Epigenomics in Plants Nozomu TAKAHASHI June 11 th

Epigenomics in Plants Nozomu TAKAHASHI June 11 th, 2012

Epigenomics n The study of epigenetics at the genome wide scale. n 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 n DNA Methylation n Histone modification

DNA methylation n Cytosine can be covalently methylated via methyltransferase activity, and transcriptionaly inactivated. e as fer ns NH 2 ra ylt th Me NH 2 O CH 3 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 n 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 / 100 k. B Length of Methylation in met 1 mutant Metyltransferase mutant plants shows hypomethylation in centromeric region Zhang, 2006

Histone modification n In Eukaryotes, DNA is wrapped around histone proteins and forms nucleosome. n Nucleosome is a basic unit of chromatin. ~ 147 bp DNA + 8 histones: 2 each H 2 A H 2 B H 3 H 4

Histone modification n n 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. n ・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. n 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 / 100 k. B Length of Methylation in met 1 mutant Zhang, 2006

An Example of Epigenetic regulation at genome wide scale: Transposon silencing Wild-type After one After three 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 (si. RNA) is derived from centromeric regions where lots of transposons are located. Kasschau, 2007

An Example of Epigenetic regulation at genome wide scale: Transposon silencing n These si. RNA 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. n Genome wide perspective of epigenetics adds further insights to the resolve this complex biological phenomenon. n

Bibliography n n n 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 si. RNAs. PLo. S Biol 5(3): e 57. 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.