Sometimes in life, we get so focused on the details that we can miss the big picture. One of the best examples of this periscope perspective is the case of Down syndrome. Although it is caused by trisomy of chromosome 21, Down syndrome patients display genome-wide alterations to their transcriptomic and epigenomic profiles; however, the differentially methylated regions (DMRs) of the Down syndrome methylome have yet to be examined under the all-seeing lens of a whole-genome bisulfite sequencing (WGBS) based analysis. That is until the lab of Janine LaSalle at the University of California, Davis (USA) came along to take a bioinformatic snapshot.
To see the forest through the trees, the group utilized low-coverage WGBS. First author Ben Laufer shares, “To make WGBS more accessible, I developed two open source bioinformatic repositories that utilize the state-of-the-art tools. The first is CpG_Me, which is a pipeline for the pre-processing, alignment, and quality control and quality assurance (QC/QA) of WGBS data through Bismark. The second is DMRichR, an R package and accompanying executable R script that utilizes dmrseq for the statistical inference of DMRs from aligned WGBS data. It also provides a number of novel downstream functions for data analysis and visualization, which are useful for identifying the biological significance of the DMRs.”
These tools allowed the team to assay over 9 million CpGs covered in all samples and provided them with more than 100,000 testable background regions to examine for DMRs in Down syndrome brain.
Here’s what the candid camera of this snap-happy team caught:
- 3,152 DMRs span the Manhattan plot skyline
- ~75% of DMRs display hypermethylation
- Despite the presence of a genome-wide profile that is not limited to chromosome 21, there is no difference in global DNA methylation
- Vacation postcards revealed that the DMRs flock towards luxurious CpG islands while avoiding other regulatory features
- Enrichment testing against a pan-tissue meta-analysis of genes mapping to CpGs with differential methylation in diverse Down syndrome tissues/cells replicated a number of them and expanded their horizons to larger scale DMRs
- Enrichment testing against genomic coordinates from a dozen other datasets and roadmap epigenomics data, as well as gene ontology testing, uncovered divergent functions for the hypermethylated and hypomethylated DMRs
- The hypermethylated DMRs demonstrate a strong cross-tissue concordance, while also displaying the most robust enrichment for brain datasets and functions related to metabolism and neuronal signaling
- The hypomethylated DMRs show a more brain-specific profile enriched for functions related to proline isomerization and glial immune functions
In summary, the team of shutterbugs synthesized their results with the literature and hypothesize that accessible chromatin is hypermethylated by excess DNA methyltransferase 3L (DNMT3L), which is located on chromosome 21, while the smaller scale hypomethylation occurs as a tissue-specific response.
Laufer adds, “Overall, we show that low-coverage whole genome bisulfite sequencing (WGBS) can be utilized to not only confirm but also expand on past investigations into DNA methylation. Ultimately, the price of low coverage WGBS has dropped to a point where it has become competitive with arrays and other reduced representation methods. We hope that the epigenetics community will benefit from our tools that make the analysis of DMRs from WGBS data more familiar and accessible.”
Senior author Janine LaSalle concludes, “The wider lens of WGBS revealed an epigenomic signature of Down syndrome brain pathology that included immune response and metabolic gene pathways that line up well with recent metabolomics studies in DS blood, suggesting some new insights relevant to therapies.”