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.