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Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Bos indicus Bos indicus x Bos taurus

PROVIDER: GSE197130 | GEO | 2022/04/22

REPOSITORIES: GEO

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Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome.

Project description:Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and gene misregulation in LOS. However, less than 4% of gene misregulation can be explained with short range (<20kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20kb in cis and in trans (other chromosomes). Our analyses focused on two imprinted domains that frequently reveal misregulation in these syndromes, namely KvDMR1 and IGF2R. Using bovine fetal fibroblasts, we identified CTCF binding at IGF2R imprinting control region but not KvDMR1, and allele-specific chromosome architecture of these domains in controls. In LOS, analyses identified erroneous long-range contacts and clustering tendency in the direction of expression of misregulated genes. In conclusion, altered chromosome architecture is associated with LOS.

| S-EPMC9079005 | biostudies-literature

Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [WGBS]

Project description:Large offspring syndrome (LOS) and Beckwith-Wiedemann syndrome are a similar epigenetic congenital overgrowth conditions in ruminants and humans, respectively. We have reported global loss-of-imprinting, methylome epimutations, and global misregulation of genes in LOS. However, less than 4% of gene misregulation can be explained with short range (<20Kb) alterations in DNA methylation. Therefore, we hypothesized that methylome epimutations in LOS affect chromosome architecture which results in misregulation of genes located at distances >20Kb in cis and also in trans (other chromosomes). Our analyses focused on two imprinted domains that frequently show misregulation in these syndromes, namely KvDMR1 and IGF2R. Using bovine fetal fibroblasts, we identified CTCF binding at IGF2R but not KvDMR1, and allele-specific chromosome architecture of these domains in controls. In LOS, analyses identified erroneous long-range contacts and clustering tendency in the direction of expression of misregulated genes. In conclusion, altered chromosome architecture is involved in the etiology of LOS.

2022-04-22 | GSE197129 | GEO

Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [4C-Seq]

2022-04-22 | GSE197127 | GEO

Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [DNA-Seq]

2022-04-22 | GSE197128 | GEO

Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome

Project description:Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome

| PRJNA809018 | ENA

Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [WGBS]

Project description:Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [WGBS]

| PRJNA809023 | ENA

Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [4C-Seq]

Project description:Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [4C-Seq]

| PRJNA809025 | ENA

Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [DNA-Seq]

Project description:Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome [DNA-Seq]

| PRJNA809024 | ENA

Allele and dosage specificity of the Peg3 imprinted domain.

Project description:The biological impetus for gene dosage and allele specificity of mammalian imprinted genes is not fully understood. To address this, we generated and analyzed four sets of mice from a single breeding scheme with varying allelic expression and gene dosage of the Peg3 domain. The mutants with abrogation of the two paternally expressed genes, Peg3 and Usp29, showed a significant decrease in growth rates for both males and females, while the mutants with biallelic expression of Peg3 and Usp29 resulted in an increased growth rate of female mice only. The mutant cohort with biallelic expression of Peg3 and Usp29 tended to have greater numbers of pups compared to the other genotypes. The mutants with switched active alleles displayed overall similar phenotypes to the wild type, but did show some differences in gene expression, suggesting potential non-redundant roles contributed by the maternal and paternal alleles. Overall, this study demonstrates a novel in vivo approach to investigate the allele and dosage specificity of mammalian imprinted domains.

| S-EPMC5937776 | biostudies-literature

Allele-specific enhancer interaction at the Peg3 imprinted domain.

Project description:The parental allele specificity of mammalian imprinted genes has been evolutionarily well conserved, although its functional constraints and associated mechanisms are not fully understood. In the current study, we generated a mouse mutant with switched active alleles driving the switch from paternal-to-maternal expression for Peg3 and the maternal-to-paternal expression for Zim1. The expression levels of Peg3 and Zim1, but not the spatial expression patterns, within the brain showed clear differences between wild type and mutant animals. We identified putative enhancers localized upstream of Peg3 that displayed allele-biased DNA methylation, and that also participate in allele-biased chromosomal conformations with regional promoters. Most importantly, these data suggest for the first time that long-distance enhancers may contribute to allelic expression within imprinted domains through allele-biased interactions with regional promoters.

| S-EPMC6804975 | biostudies-literature

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