Histone Methylation in Higher Plants
Author: Mahesh Kumar Samota


In eukaryotes, genomic DNA is tightly compacted into a complex structure known as chromatin; chromatin structure is a key regulator that influences the accessibility of factors and cofactors for all DNA-template processes. The fundamental unit of chromatin is the nucleosome, which is composed of histone octamer (containing two copies of each of the four histone protein H2A, H2B, H3 and H4) and 146 bp of DNA wrapped on a histone octamer. The structure and function of chromatin are regulated by multiple epigenetic mechanisms, including histone modification, DNA methylation, ATP-dependent chromatin remodeling, placement of histone variants, and regulation by noncoding RNA. Post-translational covalent histone modifications, together with small interfering RNA (siRNA) and DNA methylation, are implicated in modulating chromatin structure and gene activity. Histone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability.

In eukaryotes, genomic DNA is tightly packed into a complex structure known as chromatin

Chromatin structure is a key regulator that influences the accessibility of factors and cofactors for all DNA-templated processes

Fundamental unit of chromatin is the nucleosome

It composed of 146 base pairs of DNA wrapped on a Histone octamer containing two copies of each of the four histone proteins H2A, H2B,H3, and H4

Histone Methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences to maintain genome stability

Methylation marks Written on Lysine or Arginine by enzymes Histone Lysine Methyltransferases (HKMTs) or Protein Arginine Methyltransferases(PRMTs)

Histone Methylation status is dynamic : Methylation marks can be removed by Eraser enzymes, the Histone Demethylases (HDMs)

Post-translational histone modifications

Methylation
Acetylation
Phosphorylation
Ubiquitination
ADP-ribosylation
Glycosylation
Sumoylation

Histone Methylation: Enzyme Machinery

Histone Methylation occurs on Arginine and Lysine residues in Plants

Enzymes belonging to 3 distinct families of proteins :
- PRMT1 family
- SET DOMAIN protein family
- Non-SET-domain proteins Like DOT1/DOT1L3-6

Mechanism of Histone Methylation

WRITER- Enzyme responsible for adding posttranslational modifications into a given protein

READER- Protein complex that recognizes and binds specifically to a to Particular posttranslationally modified substrate

ERASER- Enzyme that removes a posttranslational modifications from a given protein

Histone methylation occurs at Arginine and Lysine amino acids. Lysine methylation by HKMTs (histone lysine methyltransferase) and Arginine methylation by PRMTs (protein arginine methyltransferase) enzymes . Maintenance of a stably hypomethylated active epiallele in rice required a CHD3 protein (CHR729) .over-expression of an H3K4me3 demethylase (JMJ703) or H3K27me3 methyltransferase (SDG711) could stably resilence the epiallele. CHR729 and JMJ703 have antagonistic function in H3K4me3 in maintaining the active state of the epiallele, whereas SDG711-mediated H3K27me3 is sufficient to stably repress the locus. Many genes are activated during callus culture but all are resilenced during plant regeneration process, except Os03g02470 (referred as to 03g) that is not repressed in regenerated plant leaves. Stable 03g activation is associated with DNA methylation loss, histone H3K27me3 Demethylation and H3K4me3 deposition.

References:

1. Chen,X., Liu,X., Zhao,Y., Zhou,DX., (2O15). Histone H3K4me3 and H3K27me3 regulatory genes control stable transmission of an epimutation in rice. nature sci rep. 19:5-13251.

2. Liu, C., Lu,F., Cui, X., Cao,X., (2010) Histone Methylation in Higher Plants. Annu. Rev. Plant Biol. 61:395-420.



About Author / Additional Info:
I am currently pursuing Ph.D. in BIOCHEMISTRY from IARI New Delhi.