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

phenylpropanoid synthesis

N & S assimilation

light perception

photosynthesis

flowering time sugar metabolism

cell elongation

cold responses

starch mobilization

hormone signaling

Epigenetic gene regulations:Two major mechanisms

DNA Methylation

Histone modification

DNA methylation

Cytosine can be covalently methylated via methyltransferase activity, and transcriptionaly inactivated.

ON

NH2

N

~

O

N

N

NH2

~

CH3

cytosine 5-methylcytosine

Methyltransfe

rase

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 Methylationin met1 mutant

Zhang, 2006

Metyltransferase mutant plants shows hypomethylation in centromeric region

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

H2BH3H4

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

Histone modification

Histone Code = The pattern of histone modification which

affects the transcriptional level.

・ Acetylation・ Methylation・ Ubiquitination・ Phosphorylation・ Sumoylation

Histone modification

Li, 2007

Examples of histone code

Position and type of modificationon histone

vsTranscriptional regulation

Histone modification

Li, 2007

Genome wide distribution Pattern of histone modifications

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 Methylationin met1 mutant

Zhang, 2006

An Example of Epigenetic regulation at genome wide scale: Transposon silencing

Wild-typeAfter onegeneration

After threegenerations

After fivegenerations

Methyltransferase mutants accumlate the mutations caused by transposon activityover the generations.

Kakutani, 1996

An Example of Epigenetic regulation at genome wide scale: Transposon silencing

Small RNAs

Small interfering RNA (siRNA) is derived from centromeric regions where lotsof transposons are located .

Silencing mechanisms

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 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):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.