Table II.
Comparative evaluation of epigenetic features and processes evaluated during human and mouse development to date.
| Tissue/cell type | Epigenetic feature/process | Mouse | Human | Reference | Relative similarity |
|---|---|---|---|---|---|
| PGCs | DNA methylation erasure | Global DNA methylation and imprinted DMRs are erased upon PGC specification | Global DNA methylation and imprinted DMRs are erased upon PGC specification | Guibert et al. (2012), Seisenberger et al. (2012), Guo et al. (2015), Gkountela et al. (2015), Guo et al. (2017b) | |
| Sperm | DNA methylation patterns in sperm | ~80% genome-wide methylation, with unmethylated regulatory domains | ~75% genome-wide methylation, with unmethylated regulatory domains | Oakes et al. (2007), Kobayashi et al. (2012), Guo et al. (2014) | |
| De novo DNMTs in spermatogenesis | DNMT3A, 3L and 3C are essential for spermatogenesis | Unknown; DNMT3A, 3B and 1 are dynamically expressed during spermatogenesis, but there is no expression of DNMT3L and no orthologous gene for DNMT3C | Bourc’his et al. (2001), Kaneda et al. (2004), Barau et al. (2016), Marques et al. (2011) | ||
| Retention of modified histones in sperm | ~1% genome-wide, enriched at developmental promoters | ~10% genome-wide, enriched at developmental promoters | Brykczynska et al. (2010), Hammoud et al. (2009) | ||
| Oocyte | DNA methylation patterns in the oocyte | ~40% genome-wide methylation and localised predominantly to expressed gene bodies | ~54% genome-wide methylation and localised predominantly to gene bodies | Okae et al. (2014), Kobayashi et al. (2012) | |
| De novo DNMTs in oogenesis | DNMT3A and 3L are essential for establishing DNA methylation in oocytes | Unknown; in human oocytes, DNMT1, 3A and 3B are expressed, but not DNMT3L | Bourc’his et al. (2001), Smallwood et al. (2011), Shirane et al. (2013), Guo et al. (2014), Okae et al. (2014) | ||
| Histone modification patterns | Non-canonical distributions of both H3K4me3 and H3K27me3 across regions lacking DNA methylation | Unknown | Zhang et al. (2016), Dahl et al. (2016), Hanna et al. (2018), Zheng et al. (2016) | ||
| Higher order chromatin organisation | Weak TADs and loops and a loss of A/B compartments upon transcriptional silencing | Unknown | Flyamer et al. (2017), Du et al. (2017), Ke et al. (2017) | ||
| Pre-implantation embryo | DNA methylation dynamics in pre-implantation development | Active loss of paternal methylation and passive loss of maternal methylation; regions of DNA methylation turnover | Active loss of paternal methylation and minimal passive loss of maternal methylation; regions of DNA methylation turnover | Guo et al. (2014), Okae et al. (2014), Smith et al. (2014), Zhu et al. (2018) | |
| ZFP57-mediated protection of imprinted DMRs | Maternal/oocyte contribution of ZFP57 is required to protect imprints in pre-implantation development | ZFP57 is required to protect imprints, but it is not expressed in human oocytes; expression is initiated in the pre-implantation embryo | Quenneville et al. (2011), Li et al. (2008), Okae et al. (2014), Mackay et al. (2008), Sanchez-Delgado et al. (2016b) | ||
| Chromatin configuration post-fertilisation | Widespread open chromatin that resolves upon ZGA | Widespread open chromatin that resolves upon ZGA | Wu et al. (2016), Wu et al. (2018) | ||
| Histone modification dynamics | Non-canonical maternal H3K4me3 resolves to canonical pattern, while maternal H3K27me3 is predominantly erased | Unknown | Zheng et al. (2016), Zhang et al. (2016), Dahl et al. (2016) | ||
| Higher order chromatin organisation | Canonical patterns of TADs, loops, and A/B compartments restored during early embryogenesis | Unknown | Flyamer et al. (2017), Ke et al. (2017), Du et al. (2017) | ||
| Blastocyst | DNA methylation patterns in blastocyst-stage embryos | Maintenance of imprinted DMRs and low levels of oocyte methylation patterns | Maintenance of imprinted DMRs and persistent oocyte methylation patterns | Kobayashi et al. (2012), Okae et al. (2014), Guo et al. (2014), Zhu et al. (2018) | |
| Post-implantation embryonic tissues | Number of imprinted genes | ~125–151, with numerous imprinted gene clusters | ~50–90, with numerous imprinted gene clusters | Crowley et al. (2015), Babak et al. (2015), Sanchez-Delgado et al. (2016a), Santoni et al. (2017), Andergassen et al. (2017) | |
| Epigenetic regulation of imprinted gene clusters | Non-coding RNAs and differential DNA methylation regulate imprinted gene expression | Non-coding RNAs and differential DNA methylation regulate imprinted gene expression | Reviewed in Reik and Walter (2001) | ||
| X chromosome inactivation (XCI) in embryogenesis | Random XCI, mediated by opposing expression of Xist and Tsix | Random XCI, mediated by expression of XIST from the inactive X | Reviewed in Furlan and Rougeulle (2016) | ||
| Genetic polymorphisms influence imprinted gene expression | Cis-acting strain-specific SNPs can influence allelic bias in imprinted gene expression | Cis-acting SNPs can influence allelic bias in imprinted gene expression | Crowley et al. (2015), Andergassen et al. (2017), Babak et al. (2015), Garg et al. (2012) | ||
| Tissue-specific imprinted gene expression | Several imprinted genes are tissue-specific | Several imprinted genes are tissue-specific | Crowley et al. (2015), Andergassen et al. (2017), Babak et al. (2015) | ||
| Post-implantation extra-embryonic tissues | Genome-wide methylation patterns | Extra-embryonic tissues are characterised by large partially methylated domains | Extra-embryonic tissues are characterised by large partially methylated domains | Rossant et al. (1986), Schroeder et al. (2013), Decato et al. (2017) | |
| XCI in extra-embryonic tissues | Imprinted inactivation of the paternal X chromosome, conferred by repression of maternal Xist by oocyte-derived H3K27me3 | Random XCI | Takagi and Sasaki (1975), Migeon and Do (1979), Penaherrera et al. (2003), Inoue et al. (2017b) | ||
| Abundance of placental-specific imprinted gDMRs | None reported | >1500 placental-specific gDMRs reported | Hanna et al. (2016), Hamada et al. (2016), Sanchez-Delgado et al. (2016a) | ||
| Polymorphic imprinted DMRs | Unknown | Pervasive in extra-embryonic tissues | Hanna et al. (2016), Sanchez-Delgado et al. (2016a) | ||
| Non-canonical imprinting | Several non-canonical placenta-specific imprinted genes mediated by maternal H3K27me3 | Unknown | Inoue et al. (2017a) | ||
| Large placenta-specific imprinted domains: KvDMR | Distal placental-specific imprinting of genes in the KvDMR locus | While the canonical imprinting at KvDMR is conserved, distal genes are not imprinted in placenta | Lewis et al. (2004); Frost et al. (2010) | ||
| Large placenta-specific imprinted domains: Chromsome 19 micro-RNA cluster | No orthologous region | Chromosome 19 micro-RNA cluster is imprinted specifically in placenta | Noguer-Dance et al. (2010) |
Colour key: green – highly similar; yellow – similar, but with key differences identified; red – highly discrepant; grey – unknown in mouse or human.