Data from: Effects of RNAi-by-feeding on DNA methyltransferases in Daphnia pulex
Data files
Jun 10, 2026 version files 16.38 KB
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ConstructSensativ_Neopermom.csv
1.41 KB
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ConstructSensativ_surv.csv
1.62 KB
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DNMT_ComparStudy_Geneexp.csv
6.76 KB
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DNMT_ComparStudy_survivorship.csv
1.24 KB
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DNMTComparStudy_neopermom.csv
2.18 KB
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README.md
3.17 KB
Abstract
DNA methyltransferases (DNMTs) are well-characterized epigenetic enzymes responsible for transferring methyl groups to and from DNA. Three main DNMT orthologues differ in function and methylation capability. They each are evolutionarily conserved across diverse taxa, but few studies investigate them jointly. We did so in Daphnia, freshwater microcrustaceans used extensively in research on genetic diversity, phenotypic plasticity, and maternal effects. Daphnia are capable of reproducing asexually through cyclic parthenogenesis, making the Daphnia system an ideal choice for studying epigenetic phenomena. Advances in gene expression control techniques, including RNA interference (RNAi), have increased the versatility and power of the Daphnia system. RNAi is a post-transcriptional gene silencing mechanism that operates through sequence-specific cleavage of endogenous messenger RNA (mRNA) transcripts. Here, we used an RNAi bacterial feeding regime to target the three DNA methyltransferase genes in two clones of Daphnia pulex. We observed significant genotypic differences in response to the RNAi feeding regime, namely, the mortality of one clone. In the other, DNMT expression significantly increased in five of the six experimental treatments, with the highest level observed in animals treated with the GFP double-stranded RNA bacterial vector control. However, DNMT expression was reduced in all three DNMT RNAi treatments relative to the GFP control. Furthermore, we found strong cross-reactivity, where targeting one DNMT resulted in a reduction in expression of the other two. This response may be associated with known immune pathways involving signal transduction that can be stimulated by viral and bacterial signals, or it may result from previously unknown aspects of DNMT biology.
Data pertaining to survivorship, fecundity, and gene expression.
Dataset DOI: 10.5061/dryad.r2280gbrq
Description of the data and file structure
The data collected are from two genotypes of Daphnia pulex: MORG 5 and TRO 3. Two experiments were conducted: "Construct Sensitivity" and "DNMT Comparison Study." Data has been curated for each study into either "survivorship," "fecundity," or "gene expression."
Files:
- ConstructSensativ_surv.csv
- ConstructSensativ_Neopermom.csv
- DNMT_ComparStudy_survivorship.csv
- DNMTComparStudy_neopermom.csv
- DNMT_ComparStudy_Geneexp.csv
Descriptions:
ConstructSensativ_surv.csv
- Treatment = assigned bacterial vector or control treatment
- lx = survivorship
- Day = numeric day of the experiment, day 1 represented the first day treatments began
- Clone = one of two genotypes used, TRO3 or MORG5
- Alive = number of animals alive on a given day
- Total = total number of animals initially setup for each treatment
ConstructSensativ_Neopermom.csv
- TotNeo = total number of neonates produced within a single beaker
- Day = day on which neonates where observed, note data was collected within an 8-12hr window
- Treatment = assigned bacterial vector treatment or control
- Clone = one of two genotypes used, TRO3 or MORG5
- #Mothers = number of adult female Daphnia capable of producing offspring
- NeoperMom = number of neonates divided by total number of living mothers on a single day
- NeoperMomperDay = total number of neonates divided by the total number of mothers divided by the number of days from the experiment start date
DNMT_ComparStudy_survivorship.csv
- Treatment = assigned bacterial vector or control treatment
- lx = survivorship
- Day = numeric day of the experiment, day 1 represented the first day treatments began
- Clone = one of two genotypes used, TRO3 or MORG5
DNMTComparStudy_neopermom.csv
- Treatment = assigned bacterial vector treatment or control
- Clone = one of two genotypes used, TRO3 or MORG5
- Day = day on which neonates where observed, note data was collected within an 8-12hr window
- TotNeo = total number of neonates produced within a treatment on a day
- #Mothers = number of adult female Daphnia capable of producing offspring
- NeoperMom = number of neonates divided by total number of living mothers on a single day
DNMT_ComparStudy_Geneexp.csv
Data from gene express output, normalized to the GFP or EV treament for plotting. Mean Cq are reported, SE and SD, Relative Quantity (RQ), SD and SE of RQ. Delta Delta Ct Method was used for calculating relative gene expression. XBP is the reference gene used.
- KDDNMT# = targeted DNMT of a vector treatement. Choices are KD DNMT1, KD DNMT2, or KD DNMT3
- KDEV = gene expression data from EV treament
- KDGFP = gene expression data from the GFP treatment
- Normalized to ### = gene expression data was normalized to either GFP or EV treatments for reporting. This header denotes which treatment data was normalized to.