Single cell multi-omics analysis reveals novel roles for DNA methylation in sensory neuron injury responses

Abstract

DNA methylation is implicated in neuronal injury response and regeneration, but its role in regulating stable transcription changes in different types of dorsal root ganglion (DRG) neurons is unclear. In this study, we simultaneously profiled both the DNA methylome and mRNA transcriptome from single DRG neurons at different ages under either control or 20 peripheral nerve injury condition. We found that age-related expression changes in Notch signaling genes and methylation changes at Notch receptor binding sites are associated with the age-dependent decline in peripheral nerve regeneration potential. Moreover, selective hypomethylation of AP-1 complex binding sites on regeneration-associated gene (RAG) promoters coincides with RAG transcriptional upregulation after injury. Consistent with the 25 findings that different subtypes of DRG neurons exhibit distinct methylome changes upon injury responses, in a hybrid CAST/Ei; C57BL/6 genetic background, we further observed allelespecific gene regulation and methylation changes for many RAGs after injury. We suggest that the genetic background determines distinct allele-specific DNA methylomes, which contribute to age-dependent regulation and neuronal subtype-specific injury-responses in different mouse 30 strains. Introduction:

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

“…Both of these examples highlight how an unbiased, data-driven approach is useful to uncover additional, often hidden, layers of the complexity underlying gene regulation. As such, our study joins several other recent papers that have shown similar potential using window-based approaches [16], and footprinting analysis [6].…”

“…Changes in DNA accessibility are a major hallmark of gene regulation [1,2], and techniques that combine chromatin accessibility with RNA sequencing are opening up novel avenues to explore the interplay between transcription factor binding and chromatin state changes in influencing gene expression [3]. These methods not only facilitate the dissection of intricate gene regulatory networks [4], but they also illuminate the extent of intercellular and intracellular variability in transcriptional and epigenomic states [5,6]. Furthermore, these techniques have great potential for both fine-mapping [7] and functional understanding [8] of non-coding genetic variation.…”

“…However, there is increasing evidence that reducing gene regulation to a coordinated effort of modular CREs may be an oversimplification. Multiple studies have highlighted inconsistencies and limitations of peak calling across cell types and methods [10,11], both within and outside of canonical CREs [6,13,15,16]. From an experimental perspective, there is an extensive body of evidence that gene regulation involves very different scales [23]: combinatorial TF binding localized at a few dozen base pairs [24,25], nucleosomal interactions at 100bp scale [26], and genome organization [27,28] combined with hub formation at kilobase scale or higher [29,30].…”