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

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

PROVIDER: PRJNA415993 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6225493_1.fastq.gz	Fastqsanger.gz
	SRR6225493_2.fastq.gz	Fastqsanger.gz
	SRR6225494_1.fastq.gz	Fastqsanger.gz
	SRR6225494_2.fastq.gz	Fastqsanger.gz
	SRR6225495_1.fastq.gz	Fastqsanger.gz

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Transfer RNA Genes Affect Chromosome Architecture and Function

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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.

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Transfer RNA Genes Affect Chromosome Architecture and Function [RNA-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.

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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.

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Saccharomyces cerevisiae

Project description:Transfer RNA Genes Affect Chromosome Architecture and Function

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Transfer RNA Genes Affect Chromosome Architecture and Function

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

2019-03-05 | GSE106250 | GEO

Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

Project description:Nuclear chromosomes transcribe far more RNA than required to code for protein. Here we investigate whether non-coding RNA broadly contributes to cytological-scale chromosome territory architecture. We develop a procedure that depletes soluble proteins, chromatin and most nuclear RNA from the nucleus, but does not delocalize XIST, a known architectural RNA, from an insoluble chromosome “scaffold.” RNA-seq analysis reveals most RNA in the nuclear scaffold is repeat-rich, non-coding, and predominantly derived from introns of nascent transcripts. This repeat-rich (C0T-1) RNA inversely correlates with chromatin compaction in normal and experimentally manipulated nuclei, demonstrating RNA physically antagonizes a propensity for chromatin to condense. C0T-1 hnRNA co-distributes on euchromatin with several known scaffold proteins including scaffold attachment factor A (SAF-A). We further show that RNA is required for SAF-A to interact with chromatin and to form structurally embedded scaffold-attachment regions (SARs) in the nuclear genome. Collectively, results indicate nascent transcripts serve a dynamic structural role in the open architecture of active chromosome territories

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