag, PhDSébastien Vigneau, PhDJason Alvarez

Sponsors/Funding Sources:National Institutes of HealthNational Science Foundationi2b2 National Center for BiocomputingHarvard-MIT Division of Health Sciences and Technology (HST)Massachusetts Institute of TechnologyHarvard Medical SchoolDana-Farber Cancer Institute

Harvard-MIT HST Summer Institute:Susanne Churchill, PhDSonal Jhaveri, PhDBarbara Mawn