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

2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists

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
2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists

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 .

2013 American Society of Plant Biologists

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..

2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists

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.
2013 American Society of Plant Biologists

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

2013 American Society of Plant Biologists

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.
2013 American Society of Plant Biologists

FLOWERING LOCUS C (FLC)

mutants flower early

flc mutant
Autumn

Winter

Spring

FLC is an inhibitor of flowering;

removing FLC removes the
vernalization requirement
2013 American Society of Plant Biologists

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
2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists

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

2013 American Society of Plant Biologists

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

2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists

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
2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists

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)
2013 American Society of Plant Biologists

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
2013 American Society of Plant Biologists

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
2013 American Society of Plant Biologists

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.

2013 American Society of Plant Biologists