Epigenetics DNA methylation II DNA methylation in plants

Epigenetics: DNA methylation II

DNA methylation in plants (Ch 9) Differences between plants and animals • Auxotroph vs. heterotroph • Sessile vs. mobile • Motionless and rigid vs. migrating and flexible cells Similarities • Chromatin structure and related machineries • Genome size and gene structures • DNA methylation (Cytosine)

Life cycle of plants - Gametophytes (Meiosis product) go through growth and more divisions (Mitosis) -> provide a window of time for epigenetic changes, and yet no known reprogramming of epigenetic modification -> transgenerational inheritance of epigenetic changes - two different methods of reproduction through germ line (seed) or through meristems (somatic embryogenesis – vegetative reproduction) reprogramming of somatic cells very easily -Mixing of two cells through plasmodesmata (cytoplasmic bridge: exchange proteins and RNAs) -> epigenetic changes can be mixed and inherited not through germ line

Epigenetics differences between plants and metazoans • Many routes of epigenetic inheritance -> provide flexibility to motionless organisms so that they can adapt to ever-changing environment

Known examples of epigenetics a) Silencing of the promoter of DFR: light purple petunia flower b) Silencing of Arabidopsis CHS gene: yellow seed c) Paramutation of the maize B-I gene: green plants d) Silencing of a transposon at Spm locus: purple kernels -> reversion by excision spotty kernels -> epigenetic mod e) Natural PTGS at the soybean CHS gene dark (extinguished) by PTGS white mottled -> revertants by a suppression of PTGS

DNA methylation in plants • Three types of DNA methylation Cp. G, Cp. Np. N (N: A, T, C) • De novo and maintenance methylation • three main enzymes Met 1: DNA methylatransferase (Cp. G) CMT 3: chromomethyltransferase (non. Cp. G) DRM 1 and 2: domain-rearranged methyltransferase (de novo) • Three demethylases HOG 1: S-adenosyl-L-homocysteine hydrolase ROS 1: DNA glycosylase-domain protein DME: DNA glycosylase-domain protein many Methyl-CG-binding proteins: 12 MBDs in Arabidopsis none in fungus

DNA methylation by RNAi in plants RNA-directed DNA methylation (Rd. DM)

DNA methylation in fungi (Neurospora crassa) - limited DNA methylation (1. 5% Cytosines) r. DNA and repeats - part of Repeat-induced point mutation (RIP) - defense mechanism - only one enzyme DMT-2, but no other machineries for recognition (MBDs)

Major questions • What triggers DNA methylation? (histone connections) • What protects Cp. G islands from DNA methylation? • How DNA methylation maintained in somatic cells (how DNMT 1 transcript and protein are controlled? )

DNA methylation analysis • Bisulfite conversion and sequencing

DNA methylation analysis • Bisulfite conversion and sequencing

Papers to be discussed • Sept 4 th : Transgenerational inheritance of stress through small non-coding RNAs Gapp K et al. Nature Neuroscience 2014.