There are many ways to “attack” a problem – head-on, from the side, with great care, or swiftly and suddenly, but as many a boxer may tell you, the classic one-two combo usually works a treat. Now, in a slugfest of a new study, a rambunctious rabble of ring-ready researchers recently hit the mark and “knocked out” a vexing problem related to gene regulation during cell fate decisions by throwing their very own epigenetic one-two combo – the new “ATAC-Me” technique.
The noted problem relates to a previous study led by Emily Hodges (Vanderbilt University School of Medicine, Tennessee, USA) that provided evidence of methylated DNA occurring alongside high chromatin accessibility at gene enhancers in pluripotent stem cells. However, in somatic cells, these sites seem to resolve via the loss of DNA methylation at active enhancers and loss of chromatin accessibility at repressed enhancers (similar to what occurs at bivalent chromatin domains) to allow for the establishment or stabilization of cell identity.
Confirming this hard-hitting hypothesis requires the ability to measure spatiotemporal relationships within the context of chromatin at high resolution on a genome-wide scale – that’s no mean feat. Luckily, the luchadores from the Hodges lab never thought about throwing in the towel, and they now report on their “ATAC-Me” protocol – a novel one-two combo of transposase-assisted enrichment of chromatin accessibility fragments from native chromatin and subsequent sodium bisulfite conversion and deep sequencing as a knockout strategy to take down this formidable scientific foe.
Ding-ding: here are the top hits from this scientific skirmish (in which the Tn5 transposase again features at the top of the bill) where the induced differentiation of monocytes into macrophages served as a model system to understand the role of DNA methylation at enhancer regions:
- ATAC-Me analysis of single DNA libraries
corroborates previous findings by establishing the persistent hypermethylation of
thousands of myeloid enhancers during monocyte-to-macrophage differentiation
that also display high chromatin accessibility
- These findings also corroborate the idea of a bivalent epigenetic state at enhancer regions, which perhaps represents an intermediate state along a continuum of enhancer activation
- At early stages of monocyte-to-macrophage differentiation,
chromatin accessibility changes correlate with the transcriptional responses of
- Chromatin accessibility at myeloid enhancers increases rapidly before plateauing at around 24 hours
- However, DNA methylation status fails to track with chromatin accessibility/gene expression
- Overall, these findings imply that DNA methylation at enhancers does not influence gene transcription or transcription factor binding on its own and in isolation has minimal influence on cell fate decisions
- Even at later time points, the authors only
observe minimal reductions in DNA methylation levels
- These data suggest a secondary role for DNA methylation removal at gene-regulatory elements
Overall, the knockout hit from this pugilistic paper is the existence of a significant enhancer-specific “disconnect” between chromatin accessibility, DNA methylation, and gene expression; however, the authors also highlight the value of ATAC-Me in “attacking” further epigenetic problems and expanding our understanding of DNA methylation in gene regulation.
For all the round-by-round highlights of the development of this one-two combo technique and the top shots from the subsequent scientific sparring session, see Molecular Cell, Jan 2020.