Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RIP-Seq]
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ABSTRACT:
PROVIDER: PRJNA1254191 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33253271.fastq.gz | Fastqsanger.gz |
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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.
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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.
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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.
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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.
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Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana
| PRJNA1254186 | ENA
Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [smallRNA-Seq]
| PRJNA1254210 | ENA
Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [RNA-Seq]
| PRJNA1254194 | ENA
Project description:Ribosomes binding to TAS transcripts buffer ta-siRNA biogenesis in Arabidopsis thaliana [Degradome-seq]
| PRJNA1254192 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2025-06-01 | GSE295326 | GEO
Project description:Purpose: To examine and characterize the expression profile of genes expressed at the neuromuscular junctions (NMJs) of extraocular muscles (EOMs) in comparison to the NMJs of tibialis anterior muscle (TA). Methods: Adult rat rectus EOMs and TAs were dissected, flash-frozen, serially sectioned and stained for acetylcholinesterase to identify NMJs. Approximately 6000 NMJs for EOM (EOMsyn) and 6000 NMJs for TA (TAsyn) and equal amounts of NMJ-free fiber regions (EOMfib, TAfib) and underlying myonuclei were captured using laser capture microdissection (LCM). RNA was isolated, processed and used for microarray-based expression profiling. Profiles were generated for genes differentially expressed at synaptic and non-synaptic regions of TA (TAsyn vs TAfib) and EOM (EOMsyn vs EOMfib) using a false discovery rate (FDR) of 5% as well as an 'interaction list' revealing the most significantly differentially expressed genes at an FDR of 1%. We validated the profiles by real-time quantitative reverse transcription-polymerase chain reaction (qPCR). Results: The regional transcriptomes associated with NMJ of EOMs and TAs were identified. We found 275 genes that were preferentially expressed in EOMsyn and 230 known transcripts that were preferentially expressed in TAsyn; 288 of the transcripts were common to both synapses; these included well-known, evolutionarily conserved, synaptic markers (e.g. nicotinic Acetylcholine receptor (ACHR) alpha and epsilon subunits, nestin) as well as a large number of novel genes. Conclusion: Transcriptome level differences exist between EOM synaptic regions and TA synaptic regions. Our definition of the synaptic transcriptome provides insight into the mechanism of formation and functioning of the unique synapses of EOM and their differential involvement in diseases noted in the EOM allotype. Tissue preparation: A total of 4 rats were killed by CO2 inhalation. The bony orbit was removed from the skull and opened at the lamina cribrosa. The globe with the four recti EOMs still attached was carefully dissected from the bony orbit. The eyeball with muscles was placed on cryomolds, covered with OCT tissue embedding medium (Tissue-Tek: Sakura Finetek, Tokyo, Japan) and flash-frozen in isopentane, cooled in liquid nitrogen and stored at -80 degreeC. The tibialis anterior (TA) muscles of all rats were dissected and frozen in the same way. The EOM and TA were then cut transversely into 10 um sections using a Microm HM 500 cryostat (Zeiss, Oberkochen, Germany), mounted on PEN (poly-ethylene-naphthalene) Membrane Slides (Arcturus) and refrozen immediately. Unfixed sections were stored at -80 degreeC until needed. Section staining: Sections for LCM were stained for acetylcholinesterase based on the method of Karnowsky and Roots to visualize NMJ. Palm microdissection: The PALM MicroBeam System was used for microdissection and for catapulting isolated tissue into a microfuge cap containing 80 ul RLT-Lysis Buffer (Quiagen). Approximately 1000 NMJ and equal amount of non-synaptic regions were collected for each muscle.
2010-04-28 | E-GEOD-15737 | biostudies-arrayexpress