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

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

PROVIDER: PRJNA809023 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18091043_1.fastq.gz	Fastqsanger.gz
	SRR18091043_2.fastq.gz	Fastqsanger.gz
	SRR18091044_1.fastq.gz	Fastqsanger.gz
	SRR18091044_2.fastq.gz	Fastqsanger.gz
	SRR18091045_1.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 [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-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.

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 [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: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

Allele-specific regulation of gene expression through enhancer function and transcriptional elongation control at imprinted loci

Project description:Genomic imprinting is a critical developmental process characteristic of parent-of-origin- specific gene expression. Here, we have identified the AFF family protein, Aff3, as a factor that functionally interacts with imprinted loci. Indeed, our genome-wide studies demonstrate that Aff3 specifically binds both imprinting control regions (ICRs) and enhancers within imprinted loci in an allele-specific manner. We have identified the molecular regulators involved in the recruitment of Aff3 to ICRs to impede transcription through the ICR, and provide a mechanism requiring Aff3 within the Super Elongation Complex-like 3 (SEC-L3) in the expression of an imprinted polycistronic transcript spanning the Dlk1-Dio3 locus. Our study also shows that DNA methylation at the ICR reinforces silencing of its related enhancers by controlling the binding and activity of Aff3 in an allele-specific manner. This study provides molecular details about the regulation of dosage-critical imprinted gene expression through Aff3’s function in transcriptional elongation control.

2016-01-01 | GSE64489 | GEO

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