group 6 xiaopeng ma, weiru liu, zhirui hu, weilong guo
TRANSCRIPT
![Page 1: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/1.jpg)
Group 6
Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo
![Page 2: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/2.jpg)
About author
• Alexander Meissner– Harvard University Department of
Stem Cell and Regenerative Biology, Broad Institute
– The epigentic mechanism of stem cell, ips
Alex Meissner`s bossRudolf Jaenisch, MD
Alex Meissner
![Page 3: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/3.jpg)
Functions of DNA methylation
• Promoter/enhancer repression• Retrotransposon silencing• Imprinting patterns
![Page 4: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/4.jpg)
Background
![Page 5: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/5.jpg)
DNA methylation dynamic in lifecycle
Smallwood et al. Trends in Genetics, January 2012, Vol. 28, No. 1
![Page 6: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/6.jpg)
RRBS: Reduced Representation Bisulfite Sequencing
• Pros: – low cost– Low cell numbers– high enrich in CpG island
• Cons: – low coverage of genome(1%)– Possible low C->U conversion rate.– Can not distinguish mC and hmC
MspI Recognition SiteInsensitive to mC
Hongcang Gu et al, 468|VOL.6 NO.4 |2011 |nature protocols
![Page 7: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/7.jpg)
Genomic coverage of typical RRBS libraries
Hongcang Gu et al, 468|VOL.6 NO.4 |2011 |nature protocols
![Page 8: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/8.jpg)
reduced representation bisulphite sequencing (RRBS) library
Recognizing site: 5’-C|CGG-3’ 3’-GGC|C-5’
Cleavage happens only when internal methylation occurs within recognizing site
![Page 9: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/9.jpg)
Result: obtained the methylation status of 1,062,216 CpGs for comparative analysis
![Page 10: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/10.jpg)
1. Murine embryogenesis
![Page 11: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/11.jpg)
BDF1 (♀) × 129X1(♂)
![Page 12: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/12.jpg)
•Oocyte methylation levels more closely resembles those of early embryonic time points than the levels in sperm, post implantation embryos, of adult tissues.
•from oocytes to the early ICM: gradual increase in the fraction of tiles that exhibit intermediate an low methylation values, which is consistent with loss of methylation over mutiple cleavage divisions
![Page 13: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/13.jpg)
CpG density vs methylation levels
Pre-implantation development represents a unique developmental period where methylation is defferentially positioned and regulated before being restored in a somatic fashion
![Page 14: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/14.jpg)
Substantial methylation changed in regional DNA
37% 66%
Most stable/increased slightly
![Page 15: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/15.jpg)
Differentially methylated regions (DMRs): differential methylated tiles between 2 gametes
The regions that are significantly hypermethylated in oocyte compared to sperm exhibit intermediate values in the zygote
Suggestion: the oocyte methylome, rather than the sperm methylome, seems to be more reflective of patterns in the early embryo.
74 CpGs within sperm-specific DMR tiles
![Page 16: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/16.jpg)
Retroelement methylation & Gametes contributed DMRs
![Page 17: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/17.jpg)
Compare between sperm and zygote methylation
• Original view:– Paternal genome actively depleted methylation at
fertilization
• 96% tiles hypermethylated in sperm, less methylated in zygote
• Already low methylation in oocyte
• Where these regions locate?
![Page 18: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/18.jpg)
Retroelement dynamics at fertilization
• LINEs: Most extreme changes in sperm to zygote transition, binomal
• LTR: similar demethylation but not binomal• SINEs: less methylated in sperm than other
repeats and thus less change, not binomal
![Page 19: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/19.jpg)
![Page 20: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/20.jpg)
Mean methylation level for Retroelements
All retrotransposons follow the same path in early developmentLess methylated in oocyte pre-implantation stagesMore methylated in E6.5/7.5 and somatic cells
![Page 21: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/21.jpg)
Summary• Does it mean retrotransposon is more active in pre-
implantation stages? – LINE-1 retrotransposon is required for early embryo
preimplantation development (Beraldi R. et al. 2006)– Associates with earliest transcriptional events during
zygotic genome activation– Not address how retrotransposon methytion related to
transcription
• Doesn’t mean paternal de-methylation in these regions– distinguish paternal and maternal methylation
• Remember the bias of RRBS (CpG rich regions)• Can’t address whether mC first convert to hmCs
![Page 22: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/22.jpg)
Gametes confer DMRsCompare between sperm and oocyte methylation• Some allele-specific methylation pattern is
maintained (e.g. ICR)• CpG methylation was lower overall in mature
oocytes than sperm; methylation in a CGI context was markedly lower in sperm (Smallwood,S.A. et al. 2011)
• DMRs contributed from either gamete– DMR: differential methylated tiles between 2 gametes– Different allelic methylation: Linear regression for
DMR with zygote methylation level half-way
![Page 23: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/23.jpg)
oocyte-contributed DMRs vs.sperm-contributed DMRs
• Differ in CpG densities• 376 oocyte-contributed DMRs– Enriched in HCP, no functional enrichment, including Dnmt1,Dmnt3b, Cpne7 (DMR near promoter)
– intermediate level from zygote to ICM and then hypomethylation (expected for HCP)
• 4894 sperm-contributed DMRs– Intergenic regions– Intermediate level to ICM and then hypermethylated
(typical in somatic)
![Page 24: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/24.jpg)
DMRs vs genomic features
Oocyte-contributed DMR Sperm-contributed DMR
Intergenic regions
![Page 25: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/25.jpg)
Methylation pattern in Cpne7oocyte-contributed DMR
![Page 26: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/26.jpg)
Promoters hypermethylated in oocytes
Intermediate through cleavage
HCP methylation structure
Mean methylation change
![Page 27: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/27.jpg)
Non-CpG• Non-CpG inherited by oocyte alleles but lost quickly– Highest mCpA in oocytes and decrease ~50% in zygote
![Page 28: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/28.jpg)
Summary
• Defining oocyte/sperm contributed DMR by linear regression is indirect
• Can’t cover much non-CpGs• Why oocyte-contributed DMR in HCP but
sperm-contributed DMR in intergenic regions?
![Page 29: Group 6 Xiaopeng Ma, Weiru Liu, Zhirui Hu, Weilong Guo](https://reader036.vdocuments.site/reader036/viewer/2022082215/56649dc85503460f94abdd1d/html5/thumbnails/29.jpg)
A model for DNA methylation dynamics during early embryogenesis