1. Nozomu TAKAHASHI June 11th, 2012
Epigenomics in Plants
Nozomu TAKAHASHI
June 11th, 2012

2. Epigenomics The study of epigenetics at the genome wide scale.
Epigenetics literally means “above genetics”, and refers to the heritable information in gene expression coded something other than DNA sequence.

3. Epigenetic gene regulation: Involved in many different biological process in plants
photosynthesis
hormone signaling
light perception
cell elongation
cold responses
N & S assimilation
THE REGULATION OF MANY DIFFERENT PROCESSES ARE CONTROLLED BY THE CIRCADIAN CLOCK
phenylpropanoid synthesis
starch mobilization
flowering time
sugar metabolism 3

4. Epigenetic gene regulations: Two major mechanisms
DNA Methylation
Histone modification

5. DNA methylation
Cytosine can be covalently methylated via methyltransferase activity, and transcriptionaly inactivated. O N
NH2 ~
CH3
cytosine
5-methylcytosine
Methyltransferase

6. DNA methylation Methyltransferases ・In Mammal
DNMT (DNA Methyltransferase), met’s CG sequence
・In Plants
MET (metyltransferase), met’s CG
CMT (chromomethyltransferase), met’s CHG
DRM (domain rearranged methyltransferase), met’s CHH
(H = A, C, or T)

7. DNA methylation: Centromeric regions are high in repeats, and highly methylated in Arabidopsis
# of Genes
Length of repeats / 100kB
Length of Methylation
Length of Methylation
in met1 mutant
Metyltransferase mutant plants shows hypomethylation in centromeric region
Zhang, 2006

8. Histone modification
In Eukaryotes, DNA is wrapped around histone proteins and forms nucleosome.
Nucleosome is a basic unit of chromatin.
~ 147 bp DNA +
8 histones:
2 each H2A
H2B H3 H4

9. Histone modification
Chromatin can be highly packed or loosely packed, and correlated to the gene expression levels.
Modifications in histone proteins affects the structure of Chromatin
Heterochromatin
= Highly packed form Low gene expression
Euchromatin
= Loosely packed form High gene expression

10. Histone modification Histone Code
= The pattern of histone modification which affects the transcriptional level.
・Acetylation
・Methylation
・Ubiquitination
・Phosphorylation
・Sumoylation

11. Histone modification Examples of histone code
Position and type of modification on histone vs
Transcriptional regulation
Li, 2007

12. Histone modification
Genome wide distribution Pattern of histone modifications
Li, 2007

13. An Example of Epigenetic regulation at genome wide scale: Transposon silencing
= DNA sequence which is able to relocate itself within a genome.
Responsible for the mutation to large scale genome rearrengements.

14. An Example of Epigenetic regulation at genome wide scale: Transposon silencing
# of Genes
Length of repeats / 100kB
Length of Methylation
Length of Methylation
in met1 mutant
Zhang, 2006

15. An Example of Epigenetic regulation at genome wide scale: Transposon silencing
Wild-type
After one
generation
After three
generations
After five
Methyltransferase mutants accumlate the mutations caused by transposon activity
over the generations.
Kakutani, 1996

16. An Example of Epigenetic regulation at genome wide scale: Transposon silencing
Silencing mechanisms
Small RNAs
Small interfering RNA (siRNA) is derived from centromeric regions where lots
of transposons are located .
Kasschau, 2007

17. An Example of Epigenetic regulation at genome wide scale: Transposon silencing
These siRNA are detected by both DNA methyltransferases and Histone modification enzymes, and promote epigenetic silencing marks

18. Conclusions
Epigenetic regulation is an important mechanism which is involved in many different biological processes not only in animals but also in plants.
Genome wide perspective of epigenetics adds further insights to the resolve this complex biological phenomenon.

19. Bibliography
Henderson IR, Jacobsen SE. (2007) Epigenetic inheritance in plants.Nature. May 24;447(7143):
Kakutani, T., Jeddeloh, J.A., Flowers, S.K., Munakata, K., and Richards, E.J. (1996) Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. PNAS 93: Copyright (1996) National Academy of Sciences, U.S.A.
Kasschau, K.D., Fahlgren, N., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., et al Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5(3): e57.
Bing Li, Michael Carey and Jerry Workman (2007) The role of chromatin during transcription Cell 128(4):
Williams M. (2011) Introduction to Epigenetic Gene Regulation : TEACHING TOOLS IN PLANT BIOLOGY The Plant Cell
Zhang, X.,  et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189–1201 with permission from Elsevier.