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Transfer RNA pools in human cells are controlled by selective gene expression [Ribo-seq]

ABSTRACT: Transfer RNA pools in human cells are controlled by selective gene expression [Ribo-seq]

PROVIDER: PRJNA947525 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23938993.fastq.gz	Fastqsanger.gz
	SRR23938994.fastq.gz	Fastqsanger.gz
	SRR23938995.fastq.gz	Fastqsanger.gz
	SRR23938996.fastq.gz	Fastqsanger.gz
	SRR23938997.fastq.gz	Fastqsanger.gz

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Transfer RNA pools in human cells are controlled by selective gene expression [Ribo-seq]

Project description:Transfer RNAs are required for translating genetic information into protein sequence. The human genome contains hundreds of tRNA genes, many of which in multiple copies. How their expression is regulated to control functional tRNA levels is unknown. Here, we combined quantitative tRNA profiling and ChIP-Seq to measure tRNA expression upon differentiation of human induced pluripotent stem cells (hiPSC) into neuronal and cardiac cells. We find that tRNA transcript pools vary substantially, while the abundance of tRNAs with distinct anticodons, which governs decoding rates, is more stable among cell types. Mechanistically, RNA Polymerase III (Pol III) samples a wide range of tRNA genes in hiPSC and becomes constrained to a housekeeping subset upon differentiation. This is mediated by diminished mTOR signaling, which activates the Pol III repressor MAF1. Our data rationalize how tRNA anticodon pools are buffered in different cellular contexts and reveal that mTOR activity drives selective tRNA expression.

2023-10-23 | GSE227926 | GEO

Transfer RNA pools in human cells are controlled by selective gene expression [ATAC-seq]

Project description:Transfer RNA pools in human cells are controlled by selective gene expression [ATAC-seq]

| PRJNA947523 | ENA

Transfer RNA pools in human cells are controlled by selective gene expression [RNA-seq]

Project description:Transfer RNA pools in human cells are controlled by selective gene expression [RNA-seq]

| PRJNA947524 | ENA

Transfer RNA pools in human cells are controlled by selective gene expression [ChIP-seq]

Project description:Transfer RNA pools in human cells are controlled by selective gene expression [ChIP-seq]

| PRJNA947526 | ENA

Transfer RNA pools in human cells are controlled by selective gene expression [tRNA-Seq]

Project description:Transfer RNA pools in human cells are controlled by selective gene expression [tRNA-Seq]

| PRJNA947527 | ENA

Transfer RNA pools in human cells are controlled by selective gene expression [tRNA-Seq]

2023-10-23 | GSE227927 | GEO

Transfer RNA pools in human cells are controlled by selective gene expression [RNA-seq]

2023-10-23 | GSE227925 | GEO

Transfer RNA pools in human cells are controlled by selective gene expression [ChIP-seq]

2023-10-23 | GSE227924 | GEO

Transfer RNA pools in human cells are controlled by selective gene expression [ATAC-seq]

2023-10-23 | GSE227923 | GEO

A small RNA controlled AND-gate regulates extrachromosomal DNA transfer in Salmonella

Project description:Horizontal gene transfer via plasmid conjugation is a major driving force in microbial evolution. Transfer of conjugative plasmids is a complex process that needs to be synchronized with the physiological state of the bacterial host. While several host transcription factors are known to control the plasmid-borne transfer control genes, RNA-based regulatory circuits for host-plasmid communication remain unknown. Here, we describe a post-transcriptional mechanism whereby the Hfq-dependent small RNA, RprA, inhibits transfer of pSLT, the virulence plasmid of Salmonella enterica. RprA employs two different seed pairing domains to recognize and activate the mRNAs of both the sigma-factor S and RicI, a cytoplasmic membrane protein. The latter is a hitherto unknown conjugation inhibitor whose transcription requires S. Together, RprA and S constitute a feed-forward loop with AND-gate logic which tightly controls RicI synthesis for selective suppression of plasmid conjugation under membrane stress. This study reports the first sRNA-controlled feed-forward loop based on double target activation and an unexpected function for a core-genome encoded small RNA in controlling extrachromosomal DNA transfer.

2015-03-24 | GSE67187 | GEO

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