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Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis

ABSTRACT: Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis

PROVIDER: PRJNA986851 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19962784_1.fastq.gz	Fastqsanger.gz
	SRR19962784_2.fastq.gz	Fastqsanger.gz
	SRR19962785_1.fastq.gz	Fastqsanger.gz
	SRR19962785_2.fastq.gz	Fastqsanger.gz
	SRR19962786_1.fastq.gz	Fastqsanger.gz

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Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [miRNA-Seq]

Project description:MicroRNAs (miRNAs) play an important role in gene regulation. In Arabidopsis thaliana, mature miRNAs are processed from primary miRNA transcripts by Dicing complex, which contains DCL1, SE and HYL1 and forms nuclear dicing bodies (D-bodies) through SE phase separation. Here we report that Cyclophilin 71 (CYP71), a peptidyl-prolyl isomerase (PPIase), positively regulates miRNA processing. We show that CYP71 directly interacts with SE and enhances its phase separation, thereby promoting the formation of D-body and increasing the activity of Dicing complex. We further show that the PPIase activity is important for the function of CYP71 in miRNA production. Our findings reveal orchestration of miRNA processing by a cyclophilin protein and suggest the involvement of proline cis-trans isomerization, a structural mechanism, in SE phase separation and miRNA processing.

2023-08-07 | GSE207396 | GEO

Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [mRNA-Seq]

2023-08-07 | GSE235656 | GEO

Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [miRNA-Seq]

Project description:Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [miRNA-Seq]

| PRJNA855233 | ENA

Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [mRNA-Seq]

Project description:Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [mRNA-Seq]

| PRJNA986858 | ENA

Genetic interactions and transcriptomics implicate fission yeast CTD prolyl isomerase Pin1 as an agent of RNA 3' processing and transcription termination that functions via its effects on CTD phosphatase Ssu72

Project description:This RNA-Seq analysis compares gene expression of the peptidyl-prolyl isomerase Pin1 mutant pin1∆ contrasting to the WT in the fission yeast S. pombe

2020-03-20 | GSE144092 | GEO

Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis

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

2023-08-07 | GSE235657 | GEO

p53 restoration in small cell lung cancer identifies a latent cyclophilin-dependent necrosis mechanism (ChIP-Seq)

Project description:The p53 tumor suppressor regulates multiple context-dependent tumor suppressive programs. Although p53 is mutated in ~90% of small cell lung cancer (SCLC) tumors, how p53 mediates tumor suppression in this context is unknown. Here, using a mouse model of SCLC in which endogenous p53 expression can be conditionally and temporally regulated, we show that SCLC tumors maintain a requirement for p53 inactivation. However, we identified tumor subtype heterogeneity between SCLC tumors such that p53 reactivation induces a canonical senescence response in a subset of tumors, while, in others, p53 induces a non-apoptotic form of cell death that culminates in necrosis. We pinpointed the cyclophilin family of peptidyl prolyl cis-trans isomerases as critical determinants of a p53-induced transcriptional program that is specific to SCLC tumors and cell lines that are poised to undergo p53- mediated necrosis. Importantly, inhibition of cyclophilin isomerase activity, or genetic ablation of specific cyclophilin genes, suppresses p53-mediated necrosis by limiting p53 transcriptional output without impacting p53 chromatin binding. Our study demonstrates that a previously unappreciated intertumoral heterogeneity in SCLC can influence the biological response to p53 restoration, describes a novel mechanism of p53-regulated cell death, and uncovers putative mechanisms for the treatment of this most-recalcitrant tumor type.

2023-06-05 | GSE231701 | GEO

p53 restoration in small cell lung cancer identifies a latent cyclophilin-dependent necrosis mechanism (RNA-Seq II)

2023-06-05 | GSE231704 | GEO

p53 restoration in small cell lung cancer identifies a latent cyclophilin-dependent necrosis mechanism (RNA-Seq I)

2023-06-05 | GSE231703 | GEO

The Ess1 prolyl isomerase is required for the transcription termination of small non-coding RNAs via Nrd1 pathway

Project description:Genome-wide studies have identified abundant small, non-coding RNAs including snRNAs, snoRNAs, cryptic unstable transcripts (CUTs), and upstream regulatory RNAs (uRNAs) that are transcribed by RNA polymerase II (pol II) and terminated by a Nrd1-dependent pathway. Here, we show that the prolyl isomerase, Ess1, is required for Nrd1-dependent termination of ncRNAs. Ess1 binds the carboxy terminal domain (CTD) of pol II and is thought to regulate transcription by conformational isomerization of Ser-Pro bonds within the CTD. In ess1 mutants, expression of ~10% of the genome was altered, due primarily to defects in termination of snoRNAs, CUTs, SUTs and uRNAs. Ess1 promoted dephosphorylation of Ser5 (but not Ser2) within the CTD, most likely by the Ssu72 phosphatase, and we provide evidence for a competition between Nrd1 and Pcf11 for CTD-binding that is regulated by Ess1-dependent isomerization. This is the first example of a prolyl isomerase required for interpreting the “CTD code.”

2009-10-16 | GSE17638 | GEO

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