Quadrana & Colot (Annual Review of Genetics, 2016) review on plant transgenerational epigenetics

Q1. Who coined the term "epigenetics" in 1942, and what was his original intention?

Conrad H. Waddington; to advocate the need to understand the mechanisms by which genes bring about phenotypic effects in the framework of the theory of epigenesis.

Q2. According to Robin Holliday, what is the definition of epigenetics used in this review?

The study of changes in gene expression that are heritable (through mitosis or meiosis) but not due to changes in DNA sequence.

Q3. What is the key difference between developmental epigenetics and transgenerational epigenetics?

Developmental epigenetics involves resetting of epigenetic states between generations; transgenerational epigenetics implies an absence of resetting in the germline or early embryo.

Q4. What is the first natural plant phenotype attributed to an epimutation rather than a DNA mutation?

The peloric variant of Linaria vulgaris (toadflax), which has radial instead of bilateral symmetry; caused by DNA hypermethylation of the Lcyc locus.

Q5. What is an epiallele?

Forms of a gene that are responsible for heritable phenotypic variation but do not entail a change in DNA sequence; caused by heritable changes in regulation or expression level.

Q6. How were the first two plant genes involved in DNA methylation (DDM1 and MET1) identified?

Through forward genetic screens for Arabidopsis mutants with reduced DNA methylation of centromeric repeats.

Q7. What was the key observation indicating lack of extensive DNA methylation reprogramming in plants?

Loss of DNA methylation in ddm1 and met1 mutants persisted after segregation of the mutant alleles.

Q8. What are epiRILs (epigenetic recombinant inbred lines), and how are they generated?

Populations derived from crossing a mutant with altered DNA methylation (e.g., ddm1 or met1) to a wild-type parent, selecting F2 progeny homozygous for the wild-type allele, then propagating by single seed descent for multiple generations.

Q9. What are the three nucleotide contexts in which DNA methylation occurs in plants?

CG, CHG, and CHH (where H = C, A, or T).

Q10. What is the unique de novo DNA methylation pathway in plants that targets transposable elements?

RNA-directed DNA methylation (RdDM), involving Pol IV, Pol V, RDR2, DCL3, AGO4, and DRM2.

Q11. Which plant DNA methyltransferase is responsible for maintaining CG methylation, and what is its mammalian homolog?

MET1; homolog of mammalian Dnmt1.

Q12. How do plants actively demethylate DNA, and how does this differ from mammals?

Plants use DNA glycosylases (ROS1, DME, DML2, DML3) that excise methylated cytosines; mammals use TET enzymes.

Q13. Which plant cell types undergo substantial DNA demethylation, and what enzyme is responsible?

The central cell (of the female gametophyte) and the vegetative nucleus of pollen grains; DME (DEMETER) DNA glycosylase.

Q14. What is the rate of spontaneous DNA methylation variation (DMPs) in Arabidopsis mutation accumulation lines compared to DNA mutation rate?

~1,000 DMPs per generation, which is three orders of magnitude higher than the DNA mutation rate.

Q15. Are differentially methylated regions (DMRs) as common as DMPs in mutation accumulation lines?

No, DMRs are as rare as DNA sequence mutations in MA lines, suggesting most spontaneous DMPs are functionally inconsequential.

Q16. What did the ddm1-derived epiRIL population reveal about the contribution of DNA methylation variation to complex traits?

Phenotypic variation in epiRILs is heritable; many traits vary; using a genetic map of stable DMRs, several QTLs were identified; rules out new TE insertions as the cause.

Q17. What is the "mantled" somaclonal variant of oil palm, and what causes it?

A homeotic transformation causing parthenocarpy and loss of oil yield; caused by hypomethylation of a retroelement called Karma inserted in the MANTLED gene.

Q18. How does the plant methylome change in response to bacterial pathogen attack?

Widespread hypomethylation of TEs, likely caused by reduced RdDM activity; associated with increased expression of immune response genes.

Q19. What is paramutation, and who coined the term?

Allelic interactions leading to non-Mendelian inheritance patterns where one epiallele imposes its methylation state on another; coined by Alexander Brink in maize.

Q20. According to the authors, what is the main cause of inherited DNA methylation variation in plants: failed reprogramming or failed reinforcement?

Failed reinforcement rather than failed reprogramming; the methylome is reinforced rather than reset during sexual reproduction