Course Title: Epigenetics Lecture Titles: Lecture I: General Overview and History of Epigenetics Lecture II: DNA methylation Lecture III: Alteration in DNA methylation and its transgenerational inheritance Lecture IV: DNA methylation and genome stability Lecture V: Epigenetic variation in genome evolution and crop improvement Lecture VI: Histone modifications Lecture VII: RNA interference Lecture VIII: Epigenetics and gene expression Lecture : TBD Lecture : Summary

Course Title: Epigenetics Lecture Titles: Lecture I: General Overview and History of Epigenetics Lecture II: DNA methylation Lecture III: Alteration in DNA methylation and its transgenerational inheritance Lecture IV: DNA methylation and genome stability Lecture V: Epigenetic variation in genome evolution and crop improvement Lecture VI: Histone modifications Lecture VII: Non-coding small RNA and RNA interference Lecture VIII: Epigenetics and gene expression Lecture : TBD Lecture : Summary

(toadflax, Leinkraut, Linaria vulgaris) Cubas, P. et al. (1999) An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401, 157–161

worker queen bee larvae DNA methyltransferase knockdown

Epigenetic Inheritance mitotic stability/heritability meiotic stability/ transgenerational inheritance Persistence of epigenetic marks. Alterations that last less than one cell cycle (green asterisk, a) do not qualify as epigenetic under the definition that strictly requires heritability, whereas non-mutational changes that are transmitted from one cell to its daughters (red asterisk, b) or between generations of an organism (blue asterisk, c) do qualify.

Epigenetic modifications are widely accepted as playing a critical role in the regulation of gene expression and thereby contributing to the determination of the phenotype of multicellular organisms. In general, these marks are cleared and re- established each generation, but there have been reports in a number of model organisms that at some loci in the genome this clearing is incomplete. This phenomenon is referred to as transgenerational epigenetic inheritance. Moreover, recent evidence shows that the environment can stably influence the establishment of the epigenome. Together, these findings suggest that an environmental event in one generation could affect the phenotype in subsequent generations, and these somewhat Lamarckian ideas are stimulating interest from a broad spectrum of biologists, from ecologists to health workers.

Heritable epigenetic polymorphisms, such as differential cytosine methylation, can underlie phenotypic variation. Moreover, wild strains of the plant Arabidopsis thaliana differ in many epialleles, and these can influence the expression of nearby genes. However, to understand their role in evolution, it is imperative to ascertain the emergence rate and stability of epialleles, including those that are not due to structural variation. We have compared genomewide DNA methylation among 10 A. thaliana lines, derived 30 generations ago from a common ancestor. Epimutations at individual positions were easily detected, and close to 30,000 cytosines in each strain were differentially methylated. In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutations. Like individual positions, the same regions were often affected by differential methylation in independent lines, with evidence for recurrent cycles of forward and reverse mutations.

Transposable elements and short interfering RNAs have been causally linked to DNA methylation. In agreement, differentially methylated sites were farther from transposable elements and showed less association with short interfering RNA expression than invariant positions. The biased distribution and frequent reversion of epimutations have important implications for the potential contribution of sequence- independent epialleles to plant evolution.

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants Robert J. Schmitz,1,2 Matthew D. Schultz,1,2,3 Mathew G. Lewsey,1,2 Ronan C. O’Malley,2 Mark A. Urich,1,2 Ondrej Libiger,4 Nicholas J. Schork,4 Joseph R. Ecker1,2,5* Epigenetic information, which may affect an organisms’ phenotype, can be stored and stably inherited in the form of cytosine DNA methylation. Changes in DNA methylation can produce meiotically stable epialleles that affect transcription and morphology, but the rates of spontaneous gain or loss of DNA methylation are unknown. We examined spontaneously occurring variation in DNA methylation in Arabidopsis thaliana plants propagated by single-seed descent for 30 generations. 114,287 CG single methylation polymorphisms (SMPs) and 2485 CG differentially methylated regions (DMRs) were identified, both of which show patterns of divergence compared to the ancestral state. Thus, transgenerational epigenetic variation in DNA methylation may generate new allelic states that alter transcription providing a mechanism for phenotypic diversity in the absence of genetic mutation. Science September 23, 2011

“Regardless of their origin, the majority of epialleles identified in this study are meiotically stable and heritable across many generations in this population. Understanding the basis for such transgenerational instability and the mechanism(s) that trigger and/or release these epiallelic states will be of great importance for future studies.” Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants Robert J. Schmitz,1,2 Matthew D. Schultz,1,2,3 Mathew G. Lewsey,1,2 Ronan C. O’Malley,2 Mark A. Urich,1,2 Ondrej Libiger,4 Nicholas J. Schork,4 Joseph R. Ecker1,2,5* Science September 23, 2011

Science (2009)

Science (2010)

“Some authors use the term “variation” in a technical sense, as implying a modification directly due to the physical conditions of life; and “variations” in this sense are supposed not to be inherited; but who can say that the dwarfed condition of shells in the brackish waters of the Baltic, or dwarfed plants on Alpine summits, or the thicker fur of an animal from far northwards, would not in some cases be inherited for at least a few generations (Darwin, 1859)?”

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