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Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RIP-Seq]

ABSTRACT: Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RIP-Seq]

PROVIDER: PRJNA1254191 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR33253270.fastq.gz	Fastqsanger.gz
	SRR33253271.fastq.gz	Fastqsanger.gz
	SRR33253272.fastq.gz	Fastqsanger.gz
	SRR33253276.fastq.gz	Fastqsanger.gz

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Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [smallRNA-Seq]

Project description:Small RNAs, including ta-siRNAs, play crucial roles in various processes in plants. Efforts have been made for decades to elucidate the biogenesis and function of ta-siRNAs. Though the key proteins involved in ta-siRNA biogenesis have been identified, the subcellular localization where ta-siRNAs are processed remains largely unexplored. Remarkably, non-coding TAS transcripts were reported to be bound by ribosomes, the machinery responsible for protein translation. Utilizing edited TAS genes in Arabidopsis, a combination of sRNA-seq, mRNA-seq, RIP-seq, and degradome-seq was employed to investigate the role of ribosomes in ta-siRNA biogenesis in this study. In the two-hit model, deletion of ribosome-binding regions resulted in a decrease in the abundance of intact TAS3 transcripts but did not significantly affect ta-siRNAs production or the efficiency of miRNA-guided cleavage. Conversely, the deletion of ribosome-binding regions led to a significant reduction in ta-siRNA abundance without affecting mRNA levels in the one-hit model. These findings indicate that in the two-hit model, ribosomes primarily stabilize TAS transcripts, while in the one-hit model, they suppress miRNA cleavage but facilitate subsequent processing. Collectively, this study proposes a model that ribosomes play distinct roles in the one-hit and two-hit models of ta-siRNA biogenesis, and provides a new angle to investigate the tangled connection between small RNAs, including miRNA and ta-siRNA, and translation.

2025-06-01 | GSE295325 | GEO

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RNA-Seq]

2025-06-01 | GSE295323 | GEO

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [Degradome-seq]

2025-06-01 | GSE295321 | GEO

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RIP-Seq]

2025-06-01 | GSE295318 | GEO

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana

Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana

| PRJNA1254186 | ENA

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RNA-Seq]

Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RNA-Seq]

| PRJNA1254194 | ENA

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [Degradome-seq]

Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [Degradome-seq]

| PRJNA1254192 | ENA

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [smallRNA-Seq]

Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [smallRNA-Seq]

| PRJNA1254210 | ENA

Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana

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

2025-06-01 | GSE295326 | GEO

Translational activators align mitochondrial mRNAs at the small ribosomal subunit for translation initiation

Project description:Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In the baker´s yeast Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats (PPRs) using selective mitoribosome profiling and cryo-EM structural analysis. These analyses revealed that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicated that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to post-initiation/pre-elongation-stalled mitoribosomes revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5' UTR of the client mRNA as well as to the mRNA exit channel to align the mRNA in the small subunit during initiation. Our findings provide a structural basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position ribosomes at start codons.

2025-07-16 | GSE282943 | GEO

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