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

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

PROVIDER: PRJNA809024 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18090837_1.fastq.gz	Fastqsanger.gz
	SRR18090837_2.fastq.gz	Fastqsanger.gz

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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 [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 [DNA-Seq]

2022-04-22 | GSE197128 | 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.

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

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-04-22 | GSE197130 | GEO

Allele-specific binding of ZFP57 in the regulation of imprinted and mono-allelic expression

Project description:Selective maintenance of genomic methylation imprints during pre-implantation development is required for parental origin-specific expression of imprinted genes. The Kruppel-like zinc finger protein ZFP57 acts as a factor necessary for maintaining the DNA methylation memory at multiple imprinting control regions (ICRs) in early mouse embryos and ES cells. Maternal-zygotic deletion of ZFP57 in mice presents a highly penetrant phenotype with no animals surviving to birth. In addition, several cases of human transient neonatal diabetes (TND) are associated with somatic mutations in ZFP57 coding sequence. Here we comprehensively map sequence-specific ZFP57 binding sites in an allele-specific manner using hybrid ES cell lines from reciprocal crosses between C57BL/6J and Cast/EiJ mice assigning allele specificity to approximately two thirds of all binding sites. While half of these are biallelic and include ERV targets, the rest show mono-allelic binding based either on parental-origin or on genetic background of the allele. Parental-origin allele-specific binding was methylation-dependent and mapped only to imprinted DMRs established in the germline (gDMRs). No binding was evident at secondary somatically-derived DMRs. ZFP57-bound gDMRs can predict imprinted gene expression and we identify new imprinted genes, including the Fkbp6 gene with a critical function in mouse male germ cell development. Genetic-background specific sequence differences also influence ZFP57 binding. We show that genetic variation that disrupts the consensus binding motif and its methylation is associated with mono-allelic expression of neighbouring genes. The work described here uncovers further roles for ZFP57 mediated regulation of genomic imprinting and identifies a novel mechanism for genetically determined mono-allelic gene expression. Input and Zfp57 CHiP-Seq profiles of hybrid Black6/Cast ES cells were generated by sequencing using the Illumina GAIIx platform.

2015-05-08 | E-GEOD-55382 | biostudies-arrayexpress

Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis

Project description:Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele, an enhancer-promoter contact formed early in development primes the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, this enhancer-promoter contact is blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.

2023-08-07 | GSE202251 | GEO

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