Download Plants` Epigenetic Secrets

PLANT METHYLATION BASICS
METHYLATION MAINTENANCE
REPRODUCTIVE REPROGRAMMING
There are three different types of DNA methylation in plants: CG, CHH (where H
is any base except G), and CHG. In Arabidopsis, CG methylation is found on some
genes, but primarily on repeat sequences that make up transposons, as well as other
repeat sequences in the genome. CHH methylation is found only where there is CG
methylation and often near transposable elements, though some evidence points to
CHH methylation on some silenced genes as well. CHG methylation is typically found
with the CHH variety.
Every time a cell divides, it must replicate its genome and its epigenome. Plants have
diverse pathways overseeing the faithful passage of the methylome to daughter cells.
During Arabidopsis reproduction, certain types of DNA methylation are reprogrammed
in the pollen. Arabidopsis pollen grains have three haploid cells: one vegetative cell that
helps produce the pollen tube and two sperm. One sperm fertilizes the egg to make the
embryo, while the other fuses with the female’s central cell to form the supportive tissue
known as endosperm.
CG METHYLATION
CHH METHYLATION
M
M
5’
CG METHYLATION
Copying CG methylation patterns to the two daughter strands is relatively straightforward. That’s
because this type of methylation is symmetrical: the complementary strand is also CG (reading
from 5’ to 3’), and that cytosine is also methylated. So when the parent DNA strand splits, the two
daughter strands that form will have methylation on the parent-strand side, and that methylation
can guide the addition of a methyl group to the newly replicated strands’ CG cytosine as DNA is
being copied.
FEMALE GAMETOPHYTE
CHG METHYLATION
Central
cell
(2n)
M
3’
C
G
C
H
H
C
H
G
G
C
G
D
D
G
D
C
3’
Replication
complex
{
Gene
H is any base except G
D is any base except C
{
Egg (n)
A methyltransferase adds
methyl marks to newly
synthesized DNA strands.
Embryo
(2n)
Sperm
Vegetative
cell
5’
M
M
Pollen tube
Sperm combine with the diploid central cell and egg to
form the triploid endosperm and the diploid embryo,
respectively.
CHH METHYLATION
CHH methylation is inherently asymmetrical, because the H is any base except guanine. CHH
methylation is passed on to both daughter genomes using a process called RNA-directed DNA
methylation, which involves small RNAs that guide RNA interference machinery to methylate
complementary regions of DNA.
Transposon
Endosperm
(3n)
Intergenic region
The small RNAs bind to
Argonaute proteins that
guide a methyltransferase to
complementary sequences of
newly synthesized DNA.
An RNA
polymerase
transcribes small
RNA molecules.
VEGETATIVE NUCLEUS
CG LOSS IN VEGETATIVE CELL
The nonreproductive nucleus loses some
CG methylation and many transposons are
activated as a result. The small RNAs that
are consequently produced can travel to the
sperm nucleus that forms the embryo, possibly
serving as guides to reinforce methylation of
those transposon sequences.
CHH
methylation
CHG
methylation
Transposon
Small RNAs
SPERM NUCLEUS
RNA
polymerase
CHH LOSS IN SPERM
CG
methylation
CHG METHYLATION
Although CHG methylation is symmetrical and thus could in principle use the same methylation
maintenance pathway as CG methylation, it also relies on RNA-directed DNA methylation
(not pictured below). In addition, this type of methylation is paired with methylation of lysine
9 on histone H3 (H3K9). The histomethyltransferase that methylates H3K9 regions binds to
methylated CHG. Conversely, the CHG-methylating enzyme binds to H3K9, then methylates
nearby CHG sites, forming a positive feedback loop between the two types of methylation.
H3
H3
After
fertilization
EMBRYO NUCLEUS
FEMALE REPROGRAMMING?
CG methylation is reprogrammed in
the central cell. No one has looked at
epigenome reprogramming in the egg.
Histone
Enzyme binds CHG methyl group and directs the
addition of a new methyl mark to nearby histone.
Conversely, sperm nuclei lose CHH
methylation, which is replaced after
fertilization under the direction of small
RNAs produced in the egg and pollen nuclei.
Enzyme binds histone methyl group and
directs the methylation of nearby DNA.
© LUCY READING-IKKANDA