While collecting blood spots may seem like a hobby best left for a TV serial killer like Dexter Morgan, a novel low-pass whole-genome bisulfite sequencing (WGBS) approach has shown that newborn dried blood spots are more than just a trophy. Their entire methylome can be assayed to answer enticing epigenomic enigmas.
DNA methylation array studies have shown that Down Syndrome is a prime example of genetics shaping epigenetics. Previously, to get a bigger picture perspective, the lab of Janine LaSalle at the University of California, Davis, applied low-pass WGBS to map the Down Syndrome brain DNA methylome. They replicated CpG methylation arrays and expanded many of the known pan-tissue CpG sites to larger scale differentially methylated regions (DMRs).
In their latest blood-borne adventure, to get at the trace amounts of DNA, they performed low-input WGBS using post-bisulfite adaptor tagging (PBAT) with terminal deoxyribonucleotidyl transferase–assisted adenylate connector–mediated single-stranded-DNA ligation. The alignments were done using CpG_Me and DMR analyses were performed with DMRichR. They sliced through tissue-specificity and chromatin state by comparing to 127 reference epigenomes from the NIH Roadmap Epigenomics Project and ENCODE Project.
Here’s what the archives of over 24 million CpGs in 86 samples held:
- Thousands of epigenome-wide significant DMRs that:
- Distinguish Down Syndrome from matched controls and idiopathic developmental delay
- Map to genes involved in neurodevelopment, metabolism, and transcriptional regulation
- When compared to previous Down Syndrome methylation studies of diverse tissues and healthy reference epigenomes:
- The hypermethylated DMRs display a pan-tissue profile
- The hypomethylated DMRs are blood-specific
- A ~28 kb block of DNA hypermethylation on chromosome 21 that overlaps the super-enhancer for the RUNX1 hematopoietic and neurodevelopmental transcription factor
- There’s also genome-wide hypomethylation of RUNX1 binding sites, which is in line with its known role of hypomethylating DNA
- A DMR profile that can distinguish Down Syndrome patients based on whether or not they have congenital heart disease
Taken together, the team hypothesizes a molecular mechanism where during early-life, overexpression of RUNX1 leads to genome-wide hypomethylation of its binding sites. Then, the overexpression of the regulatory DNA methyltransferase DNMT3L, which is also on chromosome 21, leads to the hypermethylation of the RUNX1 super-enhancer, which attenuates some of the overexpression.
First author (and EpiGenie’s Epigenetics Editor) Ben Laufer shares, “By making our computational programs and analysis scripts open source, we hope that the epigenetics community will begin to utilize low-pass WGBS to assay never before seen regions of the methylome in a variety of disorders, sample sources, and organisms.
Senior author Janine LaSalle concludes “We were really pleasantly surprised to see how well DNA derived from archived newborn blood worked for WGBS analysis. Since the methylomic signature was so clear for trisomy 21 over RUNX1 and its downstream targets despite the relatively small sample size, this bodes well for future plans to identify epigenomic signatures at birth for disorders where the genetic basis and pathogenesis are more complex.”
Check out these trophies in Human Molecular Genetics, October 2020