Genomic and Epigenomic Characterizations of Major Pancreatic Islet Endocrine Cell Types

During pancreatic development, insulin-producing beta cells, glucagon-producing alpha cells, and somatostatin-producing delta cells differentiate from a common endocrine progenitor. While these cells have been considered terminally differentiated, over the last several years it has become evident that pancreatic islet cellular identity is more plastic than previously appreciated. A cell?? ??an?c?i???me is the final outcome that stems from the interactions of both genomic and epigenomic components. Dynamic changes in chromatin accessibility alongside the recruitment of histone marks that either facilitate or repress gene transcription in tandem with transcription factor co-localization come together to define and maintain cellular identity through gene expression. Understanding of each of these components sheds further light on understanding cellular identity, with profiling the transcriptome providing signature patterns that are responsible for the functional behavior of these cells. Building on this through the interrogation of chromatin accessibility similarities and differences provides further insight into the mechanisms that govern cellular identity when coupled with the appropriate histone modification and transcription factor data. Ultimately, genomic and epigenomic characterizations of these major islet endocrine cell types can provide an avenue to further understanding the complex regulatory mechanisms that define and maintain cellular identity. Furthermore, these characterizations provide a resource for answering outstanding questions in the field

Navigating the Depths and Avoiding the Shallows of Pancreatic Islet Cell Transcriptomes.

Islet gene expression has been widely studied to better understand the transcriptional features that define a healthy β-cell. Transcriptomes of FACS-purified α-, β-, and δ-cells using bulk RNA-sequencing have facilitated our understanding of the complex network of cross talk between islet cells and its effects on β-cell function. However, these approaches were by design not intended to resolve heterogeneity between individual cells. Several recent studies used single-cell RNA sequencing (scRNA-Seq) to report considerable heterogeneity within mouse and human β-cells. In this Perspective, we assess how this newfound ability to assess gene expression at single-cell resolution has enhanced our understanding of β-cell heterogeneity. We conduct a comprehensive assessment of several single human β-cell transcriptome data sets and ask if the heterogeneity reported by these studies showed overlap and concurred with previously known examples of β-cell heterogeneity. We also illustrate the impact of the inevitable limitations of working at or below the limit of detection of gene expression at single cell resolution and their consequences for the quality of single-islet cell transcriptome data. Finally, we offer some guidance on when to opt for scRNA-Seq and when bulk sequencing approaches may be better suited

Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

BackgroundHigh throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene expression signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. However, chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity.ResultsHere, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we not only confirm and visualize previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin, but identify novel regions as well. We compiled our chromatin accessibility data in a freely accessible database of common endocrine- and cell specific-enhancer regions that can be navigated with minimal bioinformatics expertise.ConclusionsBoth alpha and delta cells appear poised, but repressed, from becoming beta cells in murine pancreatic islets. These data broadly support earlier findings on the plasticity in identity of non-beta cells under certain circumstances. Furthermore, differential chromatin accessibility shows preferentially enriched distal-intergenic regions in beta cells, when compared to either alpha or delta cells

Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

Abstract Background High throughput sequencing has enabled the interrogation of the transcriptomic landscape of glucagon-secreting alpha cells, insulin-secreting beta cells, and somatostatin-secreting delta cells. These approaches have furthered our understanding of expression patterns that define healthy or diseased islet cell types and helped explicate some of the intricacies between major islet cell crosstalk and glucose regulation. All three endocrine cell types derive from a common pancreatic progenitor, yet alpha and beta cells have partially opposing functions, and delta cells modulate and control insulin and glucagon release. While gene expression signatures that define and maintain cellular identity have been widely explored, the underlying epigenetic components are incompletely characterized and understood. However, chromatin accessibility and remodeling is a dynamic attribute that plays a critical role to determine and maintain cellular identity. Results Here, we compare and contrast the chromatin landscape between mouse alpha, beta, and delta cells using ATAC-Seq to evaluate the significant differences in chromatin accessibility. The similarities and differences in chromatin accessibility between these related islet endocrine cells help define their fate in support of their distinct functional roles. We identify patterns that suggest that both alpha and delta cells are poised, but repressed, from becoming beta-like. We also identify patterns in differentially enriched chromatin that have transcription factor motifs preferentially associated with different regions of the genome. Finally, we not only confirm and visualize previously discovered common endocrine- and cell specific- enhancer regions across differentially enriched chromatin, but identify novel regions as well. We compiled our chromatin accessibility data in a freely accessible database of common endocrine- and cell specific-enhancer regions that can be navigated with minimal bioinformatics expertise. Conclusions Both alpha and delta cells appear poised, but repressed, from becoming beta cells in murine pancreatic islets. These data broadly support earlier findings on the plasticity in identity of non-beta cells under certain circumstances. Furthermore, differential chromatin accessibility shows preferentially enriched distal-intergenic regions in beta cells, when compared to either alpha or delta cells

Additional file 14 of Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

Additional file 14: Supplemental Table 1. Quality control metrics across all ATAC-Seq replicates

Additional file 6 of Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

Additional file 6: Supplemental Figure 2. Validating more chromatin accessibility ATAC Seq and companion RNA-Seq expression in alpha, beta, and delta cells against hallmark genes governing its respective cell’s identity

Additional file 9 of Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

Additional file 9: Supplemental Figure 5. Evaluating KEGG and gene network enrichment (Alpha versus Delta)

Additional file 11 of Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

Additional file 11: Supplemental Figure 7. Transcription factor binding sites and histone mark overlap

Additional file 17 of Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers

Additional file 17: Supplemental Table 4. Validating motif-calling approach against known ChIP binding sites. A: Pancreatic islet ChIP Seq transcription factor peak calls analyzed by the motif-calling method to determine sensitivity and specificity. True positive calls ranged from 0.59-57%, and false positives ranged from 1.19-8.34%. B: Pancreatic islet ChIP Seq transcription factor peak calls limited to open chromatin determined by the consensus peak set analyzed by the motif-calling method to determine sensitivity and specificity. True positive calls ranged from 4.71-65.10%, and false positives ranged from 1.68-8.81%