Epigenetics: DNA methylation II

DNA methylation in plants (Ch9) 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 CpG, CpNpG, CpNpN (N: A,T,C) De novo and maintenance methylation three main enzymes Met1: DNA methylatransferase (CpG) CMT3: chromomethyltransferase (nonCpG) DRM1 and 2: domain-rearranged methyltransferase (de novo) Three demethylases HOG1: S-adenosyl-L-homocysteine hydrolase ROS1: 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 (RdDM)

DNA methylation in fungi (Neurospora crassa) - limited DNA methylation (1.5% Cytosines) rDNA 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 CpG islands from DNA methylation? How DNA methylation maintained in somatic cells (how DNMT1 transcript and protein are controlled?)

DNA methylation analysis Bisulfite conversion and sequencing

DNA methylation analysis Bisulfite conversion and sequencing

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