This document discusses epigenetic regulation in higher plants. It begins by defining epigenetics as heritable changes in gene function that do not involve changes to DNA sequence. It then describes several epigenetic mechanisms including DNA methylation, histone modification, and regulatory non-coding RNAs. It provides examples of epigenetic phenomena like paramutation, where one allele can alter the expression of another without changing the DNA sequence. It also discusses parent-of-origin effects like genomic imprinting. The document outlines topics including DNA methyltransferases, components of RNA-directed transcriptional gene silencing, and genes involved in the RNA-dependent DNA methylation pathway.

1. Epigenetic Regulation in Higher Plants
Xiaofeng Cao
Institute of Genetics and Developmental Biology,
Chinese Academy of Sciences, Beijing, China
2010-12-10

2. Reference
• Liu, Lu, Cui and Cao (2010) Histone
methylation in higher plant
Annu Review of Plant Biology

3. Genetics
Genotype Phenotype
Genetic information flow (central dogma):
transcription translation
DNA RNA protein

4. Epigenetics
Current Wu & Morris (2001):
“the study of changes in
gene function that are
heritable and that do not
entail a change in DNA
sequence”.
Heritable:
mitotically heritable
meioticallyheritable

5. Epigenetics
• When a cell undergoes mitosis or meiosis, the
epigenetic information is stably transmitted to the
daughter cells or subsequent generation
• Epigenetic controls add an ‘extra layer’of transcriptional
control—transcriptional memory
Epiallele—same DNA sequence but different epigenetic state
Epigenome—the epigenetic state of all sequences in a genome

6. Epigenetic mechanisms involve:
-DNA methylation
-Histone modification/histone variants
-Regulatory non-coding RNAs

7. •Epigenetic phenomena
-Paramutation
-Parent-of-origin effects
•DNA methylation and DNA methyltransferases
•Genetic screening for components in
maintenance of RNA-directed transcriptional
gene silencing
•Identification of genes involved in RdDM
Outline

8. Paramutation
Described in maize by A. Brink and E. Coe (1950’s).
An interaction between alleles that leads to a mitotically and
meiotically heritable change in the expression of one allele.
Described for a few endogenous genes and transgenes in
multiple species including plants, animals and fungi.
Only observed with specific alleles. Most alleles do not
participate in paramutation (neutral alleles).

9. Phenotypes of paramutation in maize
paramutable B-I alleles:
encodes an enzyme in
the pathway of
anthocyanin pigments
null b alleles: lack these
pigments, and these b
alleles are completely
recessive to B-I
paramutagenic allele B’:
make only a small
amount of anthocyanin
pigment.
F1
F2
B-I is recessive to B’?
3:1?

10. Paramutation at B locus
F1
The high expressing B-I
state is unstable, changes
to low expressing B’ state
at a high frequency (0.1-
10%).
When B’ and B-I are
crossed paramutation
occurs 100% of the time.
B’ is extremely stable.
UNUSUAL!
X
B’ B-I
B’/B’*
X
B-I
B’B’ B’ B’

11. Characteristic of paramutation
• Paramutation is the directed, heritable
alteration of the expression of one allele when
heterozygous with another allele.
– The newly silenced allele can further silence new targets.
– Allelism is not a strict requirement for paramutation.
– Paramutation is associated with DNA methylation changes
( both at the trigger and target sequence).
– Paramutation can be accounted by RdDM.
mediator of paramutation1 (mop1-1) mutation blocks
paramutation at the maize B, R, and Pl1 loci.

12. •Epigenetic phenomena
-Paramutation
-Parent-of-origin effects
•DNA methylation and DNA methyltransferases
•Genetic screening for components in
maintenance of RNA-directed transcriptional
gene silencing
•Identification of genes involved in RdDM
Outline

13. Genomic imprinting （基因组印记）
♂ AA x aa ♀
F1 Aa
F1 Phenotype can be A or a

14. Parent-of-origin effects
(mare) X 驴(jack)♂ ♀驴 (jenny) X 马(stallion)♂
骡(mule) ？( hinny)

15. An imprinted gene
The copy of gene A inherited from the mother is expressed. The
copy inherited from the father is silenced. By convention, gene A
is described as paternally imprinted. For some imprinted genes,
the maternal allele is silent and the paternal allele is expressed
and the gene is said to be maternally imprinted.

16. Examples of imprinting genes in mouse

17. The Igf2/H19 cluster
The Igf2/H19 gene pair is part of a cluster of
imprinted genes on mouse chromosome7.
ICR: imprinting control region; E: enhancer element

18. Deletion of the imprinting control region and changing the position of the
3’ enhancer both cause loss of imprinting of the Igf2 and H19 genes

19. The Igf2 /H19 imprinting control regions (ICR) on the maternal and
paternal chromosomes differ in CpG methylation and nuclease sensitivity