Ssed genes (DEGs) and transposable element (TE) families in Histamine Receptor Modulator Species gsnor1-3 and (B,E) Volcano plot highlighting substantial DEGs in gsnor1-3 and sahh1. Blue and red dots mark D1 Receptor Inhibitor Source considerably decreased or sahh1. (B,E) Volcano plot highlighting substantial DEGs in gsnor1-3 and sahh1. Blue and red dots mark drastically deincreased expressed genes, respectively. respectively. (C,F) Heat map showing differential households in of TE households in creased or elevated expressed genes, (C,F) Heat map showing differential expression of TE expression gsnor1-3 and sahh1. If more and a single household inside one particular household inside a superfamily is differentially expressed, superfamilies are classified gsnor1-3 than sahh1. If a lot more than a superfamily is differentially expressed, superfamilies are indicated. TEsare indicated. in accordance with www.arabidopsis.org (accessed on 24 December 2018). TEs are classified according to www.arabidopsis.org (accessed on 24 December 2018).Concerning sahh1, from 4-week-old rosette transcription aspect activity” situations RNA was extractedthe terms “DNA-bindingleaves grown beneath long-day and “metal ion binding” wereafterdominant categories amongst the molecular functions enrichedadand harvested five h the the day-time start (n = 4). Substantial criteria: log2FC 1, for downregulated genes 0.1. Gene Ontology S12). Among biological processes, terms rejusted p-value much less than(Supplemental Table(GO) term enrichment evaluation revealed that lated to “hormones” and “response molecular functional categories of the upregulated amongst one of the most drastically enrichedto chemical” were over-represented. As an example, LIPOXYGENASEwere the “catalytic activity”, “glutathione transferase”, “glycosyltransgenes in gsnor1-3 four involved within the biosynthesis in the plant hormone jasmonic acid was downregulated, as previously reported [56]. Additional, the term anthocyanin-containing ferase”, and “oxidoreductase activity” categories (Supplemental Table S11). Furthermore, bi-ological procedure categories for instance “response to light”, “response to UV”, “cellular response to reactive oxygen species”, “cellular response to oxidative stress”, and “cellularAntioxidants 2021, 10,16 ofcompound biosynthesis was located when analyzing upregulated DEGs in sahh1, that is in line with earlier studies [56]. three.six. Integrative Evaluation of WGBS and RNA-Seq Data To test whether differential methylation was related with differential expression, we looked for associations involving the WGBS and RNA-seq datasets (DEG MG candidates). The integrative analysis of DMGs and DEGs at the gene level revealed that about 4 of DMGs had been differentially expressed (percentages are relative to DMGs). Hypo- and hypermethylation had been positively and negatively correlated with transcription (Table three). Loss of GSNOR function resulted in hypermethylation of up- and downregulated TEs within the CHG context (Supplemental Figure S5). Integrative analysis of differentially methylated TEs and differentially expressed TE families revealed that DNA methylation is negatively linked with TE expression. In detail, TE households ATLINEIII, ATHATN3, and HELITRONY1A were downregulated (expression analysis performed at household level; Supplemental Table S8), and members of those TE families had been hypermethylated (Supplemental Table S4).Table 3. Integrative evaluation of DMGs and DEGs in gsnor1-3.Overlap of Significantly Downregulated Genes with DMGs Chr Chr5 Chr5 Start 8751681 9309455 bp 42 206 CH3 + Feature 3kb down 3kb up Gene ID AT5G25250 A.