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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE207396 | GEO | 2023/08/07

REPOSITORIES: GEO

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Peptidyl-prolyl isomerase Cyclophilin 71 promotes SERRATE phase separation and miRNA processing in Arabidopsis [mRNA-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 | GSE235656 | GEO

A Role for the RNA-Binding Protein MOS2 in MicroRNA Maturation in Arabidopsis

Project description:microRNAs (miRNAs) play important roles in the regulation of gene expression. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts (pri-miRNAs) by nuclear HYL1/SE/DCL1 complexes that form Dicing bodies (D-bodies). Here we report that a RNA-binding protein MOS2 bound to pri-miRNAs and was required for their efficient processing. MOS2 did not interact with HYL1, SE, and DCL1 and was not localized in D-bodies. Interestingly, in the absence of MOS2, the recruitment of pri-miRNAs by HYL1 was greatly reduced and the localization of HYL1 in D-bodies was compromised. These data suggest that MOS2 facilitates pri-miRNA processing through facilitating the recruitment of pri-miRNAs by the Dicing complexes. Examination of gene expression profiles in Col-0 and mos2-2 plants by deep sequencing

2012-10-27 | E-GEOD-41843 | biostudies-arrayexpress

A Role for the RNA-Binding Protein MOS2 in MicroRNA Maturation in Arabidopsis

2012-10-27 | GSE41843 | GEO

Dual roles of the nuclear cap binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis

Project description:The processing of Arabidopsis thaliana microRNAs (miRNAs) from longer primary transcripts (pri-miRNAs) requires the activity of several proteins, including DICER-LIKE1 (DCL1), the double stranded RNA binding protein HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). It has been noted before that the morphological appearance of weak se mutants is reminiscent of plants with mutations in ABH1/CBP80 and CBP20, which encode the two subunits of the nuclear cap-binding complex. We report that, like SE, the cap-binding complex is necessary for proper processing of pri-miRNAs. Inactivation of either ABH1/CBP80 or CBP20 results in decreased levels of mature miRNAs accompanied by increased levels of pri-miRNAs. Whole genome tiling array analyses reveal that se, abh1/cbp80 and cbp20 mutants also share similar pre-mRNA splicing defects, leading to the accumulation of many partially spliced transcripts. This is unlikely to be an indirect consequence of improper miRNA processing or other mRNA turnover pathways, since introns retained in se, abh1/cbp80 and cbp20 mutants are not affected by mutations in other genes required for miRNA processing or for non-sense-mediated mRNA decay. Taken together, our results uncover dual roles in splicing and miRNA processing that distinguish SE and the cap-binding complex from specialized miRNA processing factors such as DCL1 and HYL1. Keywords: Tiling array analysis of RNA populations from wild type, se, abh1 and cbp20 mutants

2008-05-01 | GSE11043 | GEO

Transcription profiling of wild type and serrate-1 mutant Arabidopsis seedlings to investigate regulation of miRNA levels

Project description:microRNAs function as sequence-specific guides to regulate genes by post-transcriptional gene silencing. Many miRNAs are involved in the control plant development by regulating the accumulation of transcripts encoding transcription factors. This causes pleiotropic developmental phenotypes of mutants defective in miRNA accumulation, such as dcl1, hen1, hyl1 and ago1. The serrate-1 (se-1) mutant of Arabidopsis also exhibits a highly pleiotropic phenotype which overlaps with phenotypes of mutants defective in miRNA accumulation. It has been proposed that SE functions specifically in miRNA-mediated repression of the leaf polarity genes PHABULOSA and PHAVOLUTA. Microarray analysis of transcript levels in se-1 compared to wild-type however revealed upregulation of many genes known to be targets of miRNA regulation. We show that SE is a general regulator of miRNA levels probably controlling processing of pri-miRNA to miRNA.

2006-09-18 | E-MEXP-838 | biostudies-arrayexpress

PRP4KA phosphorylates Serrate/Ars2 for degradation vs 20S proteasome to fine-tune RNA processing

Project description:We examined global expression profiles of 3-week-old prp4k3(amiR-PRP4K3) leaves compared to Col-0 using illumina sequencing. PRP4KA and its paralogs interact with Serrate (SE), a key factor in miRNA metabolism.phosphorylation of SE via PRP4KA can quickly clear accumulated SE to secure its proper amount. This study provides new insight into how protein phosphorylation regulates RNA metabolism through controlling homeostasis of SE accumulation in miRNA metabolism.

2021-12-20 | GSE190831 | GEO

Serrate modulates N6-Methyladenosine (m6A) RNA modification in Arabidopsis

Project description:N6-methyladenosine (m6A) is the most common prevalent internal modifications found in many of the eukaryotic mRNA and plays an important role in RNA metabolism including pre-mRNA processing, mRNA stability, RNA splicing, RNA export and nuclear retention. Serrate is a component of the Dicer complex, plays as a key factor in RNA metabolism. We here reported SERRATE acts as a key regulator of mRNA m6A modification in Arabidopsis. Loss function of SE results in significant global m6A level reduction in the se-1 mutant comparing to the Col-0. SE positively regulates the transcription of MTA and MTB. In addition, SE physically interacts and functionally works with the m6A writer complex MTA and MTB which affects the binding of m6A methylase to mRNA. Taking together, our data provides a molecular framework that SE modulates m6A mRNA modification in Arabidopsis.

2023-11-01 | GSE241248 | GEO

ChipSeq of Twist1 and YY1 in PLC-PRF-5 cells

Project description:Epithelial–mesenchymal transition (EMT) is an important mechanism of metastasis and malignant progression of hepatocellular carcinoma (HCC). However, the transcriptional regulation mechanism of EMT remains poorly understood. Some transcriptional co-activators can form phase-separated condensates at super-enhancers that compartmentalize and concentrate the transcription apparatus to drive robust gene expression. Here, we demonstrate that Twist1 and YY1, interact with p300 and form phase-separated local high-concentration interaction hubs at super-enhancers of miRNA-9 and activate its expression to induce EMT and promote the malignant evolution of HCC. Phase separation disrupted by metformin perturbs Twist–YY1 condensates, thereby inhibiting EMT. To explore how the Twist1 complex regulates miR-9 expression by binding SE region, we performed Twist1 ChIP-seq combined with H3K4me3, H3K4me1, H3K27ac, DNAse, p300, and YY1 ChIP-seq data to detect the SEs of miR-9. After metformin treatment, the peak of Twist1/YY1 on miR-9 SE decreased. Metformin specifically affects the binding of Twist1/YY1 to the miR-9 SE region. 1,6-hexanediol, as an aliphatic alcohol, can weaken hydrophobic interactions and inhibit liquid–liquid phase separation by disrupting hydrophobic interactions. In order to prove Twist1/YY1 interaction at these sites requires phase separation, we detect the accessibility of miR-9 SE regions in 1,6-hexanediol-treated cells. The result showed a general decrease in the accessibility of miR-9 super-enhancer regions in 1,6-hexanediol-treated cells and Twist1 / YY1 combines the SE region of miR-9 in the form of phase separation.

2019-12-13 | GSE141965 | GEO

ATAC-seq profiling of open chromatin in PLC-PRF cells

2019-12-13 | GSE141964 | GEO

Linking Key Steps of MicroRNA Biogenesis by TREX-2 and the Nuclear Pore Complex in Arabidopsis [mRNA-Seq]

Project description:Unlike in metazoans, the stepwise biogenesis of microRNAs (miRNAs) occurs within the nucleus in plants. Whether or how the major steps in miRNA biogenesis are coordinated is largely unknown. Here, we show that the plant TREX-2 complex promotes multiple steps in miRNA biogenesis, including transcription, processing and nuclear export. Core subunits of TREX-2, THP1 and SAC3A, interact and co-localize with RNA Polymerase II to promote the transcription of MIR genes in the nucleoplasm. TREX-2 interacts with the microprocessor component SERRATE and promotes the formation of Dicing bodies in the nucleoplasm. THP1 also interacts and co-localizes with a nucleoporin protein NUP1 at the nuclear envelope. NUP1 and THP1 promote the nuclear export of miRNAs and AGO1. These results suggest that TREX-2 coordinates the transcription, processing and export steps in miRNA biogenesis to ensure efficient miRNA production.

2020-08-07 | GSE150472 | GEO

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