epigenetics, epigenomics and their utilisation for crop improvement programmes

1. CREDIT SEMINAR
ON
EPIGENOMICS FOR CROP IMPROVEMENT
COURSE NO: MBB-691
PRESENTED BY
C. ANJALI
RAD/2018-37
DEPARMENT OF
MOLECULAR BIOLOGY
AND BIOTECHNOLOGY

3. Contents
• Epigenomics
• Molecular epigenetic mechanisms
• Methods for studying epigenetic modifications
• Epigenetics in crop reasearch
• Conclusion

4. What is Epigenetics ?
 Greek word “epigenesis” which means “extra growth”.
 Epigenetics means ‘above’ or ‘on top of genetics’.
 Coined by C. H. Waddington in 1942.
 The study of chromosome changes that alter the expression of
genes without any alteration in the gene sequences.
 Epigenetic modifications turn genes on or off which prevents
or allows the gene to make a protein.

5. What is Epigenomics ?
• Epigenomics is the study
of the all the epigenetic
changes in a genome of a
cell, such genome is also
called as epigenome.
• Epialleles, which refers to
the genes with identical
nucleotide sequence but
altered expression abilities
due to epigenetic events.

6. What Does “Epigenetics” Mean?
• Epigenetics describes phenomenon in which genetically
identical cells or organisms express their genomes
differently, causing phenotypic differences.
Genetically
identical cells or
individuals
Different epigenetic
modifications leading to
different expression patterns
Different
phenotypes

7. Genome and Epigenome

8. Molecular epigenetic mechanism
Epigenetic regulation during plant development and in response to
environmental conditions is attained by three epigenetic
mechanisms.

9. 1. DNA Methylation
•DNA can be covalently modified by
cytosine methylation.
• Enzyme Methyl transferases are
involved
•In plants the cytosine can be methylated
at CpG, CpHpG, and CpHpH sites, where
H represents any nucleotide

10. Mechanism of DNA methylation
Methylation demethylation
Regulates the gene expression
by transcription silencing

11. Classes of methyl transferase
Denovo methylation
Maintenance
methylation
 De novo class: Enzymes that
create new methylation mark on
DNA
Eg. DNMT3a and DNMT3b
 Maintainance class: Recognizes
the methylation marks on the
parental strand of DNA and
transfers new methylation to the
daughter strands after DNA
replication
Eg. DNMT1

12. DNA methylation induce histone de-acetylation

13. 2. Histone modification
• Refer to chemical alterations taking place on the N-tails of
nucleosomal histones
• These chemical modifications affect chromatin architecture
leading to open (active) or closed (repressive) chromatin states
which regulate transcriptional activity and are inherited by
daughter cells
Acetylation
Methylation

14. Histone modifiers
 Writers: enzymes that add a mark
 Erasers: enzymes that remove a mark
 Readers: proteins that bind to and “interpret” the mark

15. Non coding RNA
miRNA, siRNA, piRNA and lncRNA are involved in epigenetic
modifications

16. siRNA and piRNA mechanism
siRNA ( RNAi mechanism)
piRNA (silence genes by binding to certain regions
of DNA & tells to add methyl groups there

17. Methods for studying epigenetic modifications
DNA methylation–
• Bisulfite sequencing
• Methylation Sensitive Amplification Polymorphism (MSAP)
• By affinity purification
• Unmethylated C changes to U(T)
• Methylated C does not change

18. Methods for studying epigenetic modifications
Histone modification
• Chromatin
immunoprecipitation
(ChIP)
ChIP-chip ChIP-Seq

19. Methods for studying epigenetic modifications
• Non-coding RNA –Deep sequencing

20. Epigenomics in crop research
• Emerged in the past decade when whole genome data of
various crop plants (wheat, rice, maize etc) became available.
• Modifications occur in response to various environmental
pressures and it has been determined that such modifications
play a crucial role in mediating productivity and stability in
plant populations
• Many model plant species have been studied to evaluate the
changes in expression profile due to epigenetic events
• Epigenetic variants
Natural
Induced
Ex: 5-aza-deoxycytidine (DNA
methylation inhibitor)

21. Stress tolerance in plants
• Abiotic stress

22. Phenotypic diversity
• Plant population show phenotypic diversity which may be
caused by genetic and epigenetic variation.
• Recently shown that new epigenetic variants are evolved at a
higher rate than genetic variants
• If a epigenetic variant or epiallele has a phenotypic effect and
is more or less stably inherited to the progeny, it is referred to
as epimutant. Such epialleles contributed to the phenotypic
diversity of a population and hence may have a role in
adaptation and evolution
• Epigenetic variation has been suggested as an explanation for
the missing heritability in complex traits

23. Epigenetic QTL mapping
• With the help of epigenetic mapping we can identify additional
significant QTL associated with important agronomic traits.
• A total of 125 QTL associated with seven agronomic traits in
regions having a greater density of DNA methylation markers
were identified by Yan Long et al., 2012 in rice plant

24. Heterosis studies
• Epigenetic mechanisms can leads to variations of gene
expression in hybrids

25. Transient expression of transgene
• Transgene that are integrated in to genomic regions which are
subjected to epigenetic modifications during stress treatment
are susceptible to environmentally induced silencing
• To avoid this screen for lines with single copy insertion of
transgene into hypomethylated regions

26. Epialleles as a source of variation

27. Case study-1
October 2018
Accumulation of a V. dahliae
milRNA1, named VdmilR1,
was detected by RNA gel
blotting.
precursor gene VdMILR1
produce the mature VdmilR1,
in a process independent of V.
dahliae DCL (Dicer-like) and
AGO (Argonaute) proteins.
An RNaseIII domain-containing protein, VdR3, is essential for VdmilR1 biogenesis.
VdmilR1 targets a hypothetical protein-coding gene, VdHy1, at the 3’ UTR for
transcriptional repression through increased histone H3K9 methylation of VdHy1

28. Mechanism
Gene Virulence gene
VdMILR1
VdmilR1
RNaseIII domain-
containing protein,
VdR3
5’ UTR VdHy1 VdmilR1 Site
3’ UTR
5’ UTR VdHy1 VdmilR1 Site
VdmilR1binding recruits proteins
n enzymes for methylation

29. Results
• V592- wild strain

30. Case study-2
• AGO protein OsAGO2 regulates anther development in rice.
• OsAGO2 was highly expressed in anthers and knockdown of OsAGO2 led to the
overaccumulation of reactive oxygen species (ROS) and abnormal anther development,
causing premature initiation of tapetal programmed cell death (PCD) and pollen
abortion.
• The expression level of Hexokinase 1 (OsHXK1) increased significantly, and the
methylation levels of its promoter decreased.

31. Mechanism
5

32. List of epigenomics resource database

33. CONCLUSION
• Currently unexplored epigenetic variants will reveal novel
cryptic diversity, especially for species with low genetic
variation.
• The knowledge arising from epigenetic variation will allow the
exploitation of differential epigenetic marking towards useful
epibiomarker tools for superior genotype selection at early
stages.
• Collectively, breeding and the emerging area of epibreeding
will pave the way for developing optimal strategies for crop
improvement.
• Utilizing genetic and epigenetic variations for purposes of
generating improved crop varieties

34. THANK YOU