Rat and mouse imprintomes (allele-specific DNA methylomes)
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ABSTRACT:
PROVIDER: PRJNA774062 | ENA |
REPOSITORIES: ENA
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Project description:The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting.
2023-01-19 | GSE186492 | GEO
Project description:Rat and mouse imprintomes (allele-specific transcriptomes)
| PRJNA769696 | ENA
Project description:The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting.
2023-01-19 | GSE185574 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE26720: Chromosome wide analysis of parental allele specific chromatin and DNA methylation GSE26891: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr7 GSE26892: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along the central part of mouse chr7 GSE26893: Chromosome wide analysis of parental allele specific chromatin and DNA methylation along mouse distal chr15 Refer to individual Series
2011-03-31 | E-GEOD-26947 | biostudies-arrayexpress
Project description:allele specific genome editing Raw sequence reads
| PRJNA817366 | ENA
Project description:The reprogramming of parental methylomes is essential for embryonic development. In mammals, paternal 5-methylcytosines (5mCs) have been proposed to be actively converted to oxidized bases. These paternal oxidized bases and maternal 5mCs are believed to be passively diluted by cell divisions. By generating single-base resolution, allele-specific DNA methylomes from mouse gametes, early embryos, and primordial germ cell (PGC), as well as single-base-resolution maps of oxidized cytosine bases for early embryos, we report the existence of 5hmC and 5fC in both maternal and paternal genomes and find that 5mC or its oxidized derivatives, at the majority of demethylated CpGs, are converted to unmodified cytosines independent of passive dilution from gametes to four-cell embryos. Therefore, we conclude that paternal methylome and at least a significant proportion of maternal methylome go through active demethylation during embryonic development. Additionally, all the known imprinting control regions (ICRs) were classified into germ-line or somatic ICRs.
2014-05-12 | GSE56697 | GEO
Project description:We describe a method for identifying peptides that result from missense changes and identify peptides among 2 human brains that would have otherwise not been detected. Next, we use this data to estimate of allele-specific protein abundance in human brain for an average per individual, and to estimate apolipoprotein E allele specific abundance in human brain across individuals. Finally, we estimate the heritability of allele-specific protein abundance.
2017-07-31 | PXD004143 | Pride
Project description:Allele-specific expression between Arabidopsis genus
| PRJNA140331 | ENA
Project description:Extensive allele-specific translational regulation in hybrid mice
| PRJEB8233 | ENA