Closest comparison is probably the Rondon et al. 2017 diuron paper:
METHODS:
- Parents exposed to diuron during beginning and middle of gametogenesis, then gametes collected and used for spawning.
- n=6 spat used for WGBS – 3 spat from parents who experienced diuron treatment, and 3 from control parents.
methylkitfor analysis: DMRs of 500bp, using minimum coverage of 10x in all reps, minimum 25% methylation difference, with FDR-adjusted pval of 0.01.- Used visual inspection to identify DMRs for which all reps were affected in same way (ngl, this seems kind of crazy to me…)
- defined “promoter” region as 1kb upstream region.
RESULTS:
no treatment-based difference in global methylation level (GML), and samples did not cluster by treatment (consistent with preliminary
methylkitwork in the ceasmallr samples)from 57,819 eligible windows (500bp, 10X cov), found 1,967 DMRs, with roughly even split between hyper- and hypomethylation (1,060 and 907, respectively) in treated v control samples.
Rondon et al. did NOT have data from the parents. While this may be the closest comparison in the sense that they also demonstrated inheritance of treatment-induced differential methylation, they have a much smaller sample size, no parent data to try demonstrating inheritance of parental DMLs, and used methylKit. Should look elsewhere for a closer methodologically/experimentally similar example.
Feiner et al. (Daphnia paper)
METHODS:
Daphnia (F0 generation) exposed to respective = stressors (3 natural environmetnal stressors, 1 demethylation stressor), then propogated (asexually?) through to F4.
WGBS for F1, F2, and F4 (note, ommited exposed parents F0, and intermediate generation F3). After
bismarkand quality filtering, n=54 librariesmethylKit– considered CpGs wiht >=5 reads in all samples, and only variable sites with >=0.5 std dv in % methylation – average of 2.8M sites/sample.Called DMLs (they term DMPs – differentially methylated positions) using FDR-correct p=0.05 – they don’t seem to have used a minimum methylation difference. These parameters are more permissive than the p<0.01 (corrected) and >25% methylation difference used by me, Rondon, etc.
Def. of treatment-induced transgenerational DML:
treatment-induced differential methylation in F1
methylation state maintained in F2 and F4
^ don’t clarify whether this also requires maintaining direction of differential methylation (hyper- or hypo-).
some sort of permutation approach to provfide additional support for ID’d DMLs?
Peterson et al (Acropora paper w matz)
Two species – Acropora millepora and A. selago
No treatments
both pure (m1 x m2, m2 x m1, s1 x s2, s2 x s1) and hybrid (s1 x m1, s1 x m2, s2 x m1, s2 x m2) crosses
WGBS
used DSS!
Yagound et al., 2020: Intergenerational transfer of DNA methylation marks in the honey bee.
- Examines inheritance end epigenetic reprogramming in honey bees without treatment-induced differential methylation
- WGBS
- Father (sperm) v. offspring comparisons
- Basically showing that offspring methylomes are far more similar to paternal methylomes than non-parental methylomes, so (a) methylomic state is inherited, adn (b) no evidence for epigenetic reprogramming.