1. Epigenetics: DNA methylation II

2. 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)

3. 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

4. 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

5. 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

6. 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

7. DNA methylation by RNAi in plants RNA-directed DNA methylation (RdDM)

8. 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)

9. 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?)

10. DNA methylation analysis
Bisulfite conversion and sequencing

11. DNA methylation analysis
Bisulfite conversion and sequencing

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