Lessons on human beta cell biology from comprehensive methylome analysis

Yuval Dor (The Hebrew University of Jerusalem)

Yuval Dor, Ayelet Peretz, Judith Magenheim, Netanel Loyfer, Agnes Klochendler, Benjamin Glaser, Tommy Kaplan

The methylome of cells encodes and memorizes the combined influence of pre-existing genetics, cell differentiation and maintenance programs, and environmental exposures. Previous studies have described extensive plasticity of the beta cell methylome during healthy development and in diabetes. However such studies have typically relied on material from whole islets, where different preparations may have different cellular compositions. In addition, analyses have often examined the methylation status of individual CpG sites, while the actual functional unit of DNA methylation, controlling chromatin organization and protein binding, is a block of multiple adjacent CpGs that are either all methylated or all unmethylated. The purpose of this study was to characterize the methylome of human beta cells as compared to all other major human cell types.

We have generated a comprehensive cell type-specific human methylome atlas, based on whole genome bisulfite sequencing of individual cell types sorted from dissociated surgical material. The atlas contains the methylomes of 210 samples from 86 cell types, including triplicates of samples from alpha, beta and delta cells from non-diabetic donors; duplicates of alpha, beta and delta cells from donors with type 2 diabetes; and triplicates of samples from acinar cells and duct cells.

Summary of Results
Comparative analysis of the atlas provides interesting insights, including:
1. When examined through the lens of methylation blocks, the methylomes of beta cells from different donors are nearly identical. Out of 3 million methylation blocks in the genome, only 1000 (0.03%) vary in their methylation patterns between beta cells of healthy individuals. This degree of variation is seen also when comparing material from healthy donors and people with type 2 diabetes.
2. The methylome of beta cells is most similar to that of alpha and delta cells, followed by similarity to acinar cells, duct cells and hepatocytes. Strikingly, the methylomes of beta cells and neurons are highly dissimilar, despite the phenotypic similarity. Thus, methylomes reflect the lineage history of beta cells more than their current phenotype.
3. There are hundreds of loci unmethylated uniquely in beta cells. These are typically enhancers that control expression of beta cell genes.
4. Loci that are methylated uniquely in beta cells are typically binding sites to CTCF, suggesting that these are regulators of beta cell-specific chromatin looping.

The methylome of beta cells, examined in the context of the methylomes of other cell types, opens a window into beta cell biology including regulatory circuits, interpretation of GWAS hits and more.