TTPB4 Abridged 24

Epigenetics
Any potentially stable and

heritable change in gene
expression that occurs without a
change in DNA sequence
www.plantcell.org/cgi/doi/10.1105/tpc.110.tt0110
2013 American Society of Plant Biologists
What does epigenetics mean?

Literally, epigenetics means
above, or on top of, genetics.
Transcription
Usually this means information

coded beyond the DNA sequence,
such as in covalent modifications
to the DNA or modifications to the
chromatin structure.
Practically, epigenetics describes
phenomena in which genetically
identical cells or organisms
express their genomes differently,
causing phenotypic differences.
Epigenetic
Silencing
Different epigenetic
modifications
leading to different
expression patterns
Genetically identical
cells or individuals
Different
phenotypes
In plants, the
activity of many
developmental
genes and
environmentallyregulated genes
are
epigenetically
regulated, to be
stably
maintained in an
ON or OFF
position
Holec, S. and Berger, F. (2012). Polycomb group complexes mediate developmental transitions in plants. Plant Physiol. 158: 35-43.
Epigenetic marks: DNA methylation

and histone modification
n
ltra
y
th
Me
cytosine
r
sf e
e
as
5-methylcytosine
The histone proteins that

DNA is wrapped around can
be covalently modified,
affecting chromatin structure
Histone
octamer
DNA
DNA can be covalently

modified by cytosine
methylation.
Methylcytosine
TTCGCCGACTAA
NUCLEOSOME
Epigenetic
Silencing
Histone
modifications
Epigenetic marks contribute to

large-scale chromatin domains
The centromere and
regions around it are
usually densely
packaged with few
protein-coding genes
Densely packaged
heterochromatin
CENTROMERE
Euchromatin DAPI DNA stain
Less densely
packaged, generich euchromatin
Merged
Centromeric
heterochromatin
Deal, R.B., Topp, C.N., McKinney, E.C., and Meagher, R.B. (2007) Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A.Z. Plant Cell 19: 74-83.
Heterochromatin DNA is highly

methylated
BLUE = Gene
density
RED = Repetitive
element density
Plants have different

DNA methylases that act
on different sequences:
5'-CG-3'
5'-CHG-3
5'-CHH-3'
Reprinted from Zhang, X., Yazaki, J., Sundaresan, A., Cokus, S., Chan, S.W.-L., Chen, H., Henderson, I.R., Shinn, P., Pellegrini, M., Jacobsen, S.E., and Ecker., J.R.
(2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 11891201 with permission from Elsevier.;
Cokus et al., (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning Nature 452: 215-219 .
Epigenetic programming in plants

helps silence transposons and
maintain centromere function
Photo by Damon Lisch, in Gross, L. (2006) Transposon silencing keeps jumping genes in their place. PLoS Biology 4(10): e353.
Photos courtesy of the Barbara McClintock Papers, American Philosophical Society. Zhang, W., et al. (2008) Plant Cell 20: 25-34..
Transposons can cause inactive or

unstable alleles
Transposons are fragments of DNA that can insert into
new chromosomal locations. Some transposons copy
themselves and increase in number within the genome
Gene required
for pigment
biosynthesis
Wild-type allele
Pigmented kernel
Gene interrupted
by transposon
Mutant allele
Unpigmented kernel
Excision of the
transposon causes
unstable alleles
Unstable allele
Partially pigmented kernel
Transposons are
responsible for
large scale
chromosome
rearrangements
and single-gene
mutagenic events
Photo by Damon Lisch, in Gross, L. (2006) Transposon silencing keeps jumping genes in their place. PLoS Biology 4(10): e353.
Epigenetic marks silence

transposons and repetitive elements
Transposons must be tightly controlled to prevent widespread

mutagenic activity. Epigenetic controls to maintain silencing include
DNA methylation, histone modification and siRNA production.
Small interfering RNAs (siRNAs) are

preferentially derived from
pericentromeric regions
Small RNAs
The density of small RNA-homologous loci is highest in the

centromeric and pericentromeric regions which contain a high
density of repeat sequence classes, such as transposons.
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.
siRNAs recruit DNA methylases and

histone-modifying enzymes to
targets
RNA-dependent RNA
Polymerase (RdRP)
generates doublestranded RNA
RNA
Plant-specific RNA
Polymerases (IV
and V) are
involved in
silencing
RdRP
DC
AGO
P
RNA
AGO
ol V
siRNA / Argonaute (AGO)

complexes interact with RNA
transcripts and recruit silencing
machinery
Epigenetic control of flowering time

Prolonged cold
treatment
Vegetative
Development
Autumn
Reproductive
Development
Winter
Spring
Some plants require a prolonged cold

period (vernalization) - as experienced
during winter, before they will flower.
FLOWERING LOCUS C (FLC)

mutants flower early
flc mutant
Autumn
Winter
Spring
FLC is an inhibitor of flowering;

removing FLC removes the
vernalization requirement
FLC inhibits FT, an activator of

flowering
Wild-type
plant
FLC
FT gene
Transcription of FT gene
repressed by FLC binding
flc mutant
plant
FT gene
FT
FLC is silenced by vernalization
After 40 days at 4C,

FLC is not expressed.
Ten days after return
to 22C FLC
expression is still off.
Autumn
FLC gene transcribed
Winter
Spring
FLC gene silenced
Reprinted by permission from Macmillan Publishers, Ltd: NATURE Sung, S., and Amasino, R.M. (2004) Vernalization
in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427: 159-164. Copyright 2004.
FLC expression is regulated by

epigenetic modifications
H2A.Z incorporation
H3K4me, H3K36me
H3K9Ac, H3K14Ac
H3K9me2, H3K27me2
cold
Autumn
FLC gene transcribed
Winter
Spring
FLC gene silenced
Many epigenetic marks are reset

during reproduction
FLC ON
Autumn
FLC is reset to
the ON state
during
reproduction
Embryo
within seed
FLC OFF
Winter
Spring
Female gametophyte,
including egg cell
Genomic imprinting is regulated by

epigenetic processes
The zygote receives two copies of
each gene, one from the mothers
genome and one from the fathers.
At most loci, both copies are active.
Some loci, imprinted loci, show a
parent of origin effect.
Expression of these loci is
controlled by epigenetic factors.
Imprinting nuclear transplant

experiment
Placing a sperm and an egg

nucleus into an enucleated
fertilized cell leads to a
normal embryo.
Zygotes that receive only

maternal or only paternal
nuclei do not survive.
The two parental genomes

are not equivalent
The MEDEA (MEA) gene is

imprinted
MEA/mea x
MEA/MEA
All seeds viable
MEA/MEA x
MEA/mea
50% of seeds abort
In the second cross, 50% of the seeds receive the mutant mea allele from their mother.
These seed abort, even though they also have a wild-type MEA allele inherited from
their father; the paternal allele is epigenetically silenced and inactive.
From: Grossniklaus, U., Vielle-Calzada, J.-P., Hoeppner, M.A., Gagliano, W.B. (1998) Maternal control of embryogenesis by
MEDEA, a Polycomb Group gene in Arabidopsis. Science 280: 446-450. Reprinted with permission from AAAS.
Angiosperm reproduction: Development

of male and female gametophytes
Vegetative nucleus
meiosis
n
2n
Microspore
mother cell
mitosis
Microspore
meiosis
2n
Megaspore
mother cell
Generative cell
2-celled male
gametophyte
(aka pollen grain)
mitosis
Central cell
n
Megaspore
Egg cell
8-celled female
gametophyte
(aka embryo sac)
Angiosperm reproduction: Double

Fertilization
Mitotic division
of generative
cell to two
sperm cells
3n endosperm
One sperm nucleus
fertilizes the egg cell to
produce diploid
embryo.
The second sperm
nucleus fertilizes the
polar nuclei to produce
triploid endosperm.
Pollen tube
growth
2n zygote
Angiosperm reproduction:
Imprinting and epigenome resetting
Epigenetic marks can
be renewed and reset
during angiosperm
reproduction
Triploid
endosperm
Diploid embryo
Haploid
sperm
nuclei
Imprinting may ensure

a balance between
maternal and paternal
genomes, and is
necessary for
endosperm and seed
development
Summary
Expression of DNA is regulated by epigenetic
marks including DNA methylation and histone
modifications, with the contributions of
siRNAs
Epigenetic programming silences
transposons and controls the timing of many
genes that control plant development.

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Epigenetics

Any potentially stable and

What does epigenetics mean?

Usually this means information

2013 American Society of Plant Biologists

2013 American Society of Plant Biologists

Epigenetic marks: DNA methylation

The histone proteins that

DNA can be covalently

Epigenetic marks contribute to

Euchromatin DAPI DNA stain

2013 American Society of Plant Biologists

Heterochromatin DNA is highly

Plants have different

2013 American Society of Plant Biologists

Epigenetic programming in plants

2013 American Society of Plant Biologists

Transposons can cause inactive or

2013 American Society of Plant Biologists

Epigenetic marks silence

Transposons must be tightly controlled to prevent widespread

2013 American Society of Plant Biologists

Small interfering RNAs (siRNAs) are

The density of small RNA-homologous loci is highest in the

siRNAs recruit DNA methylases and

siRNA / Argonaute (AGO)

2013 American Society of Plant Biologists

Epigenetic control of flowering time

Some plants require a prolonged cold

FLOWERING LOCUS C (FLC)

FLC is an inhibitor of flowering;

FLC inhibits FT, an activator of

FLC is silenced by vernalization

After 40 days at 4C,

FLC gene transcribed

FLC gene silenced

2013 American Society of Plant Biologists

FLC expression is regulated by

FLC gene transcribed

FLC gene silenced

2013 American Society of Plant Biologists

Many epigenetic marks are reset

2013 American Society of Plant Biologists

Genomic imprinting is regulated by

2013 American Society of Plant Biologists

Imprinting nuclear transplant

Placing a sperm and an egg

Zygotes that receive only

The two parental genomes

The MEDEA (MEA) gene is

2013 American Society of Plant Biologists

Angiosperm reproduction: Development

Angiosperm reproduction: Double

Imprinting may ensure

2013 American Society of Plant Biologists

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