This slides include projects analyzed using next-generation sequencing method in genomic imprinting, X chromosome dosage compensation and DNA methylome in bovine early embryos.

1. Genomic Imprinting and X
Chromosome Dosage Compensation
in Domestic Ruminants
Jingyue (Ellie) Duan
Department of Animal Science, UCONN
11/19/2018
Major Advisor: Dr. X. Cindy Tian
Committees: Dr. Ion Mandoiu
Dr. Lynn Kuo
Dr. Michael O’Neill

2. • Project 1: Genomic imprinting in sheep
• Project 2: X Chromosome dosage compensation in bovine
• Project 3: DNA methylome dynamic in bovine early embryos
• Project 4: X Chromosome dosage compensation in sheep
• Project 5: Abundance of mRNA for histone variants and DNA
modifier in bovine early embryo
2
Projects

3. Outline
• Introduction
• Project 1: Genomic imprinting in sheep
• Project 2: X Chromosome dosage compensation in bovine
• Project 3: DNA methylome dynamic in bovine early embryos
• Conclusion
3

4. Epigenetics
• Epigenetics: changes above or in addition to genetics to explain
differentiation
4
C.H. Waddington
1942
Epigenetics landscape
• Cell fate is established
• Totipotent state

5. Epigenetics
Epigenetics
• Switch-like changes in gene expression, phenotype
• Does not involve in DNA mutation
• Chemical modification of DNA or histone proteins
• DNA methylation
• Histone modification
• Non-coding RNA

6. Epigenetic features
• Gene expression switch: ON/OFF
• Epigenetic markers transmitted
during DNA replication/cell division
• Can be influenced by many factors
eg. age, stress, environment, diets,
toxic chemicals, life style etc.
• Erasable
• Embryonic development
• Germline specification
6
ON OFF

7. Epigenetic phenomenon
• Different hair colors
• Diseases are not the same in identical twins
• Yellow indicates shared epigenetic markers
• Environmental influence
• Epigenome of twins has diverged
Fraga et al., 2005, PNAS

8. Epigenetic processes
8
• Genomic imprinting
• X chromosome inactivation
• Cell differentiation
• Gene silencing
• Cancer formation
• Aging

9. Project 1: Genomic imprinting in sheep
9
Collaboration with the labs of Drs. Govoni, Reed, Zinn and Mandoiu

10. Non-imprinted
gene
Genomic imprinting
Koerner et al. 2009, Development
10

11. Examples of genomic imprinting in
animal science
11
Mule
Horse X Donkey
Hinny
Donkey X Horse
• Parental specific effect: size, coat, strength, etc
Donkey
Horse

12. Identified imprintedgenes
Species Number of identified
imprinted genes
Mouse1,3 163
Human2,3 114
Cow4,8 52
Pig3,5 25
Sheep3,6,7 21
Horse3,9 17
1 http://mousebook.org/imprinting-gene-list; 2 http://igc.otago.ac.nz/Search.html;
3 http://www.geneimprint.com/site/genes-by-name; 4 Chen et al.,2009; 5 Bischoff et al., 2009,
6 Tian, 2014; 7 Magee et al.,2014, 8 Chen et al.,2016; 9 Want et al. 2013
12

13. Environmental effects of genomic imprinting
Ramamoorthy et al., Front. Neurosci., 2015
13

14. Objectives
• To use single nucleotide polymorphisms (SNPs)
from DNA-seq and allelic expression from
RNA-seq to identify novel imprinted genes in
sheep
• To determine the effect of maternal nutrition
on
• imprinted gene allelic expression patterns
• imprinted gene expression levels
14

15. Experimental Design and Materials
Ram blood (n=4)
HiSeq 2000
DNA sequencing
Ram
Nextseq 500
Tissues from 15 Day 135 fetuses: Brain, Kidney,
and Lung
RNA sequencing
15
Duan et al., Epigenetics, 2018
Restricted (n=4)
(60% NRC)
Control (n=4)
(100% NRC)
Overfed (n=4)
(140% NRC)
Pregnant Ewes at day 30 (n=12)
National Research Council Total Digestible Nutrients

16. SNP1
A=25
C = 5
P > M
SNP quality filtering; Identify Informative SNPs;
Assign reads to two alleles;
Calling SNPsCalling SNPs
Fetus RNA seq reads (pooled from B, K, L)
Map to Oar_v4.0
Ram DNA seq reads
Map to Oar_v4.0
16
Bioinformatics pipeline

17. Fisher’s exact test for significance of allelic
expression bias (q<0.05; ASE>70%)
Monoallelically expressed in 3 tissues
Validate by Sanger sequencing;
Differential gene expression analysis
Reads aggregation
P M
P=20 M=1
Allele-specific gene expression
PEG3
Candidate novel imprinted genes
Known in sheep
Known imprinted gene list (255)
17

18. Data summary
Data category Numbers
Informative SNPs ~10/gene
Allelic expression bias genes 4,537
Monoallelically expressed in 3
tissues
80
Candidate imprinted genes 18
Known in sheep 5
Novel imprinted genes in sheep 13
18

19. Genome visualization of sheep imprinted genes
19
Duan et al., Epigenetics, 2018

20. 20
PPP1R9A
Duan et al., Epigenetics, 2018

21. Paternally expressed genes: 8; Maternally expressed genes: 10
Maternal nutrition influence on fetal allelic expression patterns
21
Duan et al., Epigenetics, 2018

22. Down regulated Up regulated
PHLDA2 in lung PHLDA2 in brain
SLC22A18 in kidney
Down regulated Up regulated
PHLDA2 in lung PHLDA2 in brain
IGF2 in brain
DIRAS3 in lung
Differential gene expression analysis
Control vs. Restricted Control vs. Overfed
• IGF2, PHLDA2 and SLC22A18 are in imprinted cluster on chromosome 21
• IGF2: involved in development and growth, promotes growth of fetus
• Beckwith-Wiedemann syndrome
• Prostate caner
22
PHLDA2
SLC22A18
KCNQ1
Duan et al., Epigenetics, 2018
• Russell-Silver syndrome
• Wilms tumor

23. Summary of project 1
• Identified 13 novel imprinted in sheep
• Sanger sequencing confirmed 7 new sheep imprinted genes
COPG2, DIRAS3, SLC22A18, INPP5F, PLAGL1, CASD1 and
PPP1R9A
• Identified four imprinted clusters
• MEST domain on chromosome 4
• PEG10/SGCE domain on chromosome 4
• DLK1/GTL2 domain on chromosome 18
• KCNQ1 on chromosome 21
• PHLDA2, SLC22A18, DIRAS3, and IGF2 differentially expressed
• No allelic expression patterns were reversed among three maternal
nutritional groups
23

24. Project 2: X Chromosome dosage
compensation in bovine
24
Collaboration with the labs of Drs. O’Neill and Kuo

25. X chromosome inactivation
2n
For every 2n, one active X (Xa)
25

26. XCI in mammals
The Barr body = the inactivated X (Xi)
condensed heterochromatin
• XCI escapee: 5-15% of X-linked genes escape XCI in female, pseudoautosomal
region (PAR)
• Dosage sensitive genes: X-specific region, with housekeeping functions, more
likely affected by dosage imbalance.
26

27. XY
AA
Male
1 : 2
XY AA
2 : 2
Female
AA
XX
4 : 2
Xx AA
2 : 2
Ohno’s Hypothesis: X chromosome
dosage compensation in mammals
Susumu Ohno
XCI
Confirmed!
X upregulation:
X:AA=1?
No consensus
27

28. Objectives
• To determine X chromosome upregulation in bovine
germline, embryos (2-cell to blastocyst) , pre-attachment
conceptuses (days 7, 10, 13, 16, 19), and adult somatic
tissues
28

29. Materials
Mature
oocyte
♀♂
Somatic cell
Immature
oocyte 2C 4C 8C CM BL D7 D10 D13 D16 D19
Embryogenesis
29
Duan et al., GEB, under revision

30. Methods
Duan et al., GEB, under revision
RNA-seq dataset download
Data trimmed
Align to bovine genome UMD3.1.1
Quantify the expression levels (TPM)
Hisat2
Trimmomatic
IsoEM
X:A median ratio
Confident interval: 95% certain that
contains the true median
X:AA ≥ 1, Complete
X:AA < 1, Incomplete
X:AA ≤ 0.5, No dosage compensation
30
Expressed gene: TPM>1
Dosage sensitive genes: TPM >1 in all

31. Expression range of autosomes and X chromosome
31
Duan et al., GEB, under revision

32. Hypothalamus
Fat
Kidney
Liver
M
uscle
Pituitary
Lung
Duodenum
Hypothalamus
Fat
Kidney
Liver
M
uscle
Pituitary
Lung
Duodenum
♂ tissues, expressed genes Dosage sensitive genes
X chromosome up-regulation in male (♂) adult tissues
32
Duan et al., GEB, under revision

33. X chromosome up-regulation in female (♀) adult tissues
33
Duan et al., GEB, under revision
Brain Fat
Kidney
Liver
M
uscle
Pituitary
Corpus Luteum
Endometrium
♀ tissues, expressed genes Dosage sensitive genes
Brain Fat
Kidney
Liver
M
uscle
Pituitary
Corpus Luteum
Endometrium

34. 34
Duan et al., GEB, under revision
X chromosome up-regulation in in vivo produced oocytes and embryos
In vivo produced, expressed genes
M
II 2C 4C 8C
16C
32C
Compact morula
Blastocyst
D7
D10
D13
D16
D19
Dosage sensitive genes
M
II 2C 4C 8C
16C
32C
Compact morula
Blastocyst
D7
D10
D13
D16
D19

35. X chromosome up-regulation in in vitro produced oocytes and embryos
35
Duan et al., GEB, under revision
In vitro produced, expressed genes Dosage sensitive genes
GV M
II 4C 8C
16C
Blastocyst
GV M
II 4C 8C
16C
Blastocyst

36. X chromosome up-regulation in different subsets of genes
Rem
ovalXCIescapees
36
Duan et al., GEB, under revision

37. Summary of project 2
37
• Up-regulation of X chromosome in bovine supports
a balanced expression between a single active X and
autosome pairs
• No difference was observed between bovine female
and male somatic tissues
• Complete X upregulation process for “dosage-
sensitive” genes
• X dosage compensation is a very dynamic process
during embryonic development

38. Project 3: DNA methylome dynamic
in bovine early embryos
38
Collaboration with the lab of Dr. Mandoiu

39. DNA Methylation
• Best characterized epigenetic marker
• A methyl group added to C next to a G
5mC

40. Immunostaining of 5mC in bovine pre-implantation embryos
Dean et al., 2001
• De novo methylation occurs in
bovine embryos at 16-cell stage
40
Zygote 2-Cell 4-Cell 8-Cell 16-Cell
Mouse
Bovine
5mCBlastocyst
• Not detailed
• Not quantified
• Not accurate

41. Objective
1. Profile the global methylome of bovine pre-
implantation embryos (2-cell to 16-cell) and gametes
using Whole Genome Bisulfite Sequencing (WGBS)
2. Characterize of gamete-specific differentially
methylated regions (DMRs)
3. Relationship between DNA methylation and gene
expression
4. Characterize the DNA methylation of known
imprinted genes
41

42. Materials
Gametes & Single embryo
• Sperm (n=3 pools of 20)
• GV oocyte (n=4)
• In vivo MII oocyte (n=6)
• In vitro MII oocyte (n=6)
• 2-Cell (n=4)
• 4-Cell (n=5)
• 8-Cell (n=4)
• 16-Cell (n=3)
42
In vivo
MII
Immature
(GV)
2C 4C 8C 16C
In vitro
MIISperm
Oocyte

43. WGBS (Whole-genome
bisulfite sequencing)
https://www.nucleomeinfo.com/services/epigenomics/
43
• Library sequencing
• Bioinformatics analysis
• Genomic DNA extraction
• Fragmentation and add adaptors
• Bisulfite treatment
• PCR amplification

44. Calculation of CpG methylation
Average CpG me-level =
!"
!"
#! $ =
!
!#%
Genome
CpGs
300bp windows
Wardenaar et al., 2013, methods in molecular biology
TC
300-bp windows of the genome

45. 1.1. Global methylome dynamics during embryonic
development
45
GV
Sperm
In vivo M
II
In vitro M
II
2-Cell
4-Cell
8-Cell
16-Cell

46. 1.2. Genomic elements methylome dynamics during
embryonic development
46

47. 2.1. DNA methylation changes in consecutive stages
47
• Changing tiles:
> 40% changes in comparison
• More stable tiles than changing tiles
• Sperm to 2 cell: decreasing
• 8 to 16 cell: increasing

48. Stages No. of DMRs No. of genes
Sperm vs. GV 4,654 543
Sperm vs. In vivo MII 2,653 354
Sperm vs. In vitro MII 6,211 668
GV vs. In vivo MII 755 77
GV vs. In vitro MII 936 93
In vivo MII vs. In vitro MII 801 68
48
2.2. Differentially methylated regions (DMRs) in gametes

49. 2.2. DMRs in gametes during the embryonic development
GV
Sperm
In vivo M
II
In vitro M
II
2-Cell
4-Cell
8-Cell
16-Cell
GV
Sperm
In vivo M
II
In vitro M
II
2-Cell
4-Cell
8-Cell
16-Cell
Sperm-specific DMRs
• Largely demethylated
In vivo MII-specific DMRs
• Follow the global pattern

50. 3. Relationship between promoter DNA methylation and gene expression
50
• Low and negative correlation
• Sperm has the strongest negative correlation
ON OFF

51. 4. DNA methylation of imprinted gene PEG3
51

52. • The major wave of genome-wide DNA
demethylation was complete at the 8-cell stage when
de novo methylation became prominent
• Sperm and oocytes were differentially methylated in
numerous regions (DMRs)
• DMRs were also identified between in vivo and in vitro
matured oocytes
• Inverse correlation between gene expression and
promoter methylation
Summary of project 3
52

53. • Maternal diets affect levels of imprinted gene
expression while the allelic expression pattern was not
affected
• Up-regulation of X chromosome in bovine germline,
embryos and somatic tissues
• Global demethylation during bovine embryo cleavage
up to 8-cell stage and de novo methylation at 16-cell
stage
Conclusion

54. Acknowledgements
Major Advisor:
Dr. Xiuchun (Cindy) Tian
Committee Members:
Dr. Ion Mandoiu
Dr. Lynn Kuo
Dr. Michael O’Neill
Collaborators:
Dr. Sahar Al Seesi
Wei Shi
Dr. Nathaniel Jue
Dr. Kristen Govoni
Dr. Sarah Reed
Dr. Steven Zinn
Dr. Sadie Marjani
Dr. Isabelle Hue
Reed & Govoni Labs:
Dr. Amanda Jones
Dr. Sambhu Pillai
Dr. Maria Hoffman
Ms. Joseline Raja
Tian Lab previous and
current Members:
Dr. Zongliang Jiang
Dr. Mingyuan Zhang
Kaleigh Flock
Linkai Zhu
Dr. Kanokwan
Srirattana
Elizabeth Johnson
Shyann Williams
Liqi An
Tang Lab Members:
Dr. Young Tang
Ling Wang
Chang Huang
54

55. Thankyou for yourattention.
Doewehaveanyquestion?
55

56. 56
• Happens in cycles
• Erased and re-set in the gonads
• Multi-generational effects
Epigenetic features

58. Examples of genetic imprinting in
animal science
horse donkey
mule hinny
Callipyge (CLPG) locus mutation
Polar overdominance, inherited from the father
Two copies--- normal phenotype
58

59. 4. DNA methylation of 34 known imprinted genes in bovine
59
(Methylation)
17 Paternally expressed genes
• 9 expressed allele low methylation
• 8 expressed allele high methylation
17 Maternally expressed genes
• 11 expressed allele low methylation
• 6 expressed allele high methylation
Sperm
In vivo MII