th,

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

Epigenetic gene regulation:
Involved in many different biological process in plants hormone signaling photosynthesis light perception cell elongation
N & S assimilation cold responses phenylpropanoid synthesis flowering time starch mobilization sugar metabolism

 DNA Methylation
 Histone modification

 Cytosine can be covalently methylated via methyltransferase activity, and transcriptionaly inactivated.
NH
2
N
O
N
~ cytosine
NH
2
N
N
O
~
5-methylcytosine
CH3

 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)

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

 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



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

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

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

Genome wide distribution Pattern of histone modifications
Li, 2007

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

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

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

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

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

 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.

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Henderson IR, Jacobsen SE. (2007) Epigenetic inheritance in plants.Nature. May
24;447(7143):418-24.
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: 12406-12411. 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. 2007 Genomewide 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):707-19.
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.