The dynamic methylome of islets in health and disease

Abstract

Background: Epigenetic processes control timing and level of gene expression throughout life, during development, differentiation, and aging, and are the link to adapting gene expression profiles to environmental cues. To qualify for the definition of 'epigenetic', a change to a gene's activity must be inherited through at least one mitotic division. Epigenetic mechanisms link changes in the environment to adaptions of the genome that do not rely on changes in the DNA sequence. In the past two decades, multiple studies have aimed to identify epigenetic mechanisms, and to define their role in development, differentiation and disease.

Scope of review: In this review, we will focus on the current knowledge of the epigenetic control of pancreatic beta cell maturation and dysfunction and its relationship to the development of islet cell failure in diabetes. Most of the data currently available have been obtained in mice, but we will summarize studies of human data as well. We will focus here on DNA methylation, as this is the most stable epigenetic mark, and least impacted by the variables inherent in islet procurement, isolation, and culture.

Major conclusions: DNA methylation patterns of beta cell are dynamic during maturation and during the diabetic process. In both cases, the changes occur at cell specific regulatory regions such as enhancers, where the methylation profile is cell type specific. Frequently, the differentially methylated regulatory elements are associated with key function genes such as PDX1, NKX6-1 and TCF7L2. During maturation, enhancers tend to become demethylated in association with increased activation of beta cell function genes and increased functionality, as indicated by glucose stimulated insulin secretion. Likewise, the changes to the DNA methylome that are present in pancreatic islets from diabetic donors are enriched in regulatory regions as well.

Keywords: Aging; Beta cells; DNA methylation; Endocrine pancreas; Epigenetics.

Figure 1

The cytosine methylation and demethylation system. Cytosine in the CpG context can be methylated de novo by DNA methyltransferase 3a and 3b (DNMT3) to 5′-methyl cytosine (5 mC). Following copying of the DNA during S-phase of the cell cycle, the now hemi-methylated CpGs are recognized by DNMT1 and restored to the fully methylated state. In specific contexts, likely driven by tissue-specific DNA binding transcription factors, selected 5 mC residues are oxidized by TET enzymes to produce 5hmC (5-hydroxymethyl cytosine), which can be further oxidized to 5 fC (5-formyl cytosine) and 5caC (5-carboxy cytosine), and glycosylated by thymidine DNA glycosylase (TDG), after which the modified base is removed by base excision repair (active demethylation). Alternatively, and possibly quantitatively more impactful, CpG methylation can be removed at selected sites through several rounds of DNA replication once a site has been converted to 5hmC, as this base cannot be recognized by DNMT1 (passive demethylation).

Figure 2

Structure of commonly used targeted epigenome modifying systems. (A) A three zinc finger protein (green) in complex with DNA (gray). Inset shows one of the zinc finger modules and its binding to residues −1, 2, 3, and 6 (B) A TALE protein (blue) in complex with DNA (gray). Inset shows TALE repeat-variable di-residues (RVDs) labeled in red and corresponding DNA bases labeled in gray. (C) Nuclease-null dCas9 protein (purple) with designed sgRNA (orange) in complex with DNA (gray). Inset shows the interaction between the sgRNA and DNA. Reprinted with permission from Waryah and colleagues .

Figure 3

Targeted epimutation at the CDKN1C locus increases replication of human beta cells. (A) Schematic of the imprinted Chr11p15.5 locus. The ICR2 is methylated (depicted by black circles) at the promoter of lncRNA KCNQ1OT1 on the maternal allele, which correlates with maternal allele-specific expression of CDKN1C/p57^kip2. A TALE-TET1 fusion protein was designed to target the ICR2 and remove the methylCpGs at the ICR2 in order to deactivate CDKN1C and increase cell proliferation. (B) Percent methylation of unique CpGs in the ICR2 of human fibroblasts after transduction with either the control ICR2-deadTET1 or ICR2-TET1 adenovirus (*,p < 0.05, **,p < 0.01). (C) Immunocytochemistry of beta cells (identified by C-peptide, red) transduced with the ICR2-TET1 adenovirus. Control beta cells were identified by the absence of GFP staining. Note the absence of nuclear p57^kip2 protein in beta cells expressing ICR2-TET1. (D) BrdU⁺ beta cells in sectioned islet xenografts. C-peptide stained in red, BrdU in blue. Reprinted with permission from .