scholarly journals KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1

2015 ◽  
Vol 112 (45) ◽  
pp. 14096-14101 ◽  
Author(s):  
Patricia Karlsson ◽  
Michael Danger Christie ◽  
Danelle K. Seymour ◽  
Huan Wang ◽  
Xi Wang ◽  
...  
Keyword(s):  
Mirna Target ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Mirna Biogenesis ◽  
Plant Tissues ◽  
Double Stranded Rna ◽  
Plant Mirna ◽  
Kh Domain ◽  
Domain Protein ◽  
Processing Steps

The biogenesis of microRNAs (miRNAs), which regulate mRNA abundance through posttranscriptional silencing, comprises multiple well-orchestrated processing steps. We have identified the Arabidopsis thaliana K homology (KH) domain protein REGULATOR OF CBF GENE EXPRESSION 3 (RCF3) as a cofactor affecting miRNA biogenesis in specific plant tissues. MiRNA and miRNA-target levels were reduced in apex-enriched samples of rcf3 mutants, but not in other tissues. Mechanistically, RCF3 affects miRNA biogenesis through nuclear interactions with the phosphatases C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 and 2 (CPL1 and CPL2). These interactions are essential to regulate the phosphorylation status, and thus the activity, of the double-stranded RNA binding protein and DICER-LIKE1 (DCL1) cofactor HYPONASTIC LEAVES1 (HYL1).

scholarly journals Hyponastic Leaves 1 protects pri-miRNAs from nuclear exosome attack

2020 ◽  
Vol 117 (29) ◽  
pp. 17429-17437
Author(s):  
Shuai Gao ◽  
Jingyu Wang ◽  
Ning Jiang ◽  
Shiting Zhang ◽  
Yuan Wang ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Protein ◽  
Mature Mirnas ◽  
Mirna Biogenesis ◽  
Dual Roles ◽  
Antagonistic Action ◽  
Additional Function ◽  
Double Stranded Rna ◽  
Passenger Strand ◽  
Nuclear Exosome

Biogenesis of plant microRNAs (miRNAs) takes place in nuclear dicing bodies (D-bodies), where the ribonulease III-type enzyme Dicer-like 1 (DCL1) processes primary transcripts of miRNAs (pri-miRNAs) into miRNA/miRNA* (*, passenger strand) duplexes from either base-to-loop or loop-to-base directions. Hyponastic Leaves 1 (HYL1), a double-stranded RNA-binding protein, is crucial for efficient and accurate processing. However, whether HYL1 has additional function remains unknown. Here, we report that HYL1 plays a noncanonical role in protecting pri-miRNAs from nuclear exosome attack in addition to ensuring processing. Loss of functions in SOP1 or HEN2, two cofactors of the nucleoplasmic exosome, significantly suppressed the morphological phenotypes ofhyl1-2. Remarkably, mature miRNAs generated from loop-to-base processing were partially but preferentially restored in thehyl1 sop1andhyl1 hen2double mutants. Accordingly, loop-to-base–processed pri-miRNAs accumulated to higher levels in double mutants. In addition, dysfunction of HEN2, but not of SOP1, inhyl1-2resulted in overaccumulation of many base-to-loop–processed pri-miRNAs, with most of their respective miRNAs unaffected. In summary, our findings reveal an antagonistic action of exosome in pri-miRNA biogenesis and uncover dual roles of HYL1 in stabilizing and processing of pri-miRNAs.

scholarly journals DRB1 as a mediator between transcription and microRNA processing

2019 ◽  
Author(s):  
Dawid Bielewicz ◽  
Jakub Dolata ◽  
Mateusz Bajczyk ◽  
Lukasz Szewc ◽  
Tomasz Gulanicz ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Mirna Biogenesis ◽  
Transcriptional Level ◽  
Core Component ◽  
Double Stranded Rna ◽  
Mirna Processing ◽  
It Impacts ◽  
Microrna Processing

AbstractDRB1 (HYL1) is a double-stranded RNA binding protein involved in miRNA processing in plants. It is a core component of the Microprocessor complex and enhances the efficiency and precision of miRNA processing by DCL1 protein. In this work, we report a novel function of DRB1 protein in the transcription of MIR genes. DRB1 co-localizes with RNA Polymerase II and affects its distribution along MIR genes. Moreover, proteomic experiments revealed that DRB1 protein interacts with many transcription factors. Finally, we show that the action of DRB1 is not limited to MIR genes as it impacts expression of many other genes, majority of which are involved in plant response to light. These discoveries add DRB1 as another player of gene regulation at transcriptional level, independent of its role in miRNA biogenesis.

scholarly journals Cellular functions of the microprocessor

2013 ◽  
Vol 41 (4) ◽  
pp. 838-843 ◽  
Author(s):  
Sara Macias ◽  
Ross A. Cordiner ◽  
Javier F. Cáceres
Keyword(s):  
Digeorge Syndrome ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Mirna Biogenesis ◽  
Cross Linking ◽  
Cellular Functions ◽  
Rnase Iii ◽  
Double Stranded Rna ◽  
Functional Roles

The microprocessor is a complex comprising the RNase III enzyme Drosha and the double-stranded RNA-binding protein DGCR8 (DiGeorge syndrome critical region 8 gene) that catalyses the nuclear step of miRNA (microRNA) biogenesis. DGCR8 recognizes the RNA substrate, whereas Drosha functions as an endonuclease. Recent global analyses of microprocessor and Dicer proteins have suggested novel functions for these components independent of their role in miRNA biogenesis. A HITS-CLIP (high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation) experiment designed to identify novel substrates of the microprocessor revealed that this complex binds and regulates a large variety of cellular RNAs. The microprocessor-mediated cleavage of several classes of RNAs not only regulates transcript levels, but also modulates alternative splicing events, independently of miRNA function. Importantly, DGCR8 can also associate with other nucleases, suggesting the existence of alternative DGCR8 complexes that may regulate the fate of a subset of cellular RNAs. The aim of the present review is to provide an overview of the diverse functional roles of the microprocessor.

scholarly journals MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities

2020 ◽  
Vol 117 (38) ◽  
pp. 23982-23990 ◽  
Author(s):  
Shengjun Li ◽  
Mu Li ◽  
Kan Liu ◽  
Huimin Zhang ◽  
Shuxin Zhang ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Protein ◽  
Dual Role ◽  
Mirna Biogenesis ◽  
Core Component ◽  
Stem Loop ◽  
Loop Region ◽  
Nuclear Rna ◽  
Efficient Processing ◽  
The Stability

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels inmac5is partially caused by XRN2/XRN3, the nuclear-localized 5′-to-3′ exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.

scholarly journals Cytoplasmic Granule Formation and Translational Inhibition of Nodaviral RNAs in the Absence of the Double-Stranded RNA Binding Protein B2

2013 ◽  
Vol 87 (24) ◽  
pp. 13409-13421 ◽  
Author(s):  
J. E. Petrillo ◽  
P. A. Venter ◽  
J. R. Short ◽  
R. Gopal ◽  
S. Deddouche ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cytoplasmic Granule ◽  
Granule Formation ◽  
Double Stranded Rna ◽  
Translational Inhibition

Nuclear Localization of a Double-Stranded RNA-Binding Protein Encoded by the Vaccinia Virus E3L Gene

Virology ◽  
1993 ◽  
Vol 195 (2) ◽  
pp. 732-744 ◽  
Author(s):  
Hao Yuwen ◽  
Josephine H. Cox ◽  
Jonathan W. Yewdell ◽  
Jack R. Bennink ◽  
Bernard Moss
Keyword(s):  
Vaccinia Virus ◽  
Nuclear Localization ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Double Stranded Rna

scholarly journals NF90 modulates processing of a subset of human pri-miRNAs

2020 ◽  
Vol 48 (12) ◽  
pp. 6874-6888
Author(s):  
Giuseppa Grasso ◽  
Takuma Higuchi ◽  
Victor Mac ◽  
Jérôme Barbier ◽  
Marion Helsmoortel ◽  
...  
Keyword(s):  
Rna Binding ◽  
Mirna Biogenesis ◽  
Biological Processes ◽  
Mobility Shift ◽  
Double Stranded Rna ◽  
Genome Wide ◽  
Mammalian Genes ◽  
Mobility Shift Assay ◽  
Host Genes ◽  
Stable Structures

Abstract MicroRNAs (miRNAs) are predicted to regulate the expression of >60% of mammalian genes and play fundamental roles in most biological processes. Deregulation of miRNA expression is a hallmark of most cancers and further investigation of mechanisms controlling miRNA biogenesis is needed. The double stranded RNA-binding protein, NF90 has been shown to act as a competitor of Microprocessor for a limited number of primary miRNAs (pri-miRNAs). Here, we show that NF90 has a more widespread effect on pri-miRNA biogenesis than previously thought. Genome-wide approaches revealed that NF90 is associated with the stem region of 38 pri-miRNAs, in a manner that is largely exclusive of Microprocessor. Following loss of NF90, 22 NF90-bound pri-miRNAs showed increased abundance of mature miRNA products. NF90-targeted pri-miRNAs are highly stable, having a lower free energy and fewer mismatches compared to all pri-miRNAs. Mutations leading to less stable structures reduced NF90 binding while increasing pri-miRNA stability led to acquisition of NF90 association, as determined by RNA electrophoretic mobility shift assay (EMSA). NF90-bound and downregulated pri-miRNAs are embedded in introns of host genes and expression of several host genes is concomitantly reduced. These data suggest that NF90 controls the processing of a subset of highly stable, intronic miRNAs.

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