Notch signaling genes

Abstract

Notch intercellular signaling is critical for diverse developmental pathways and for homeostasis in various types of stem cells and progenitor cells. Because Notch gene products need to be precisely regulated spatially and temporally, epigenetics is likely to help control expression of Notch signaling genes. Reduced representation bisulfite sequencing (RRBS) indicated significant hypomethylation in myoblasts, myotubes, and skeletal muscle vs. many nonmuscle samples at intragenic or intergenic regions of the following Notch receptor or ligand genes: NOTCH1, NOTCH2, JAG2, and DLL1. An enzymatic assay of sites in or near these genes revealed unusually high enrichment of 5-hydroxymethylcytosine (up to 81%) in skeletal muscle, heart, and cerebellum. Epigenetics studies and gene expression profiles suggest that hypomethylation and/or hydroxymethylation help control expression of these genes in heart, brain, myoblasts, myotubes, and within skeletal muscle myofibers. Such regulation could promote cell renewal, cell maintenance, homeostasis, and a poised state for repair of tissue damage.

Myogenic Differential Methylation: Diverse Associations with Chromatin Structure

“…Evidence is accumulating that changes in DNA methylation also help direct alternative splicing [15]. Our previous analyses of myogenesis-associated differential DNA methylation and gene expression from whole-genome profiles reinforce the hypothesis that vertebrate DNA methylation plays multiple roles in regulating gene expression including little-studied ones, such as helping to finely tune expression levels, limiting the spread of promoter- or enhancer-type chromatin, and silencing repressive DNA elements [16,17,18]. …”

Overlapping Requirements for Tet2 and Tet3 in Normal Development and Hematopoietic Stem Cell Emergence

“…Analysis of double mutant larvae revealed a combined requirement for tet2/3 in regulating Notch signaling in the hemogenic endothelium, suggesting a role for 5hmC in the specification or early function of this tissue. Enrichment of 5hmC has been reported at Notch receptor and ligand genes in other tissues, but the functional significance of these changes has not been determined (Terragni et al, 2014). Intriguingly, we find Notch signaling to be relatively intact in other tissues of tet2/3 DM larvae, indicating that Tet2/3 are likely be involved in fine-tuning the activation of this pathway in select cell types.…”

DNA Cytosine Methylation and Hydroxymethylation at the Borders

“…Because elevated 5hmC and low 5mC levels are associated with poised or active enhancers [9,13,16,27], we hypothesize that 5hmC at the borders of active promoters favors forming or maintaining enhancer chromatin there. Although a higher level of 5mC than 5hmC is usually observed at a given 5hmC-containing CpG in a steady-state population of cells [1,16], exceptional CpG sites, especially in non-cycling cell populations, can be found with average 5hmC contents higher than those of 5mC [14,16]. …”

“…In contrast, at the borders of some active-promoter chromatin regions [26], we found myoblast-associated differentially methylated regions (DMRs) that were hypermethylated in myoblasts and not present in nonexpressing cell types [15,28]. Although the methylation was monitored by reduced representation bisulfite sequencing, which does not distinguish between 5mC and 5hmC, the low levels of genomic 5hmC in myoblasts [4,14–15] make it likely that these DMRs contain mostly 5mC. The unexpected association of hypermethylated DMRs with the borders of certain active-promoter regions could be due to DNA methylation stopping the spread of polycomb silencing into the promoter [29]; counteracting the activity of a silencer element; or inhibiting repressive noncoding RNA transcription from the promoter flanks.…”

“…This evidence includes cell-type-specific changes in 5hmC and 5mC at cis-acting transcription-regulatory elements, including among functionally related sets of genes [3,13,14]. Moreover, although the global levels of 5hmC in brain are very much higher than in other tissues, the importance of 5hmC in non-neural tissues is indicated by the finding that compared to brain, skeletal muscle or heart have much higher levels of 5hmC in certain DNA sequences [14,15]. …”