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Transfer RNA Genes Affect Chromosome Architecture and Function

ABSTRACT: Transfer RNA Genes Affect Chromosome Architecture and Function

PROVIDER: PRJNA415991 | ENA |

REPOSITORIES: ENA

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Transfer RNA Genes Affect Chromosome Architecture and Function [ChIP-seq]

Project description:Transfer RNA Genes Affect Chromosome Architecture and Function [ChIP-seq]

| PRJNA415992 | ENA

Transfer RNA Genes Affect Chromosome Architecture and Function [RNA-seq]

Project description:Transfer RNA Genes Affect Chromosome Architecture and Function [RNA-seq]

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Transfer RNA Genes Affect Chromosome Architecture and Function

Project description:Chromosomes are packaged and organized in the nucleus in an ordered, non-random manner. This organization influences many nuclear processes such as transcription, gene silencing and mitosis. While transfer RNA genes (tDNAs) are essential for the generation of tRNAs these gene loci are also binding sites for transcription factors and chromosomal architectural proteins. In the yeast Saccharomyces cerevisiae, tDNAs are dispersed along all sixteen chromosomes. In this study, we investigated the role of tDNAs in genomic organization and nuclear function by editing a chromosome so that it lacks any tDNAs. Our analyses of this tDNA-less chromosome show that loss of tDNAs affect nucleosome positioning, binding of SMC proteins, centromere clustering, long-range chromosome folding and epigenetic gene silencing. We propose that these effects are primarily mediated via changes in local interactions between tDNAs and other regulatory sequences that then manifest as alterations in long-range chromosome architecture with effects on gene regulation over large distances.

2017-10-30 | GSE98543 | GEO

Transfer RNA Genes Affect Chromosome Architecture and Function

Project description:In this study we investigated the role of tDNAs in genomic organization and nuclear function by editing a chromosome so that it lacks any tDNAs.

2019-03-06 | GSE98304 | GEO

Transfer RNA Genes Affect Chromosome Architecture and Function [ChIP-seq]

Project description:In this study, we investigated the role of tranfer RNA genes (tDNAs) in genome organization and nuclear function by generating a chromosome lacking all its tDNAs. Our analyses of this tDNA-less chromosome show that loss of these genes affects nucleosome postioning, SMC protein binding, centromere clustering, long range chromosome folding and epigenetic silencing.

2019-03-05 | GSE106249 | GEO

Transfer RNA Genes Affect Chromosome Architecture and Function [RNA-seq]

2019-03-05 | GSE106248 | GEO

Saccharomyces cerevisiae

Project description:Transfer RNA Genes Affect Chromosome Architecture and Function

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Saccharomyces cerevisiae

Project description:Transfer RNA Genes Affect Chromosome Architecture and Function

| PRJNA384632 | ENA

Transfer RNA Genes Affect Chromosome Architecture and Function

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

2019-03-05 | GSE106250 | GEO

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

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