Authors: Iris Sammarco, Anupoma Niloya Troyee, Morgane van Antro, Dario Galanti, John Juma, Bárbara Díez Rodríguez, Daniela Ramos Cruz, Cristian Peña, Adam Nunn, Nilay Can, Adrián Contreras, María Estefanía López, Bhumika Dubay, Samar Fatma, Panpan Zhang

Introduction

How to read this book

Starting from epigenetics as concept: why, when and how is epigenetics relevant

Molecular mechanisms in epigenetics

Chapter 1 | DNA Methylation

Molecular functions of DNA methylation (epimutations)

DNA methlyation de novo, establishing and erasing (Methylstats)

RdDM canonical pathway-noncanonical pathway (TE and repetitve regions)

Chapter 2 | Histone modifications

Chapter 3 | Small RNAs

Chapter 4 | TEs and mobilomes

Chapter 5 | Consequences of epigenetic modifications

Gene Expression

Phenotypes

Responses to environmental stimuli

Chapter 6 | Transgenerational adaptation

Chapter 7 | Wetlab techniques

Tissue

Extraction

Reduced representation techniques

RNAseq

NGS

Epigenetics in ecology and evolution

Chapter 1 | Introduction to ecology and the merging between the 3 disciplines

Chapter 2 | Life history strategies

Chapter 3 | Biotic vs abiotic stress

Genome stability is affected by stress

Plants are sessile organisms that do not have a predetermined germline. During their life cycle, they are constantly challenged by various stresses that may have negative impacts on growth, development and reproduction [1,2]. The vast majority of biotic and abiotic stimuli are found to alter genome stability by changing the frequency of homologous recombination (HR) events in somatic and meiotic cells. These stimuli include pathogen attacks, the bacterial elicitor flagellin, high and low temperatures, day length, UVB and UVC, drought and flood, salt, osmotic and oxidative stresses, as well as drugs that modify chromatin and change DNA methylation patterns [3,4••,5–7,8••,9,10•,11•]. Many of these stresses do not damage DNA directly. An increased frequency of somatic HR events in response to the majority of stresses tested suggests that changes in genome stability are part of a general plant response to stress (Figure 1) . (https://doi.org/10.1016/j.pbi.2011.03.003)

Regulation of gene expression by DNA methylation is crucial for defining cellular identities and coordinating organism-wide developmental programs in many organisms. In plants, modulation of DNA methylation in response to environmental conditions represents a potentially robust mechanism to regulate gene expression networks; however, examples of dynamic DNA methylation are largely limited to gene imprinting. Here we report an unexpected role for DNA methylation in regulation of the Arabidopsis thaliana immune system. Profiling the DNA methylomes of plants exposed to bacterial pathogen, avirulent bacteria, or salicylic acid (SA) hormone revealed numerous stress-induced differentially methylated regions, many of which were intimately associated with differentially expressed genes. In response to SA, transposon-associated differentially methylated regions, which were accompanied by up-regulation of 21-nt siRNAs, were often coupled to transcriptional changes of the transposon and/or the proximal gene. Thus, dynamic DNA methylation changes within repetitive sequences or transposons can regulate neighboring genes in response to SA stress (Dowen et al., 2012).\cite{Dowen_2012})

how changes in genome stability and epigenetically mediated changes in gene expression could contribute to plant adaptation. We provide examples of environmentally induced transgenerational epigenetic effects that include the appearance of new phenotypes in successive generations of stressed plants. We also describe several cases in which exposure to stress leads to nonrandom heritable but reversible changes in stress tolerance in the progeny of stressed plants.