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SERRATE recruits the NEXT complex to control the levels of miRNA precursors in Arabidopsis

ABSTRACT: SERRATE recruits the NEXT complex to control the levels of miRNA precursors in Arabidopsis

PROVIDER: PRJNA543989 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11296925_1.fastq.gz	Fastqsanger.gz
	SRR11296925_2.fastq.gz	Fastqsanger.gz
	SRR11296926_1.fastq.gz	Fastqsanger.gz
	SRR11296926_2.fastq.gz	Fastqsanger.gz
	SRR11296927_1.fastq.gz	Fastqsanger.gz

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SERRATE recruits the NEXT complex to control the levels of miRNA precursors in Arabidopsis

Project description:total RNA from plant tissues was performed followed by sequencing of NGS libraries

2020-07-20 | GSE131542 | GEO

SERRATE interacts with the nuclear exosome targeting (NEXT) complex to degrade primary miRNA precursors in Arabidopsis.

Project description:SERRATE/ARS2 is a conserved RNA effector protein involved in transcription, processing and export of different types of RNAs. In Arabidopsis, the best-studied function of SERRATE (SE) is to promote miRNA processing. Here, we report that SE interacts with the nuclear exosome targeting (NEXT) complex, comprising the RNA helicase HEN2, the RNA binding protein RBM7 and one of the two zinc-knuckle proteins ZCCHC8A/ZCCHC8B. The identification of common targets of SE and HEN2 by RNA-seq supports the idea that SE cooperates with NEXT for RNA surveillance by the nuclear exosome. Among the RNA targets accumulating in absence of SE or NEXT are miRNA precursors. Loss of NEXT components results in the accumulation of pri-miRNAs without affecting levels of miRNAs, indicating that NEXT is, unlike SE, not required for miRNA processing. As compared to se-2, se-2 hen2-2 double mutants showed increased accumulation of pri-miRNAs, but partially restored levels of mature miRNAs and attenuated developmental defects. We propose that the slow degradation of pri-miRNAs caused by loss of HEN2 compensates for the poor miRNA processing efficiency in se-2 mutants, and that SE regulates miRNA biogenesis through its double contribution in promoting miRNA processing but also pri-miRNA degradation through the recruitment of the NEXT complex.

| S-EPMC7337926 | biostudies-literature

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

Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

Project description:Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions play important roles in key biological processes.Analysis of published transcriptom datasets suggested some lincRNAs may be regulated by SERRATE,CBP20 and CBP80 in Arabidopsis. To further investigate the regulation, we use Arabidopsis lincRNA arrays v1 to detect lincRNA expression in se-2 and cbp20/80 double mutants.We found the expression levels of 940 lincRNAs (20%) out of the 4,634 lincRNAs with probes in array were significantly alerted in all mutants (P-value of eBays ANOVA < 0.05 & fold change of signal intensity > 2). This group included 525 up-regulated and 415 down-regulated lincRNAs. Seedlings(Col-0), Seedlings(se-2), Seedlings(cbp20,80 double mutant) x 3 biological replicates

2012-09-29 | E-GEOD-35963 | biostudies-arrayexpress

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

Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

2012-09-29 | GSE35963 | GEO

mRNA sequencing of wild type Columbia and serrate-1 globular stage embryos of Arabidopsis thaliana

Project description:Wild type Columbia and serrate-1 globular stage embryos were sequenced in order to profile miRNAs which are expressed in embryogenesis in Arabidopsis thaliana

2017-06-27 | GSE100450 | 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

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

| PRJNA1007576 | ENA