PPT ON GENEOME IMPRINTING PRESENTED BY Neeraja Puthiamadom PHD SCHOLAR, GENETICS AND PLANT BREEDING

1. Mendelian inheritance
Parents
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PP
pp
Pp
Pp
3:1

2. Genome imprinting
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Neeraja Puthiamadom
2017-21-004

3. Contents
 What is genome imprinting?
 History of genome imprinting
 Mechanism of genome imprinting
 The evolution of genome imprinting: theories
 Genome imprinting in plants
 Role of genome imprinting
 Complications in genome imprinting
 Summary
 Future thrust
 Conclusion
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4. What is genome imprinting?
“An epigenetic phenomenon found in mammals and
flowering plants that causes genes to adopt a parent-
of-origin-specific mode of expression”
(Feil and Berger, 2007)
4
Paternal imprinting
Maternal imprinting

5. Paternal imprinting
(Razaq, 2014)
5
aaBB bb
Bb Bb
Gene for
pigmentation

6. Maternal imprinting
(Razaq, 2014)
6
aa AABBbb
Bb Bb
Gene for
pigmentation

7. Imprinted gene expression
(Rodrigues and Zilberman, 2019) 7

8. Time line of genome imprinting
(Renfree et al., 2013) 8

9. History of genome imprinting
9
1960 - Helen Crouse
Spermatogenesis in sciarid fly
1970 - Kermicle
endosperm- expressed r1 gene of maize
1991-Robinson
insulin-like growth factor-2 (IGF2)
first in mammals

10. Mules vs Hinny
10
(Hunter, 2007)
Mule Hinny

11. Mechanism of genome imprinting
Epigenetics
DNA
methylation
Histone
modification
11

12. Epigenetic phenomenon
xAA aa
TTAC………..C
TTAC………..C
A a
Aa
F1 X
AaAA aa
1 2 1
Aa
Aa
12
Study of heritable phenotypic
changes that do not involve
alterations in the DNA sequence
(Iwasaki, 2014)

13. DNA methylation
Process by which methyl groups are added to
the DNA molecule
(Feng et al., 2014)
13

14. …DNA methylation
• CpG islands - DNA sequence with high frequency of
CpG
• Important source code in regulating gene expression
• Hypermethylation - gene suppression
• Demethylation - gene expression
• Enzyme - DNA methyltransferases
14

15. …DNA methylation
15(Vrana, 2007)

16. …DNA methylation
• Silencing of genes
• Promotes gene activity
• Differential methylation of maternal and paternal
alleles - imprinted expression
16

17. …DNA methylation
Methylation
fwa1
17
Expression of plant with methylated fwa 1
Wild type
(Rodrigues and Zilberman, 2019)

18. Histone modification
A post translational modification (PTM)
of histone proteins that affects gene expression by
altering chromatin structure
Trimethylation of lysine 27 in
histone H3 (H3K27me3)
18

19. Theories for the evolution of
genome imprinting
Kinship theory
Parental - offspring co-adaptation theory
Ovarian time bomb theory
19

20. Kinship theory
“Inequality between parental genomes due to imprinting
is a result of the differing interests of each parent in terms
of the evolutionary fitness of their genes”
(Haig, 2006)
20

21. “The fitness of a genotype depends not only on its direct
phenotypic effect on its bearer but also on the interactions
between the phenotypes of different individuals”
Maternal-offspring co-adaptation theory
(McGlothlin et al., 2010)
21

22. Ovarian time bomb theory
22
“Imprinting evolved in mammals to prevent
spontaneous development of unfertilized eggs”
(Varmuza and Mann, 1994)

23. Genome imprinting in plants
23
(Kinoshita, 2007)
DEMETER (DME)
Medea: Maternal effect dominant embryonic arrest
Fis2: fertlization independent seed 2
fwa: flowering wageningen
phe1: Pheres

24. Genome imprinting in plants
24(Kinoshita, 2007)

25. Imprinting cycle
(Dickinson and Scholten, 2013) 25

26. Comparison of Mendelian genetic inheritance
and imprinted inheritance
(Bai and Settles, 2015) 26

27. (Zhang et al., 2016) 27
Identification of imprinted genes in sorghum

28. …identification of imprinted genes in sorghum
Plant tissue collection
RNA-seq data generation and processing
Identification of SNPs between parental
orthologs
Identification of imprinted genes
Clustering analysis
28
BTx 623(B) and Y49 (Y)
Tophat 2.0
Sliding windows

29. Gene ontology (GO) analysis
RNA preparation, reverse transcription and
locus-specific pyrosequencing
Gene expression analysis by quantitative
RT-PCR
Genomic DNA extraction and bisulfite
sequencing
…identification of imprinted genes in sorghum
29

30. …identification of imprinted genes in sorghum
30

31. …identification of imprinted genes in sorghum
Heat map for tissue-
specific expression of
sorghum
imprinted genes
31
Venn diagram

32. …identification of imprinted genes in sorghum
Chromosomal location of sorghum imprinted genes
32
Chromosomelength(M)

33. Salient findings
• 85 maternal expressed genes (MEGs)
• 16 paternal expressed genes (PEGs)
• 71 genes are sorghum-specific imprinted genes
33

34. (Liu et al., 2018) 34
Screening and analysis of imprinted genes in
rapeseed endosperm

35. …screening and analysis of imprinted
genes in rapeseed endosperm
Plant tissue collection
RNA-seq data generation and processing
Identification of SNPs between parental orthologs
Identification of imprinted genes
DNA preparation and locus-specific sequencing
Gene expression analysis by RT-PCR
Gene MapMan analysis
Genomic DNA extraction and bisulphite sequencing
35

36. Heat map analysis of
MEGs and PEGs
…screening and analysis of imprinted genes in
rapeseed endosperm
36

37. Heat map analysis of
MEGs and PEGs
…screening and analysis of imprinted genes in
rapeseed endosperm
37

38. …screening and analysis of imprinted genes in
rapeseed endosperm
Chromosomal location of rapeseed imprinted genes 38

39. …screening and analysis of imprinted genes in
rapeseed endosperm
Functional classification analysis of the 183 rapeseed
imprinted genes 39

40. …screening and analysis of imprinted genes in
rapeseed endosperm
Functional classification analysis of the 183 rapeseed
imprinted genes 40

41. Role of imprinted genes
 Normal growth and development
 Endosperm in angiosperms
 Placenta in mammals
 Normal metabolism
 Prevention of tumorous growth
41

42. …role of imprinted genes
42
 Failure of imprinting in somatic cells - cancer
 Accidental inheritance of two copies of same gene – fatal
 Prevents parthenogenesis
 Suppresses duplicated gene
 Leads to evolution and speciation

43. Genome imprinting in reproductive isolation
43
(Coughlan et al., 2018)

44. 44
Phenotypic and genetic survey
Crossing survey between M. guttatus and M. decorus
Evolutionary mechanisms for variation in hybrid seed
inviability
Crossing survey within species
…genome imprinting in reproductive isolation

45. 45
RI= Average hybrid seed viability in interspecific cross
Average seed viability in intraspecific cross
SRI=Viable seeds (D X G) - Viable seeds (G X D)
Viable seeds (D X G)+ Viable seeds (G X D)
RI - Reproductive Index
SRI – Symmetry of Reproductive Index
D - M. guttatus
G - M. decorus
…genome imprinting in reproductive isolation

46. 46
Reciprocal F1 seed size
…genome imprinting in reproductive isolation
ND
SD
G

47. Database for imprinted genes
www.geneimprint.org
47

48. Application of genome imprinting in crop
improvement
 Trait specific manipulation of genome
imprinting
 Demethylation
 Epigenetic resetting of imprinted genes
(Jahnke and Scholten, 2009)
48

49. Epigenetic resetting of imprinted genes
(Jahnke and Scholten, 2009)
49

50. …epigenetic resetting of imprinted genes
50
SSRP – Structure Specific Recognition Protein
DME - DEMETER

51. Complications of genome imprinting
• Tissue specific imprinting
• Stage specific imprinting
• Monoallelic gene expression
• Prevents wide hybridization
• Improper imprinting - imprinting disorders
(Razak et al., 2014)
51

52. Imprinting disorders
52

53.  Normal development - one active copy of an
imprinted gene
 Improper imprinting - two active copies or two
inactive copies
…imprinting disorders
Prader-Willi syndrome
Angelman syndrome
Male infertility
Uniparental disomy
Wilms´ tumor
53

54. Prader-Willi syndrome
 Paternal imprinting - chromosome 15
 Severe hypotonia
 Difficulties with feeding
 Obesity due to an insatiable appetite
 Small hands and feet
 Hypogonadism
54

55. Angelman syndrome (AS)
 Maternal imprinting - chromosome 15
 Severe mental retardation
 Severe speech impairment
 Tremulousness of the limbs
 Inappropriate laughter and excitement
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56. Male infertility
Epigenetic disregulation of imprinted gene H19 in sperm
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57. Wilms’ tumour
 Two active copies of IGF2
 Constipation
 Abdominal pain, swelling or
discomfort
 Nausea and vomiting
 Weakness and fatigue
 Loss of appetite
 Fever
 Blood in urine
57

58. Uniparental disomy
“Inheritance of both copies of a chromosome
from one parent and none from the other”
58

59. Other imprinting disorders
Diabetes in infants
Autism
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60. Summary
 Parent- of- origin specific mode of expression
 Epigenetic mechanism
 Improper imprinting - disorders
 Imprinted genes in plants
 Genome wide association studies
 Evolution and speciation
 Improper imprinting - disorders
60

61. Future thrust
 Elucidation of biological functions of imprinting
 Exploitation of genome imprinting
 Eugenics
 Gene therapy
 Crop improvement
(Kinoshitha, 2018)
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62. Conclusion
 Epigenetic modification
 Both desirable and undesirable
Trait specific manipulation
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63. Thank you
63