Transcript Silencing mechanisms

Epigenomics in
Plants
Nozomu TAKAHASHI
June 11th, 2012
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.
Epigenetic gene regulation:
Involved in many different biological process in plants
photosynthesis
light perception
hormone signaling
cell elongation
cold responses
N & S assimilation
phenylpropanoid synthesis
flowering time
starch mobilization
sugar metabolism
Epigenetic gene regulations:
Two major mechanisms

DNA Methylation

Histone modification
DNA methylation

Cytosine can be covalently methylated via
methyltransferase activity, and transcriptionaly
inactivated.
NH2
NH2
O
CH3
N
N
N
~
cytosine
O
N
~
5-methylcytosine
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)
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
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
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
Euchromatin
= Loosely packed form
Low gene expression
High gene expression
Histone modification
Histone Code
= The pattern of histone modification which
affects the transcriptional level.

・Acetylation
・Methylation
・Ubiquitination
・Phosphorylation
・Sumoylation
Histone modification
Examples of histone code
Position and type of modification
on histone
vs
Transcriptional regulation
Li, 2007
Histone modification
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
After three After five
generation generations 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
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.

Bibliography






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.