Understanding the structure/sequence preference of plant miRNA biogenesis machinery
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana tabacum
PROVIDER: GSE99094 | GEO | 2017/07/15
SECONDARY ACCESSION(S): PRJNA387281
REPOSITORIES: GEO
Similar Datasets
Project description:MicroRNAs (miRNAs) regulate plant development by post-transcriptional regulation of target genes. In Arabidopsis thaliana, DCL1 processes precursors (pri-miRNAs) to miRNA duplexes, which associate with AGO1. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) or AGO1, respectively, to facilitate efficient and precise pri-miRNA processing and miRNA loading. In this study, we show that the accumulation of plant microRNAs depends on RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), a scaffold protein found in all higher eukaryotes. miRNA levels are reduced in rack1 mutants and our data suggest that RACK1 affects the microRNA pathway via several distinct mechanisms involving direct interactions with known microRNA factors: RACK1 ensures the accumulation and processing of some pri-miRNAs, directly interacts with SERRATE and is part of an AGO1 complex. As a result, mutations in RACK1 lead to misregulation of miRNA target genes, which is important for ABA responses and phyllotaxy. In conclusion, our study discovered complex functioning of RACK1 proteins in the Arabidopsis miRNA pathway, which are important for miRNA production and therefore plant development.
2013-07-01 | GSE40579 | GEO
Project description:MicroRNAs (miRNAs) are processed from longer precursors with fold-back structures. While animal MIRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach (SPARE) to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the evolutionary conserved miRNAs present in Arabidopsis thaliana. We found that plant MIRNAs are processed by four mechanisms, depending on the sequential direction of the processing machinery and the number of cuts required to release the miRNA. Classification of the precursors according to their processing mechanism revealed specific structural determinants for each group. We found that the complexity of the miRNA processing pathways occurs in both ancient and evolutionary young sequences, and that members of the same family can be processed in different ways. We observed that different structural determinants compete for the processing machinery and that alternative miRNAs can be generated from a single precursor. The results provide a mechanistic explanation for the structural diversity of MIRNA precursors in plants and new insights towards the understanding of the biogenesis of small RNAs. Approach to systematically analyze miRNA processing intermediates and characterize the biogenesis of conserved and young miRNAs present in Arabidopsis thaliana. MiRNA processing intermediates profiles of Wild type and Fiery mutants Arabidopsis plants were analyzed, using Illumina GAIIx.
2013-06-12 | E-GEOD-46429 | biostudies-arrayexpress
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
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 | GSE150471 | GEO
Project description:MicroRNAs (miRNAs) are processed from longer precursors with fold-back structures. While animal MIRNA precursors have homogenous structures, plant precursors comprise a collection of fold-backs with variable size and shape. Here, we design an approach (SPARE) to systematically analyze miRNA processing intermediates and characterize the biogenesis of most of the evolutionary conserved miRNAs present in Arabidopsis thaliana. We found that plant MIRNAs are processed by four mechanisms, depending on the sequential direction of the processing machinery and the number of cuts required to release the miRNA. Classification of the precursors according to their processing mechanism revealed specific structural determinants for each group. We found that the complexity of the miRNA processing pathways occurs in both ancient and evolutionary young sequences, and that members of the same family can be processed in different ways. We observed that different structural determinants compete for the processing machinery and that alternative miRNAs can be generated from a single precursor. The results provide a mechanistic explanation for the structural diversity of MIRNA precursors in plants and new insights towards the understanding of the biogenesis of small RNAs.
2013-06-12 | GSE46429 | GEO
Project description:Many evolutionarily conserved miRNAs in plants regulate transcription factors with key functions in plant development. Hence, mutations in core components of the miRNA biogenesis machinery causes strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from an arm of the fold-back precursor. Defects in the selection of the correct miRNA sequence will ultimately affect miRNA target specificity, plant development and other processes controlled by these small RNAs. Intriguingly, plant miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized genomic approaches to detect processing intermediates during miRNA biogenesis. We identified and characterized an endogenous miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes suggesting intrinsic differences between miRNA biogenesis pathways. Despite the various potential structural determinants present in a single a miRNA precursor, we found that DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, genomic studies of miRNA processing intermediates in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative or cryptic processing determinants in miRNA precursors. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.
2018-09-11 | GSE112632 | GEO
Project description:Many evolutionarily conserved miRNAs in plants regulate transcription factors with key functions in plant development. Hence, mutations in core components of the miRNA biogenesis machinery causes strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from an arm of the fold-back precursor. Defects in the selection of the correct miRNA sequence will ultimately affect miRNA target specificity, plant development and other processes controlled by these small RNAs. Intriguingly, plant miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized genomic approaches to detect processing intermediates during miRNA biogenesis. We identified and characterized an endogenous miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes suggesting intrinsic differences between miRNA biogenesis pathways. Despite the various potential structural determinants present in a single a miRNA precursor, we found that DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, genomic studies of miRNA processing intermediates in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative or cryptic processing determinants in miRNA precursors. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.
2018-09-11 | GSE116330 | GEO
Project description:MicroRNAs (miRNAs) regulate different aspects of plant development by post-transcriptional regulation of target genes. In Arabidopsis, DICER-LIKE 1 (DCL1) processes miRNA precursors (pri-miRNAs) to miRNA duplexes, which associate with ARGONAUTE 1 (AGO1). AGO1 together with the miRNA guide strand binds complementary RNA sequences within target mRNAs. Additional proteins act in concert with DCL1 (e.g. HYL1 and SERRATE) and AGO1, respectively, to facilitate efficient and precise pri-miRNA processing and loading into the effector protein. Here, we show that RECEPTOR OF ACTIVATED C KINASE 1 (RACK1) is a novel component of the Arabidopsis miRNA pathway. RACK1 is a seven-bladed WD-repeat protein that has previously been shown to act as a scaffold protein mediating multiple simultaneous protein-protein interactions. Our molecular analyses demonstrate that RACK1 function is required for controlling miRNA-mediated gene expression. rack1 mutants contain only low levels of mature miRNAs without affecting the first step of pri-miRNA processing. Physical and genetic interaction studies revealed that RACK1 acts in concert with AGO1 and also interacts with a SERRATE, a component of the miRNA processing machinery. These results suggest that RACK1 also functions as a scaffold protein in the miRNA pathway to orchestrates miRNA maturation steps after the initial events of pri-miRNA processing. sequencing of small RNAs from WT and rack1abc mutants (two biological replicates each)
2013-07-01 | E-GEOD-40579 | biostudies-arrayexpress
Project description:During microRNA-biogenesis, stem-loop structured precursors are processed in two endonucleolytic steps, giving rise to mature microRNAs (miRNAs). This process is not only regulated at the level of transcription but also posttranscriptionally by RNA-binding proteins (RBPs). Here we have used a proteomics-based pull-down approach to map and characterize the interactome of 72 pre-miRNAs in eleven cell lines. We identify over 150 RBPs that interact specifically with distinct pre-miRNAs. To demonstrate their functional relevance, we used RNAi knockdown and CRISPR/Cas-mediated knockout experiments and analyzed changes in miRNA levels. Indeed, a large number of the investigated candidates have effects on miRNA-processing under our experimental conditions, including several C3H-zinc-finger proteins. Ultimately, we show that TRIM71/Lin41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. In summary, we provide an extended database of RBPs that interact with pre-miRNAs in different cell types helping to elucidate posttranscriptional regulation of miRNA biogenesis on a global scale.
2017-04-26 | PXD004193 | Pride
Project description:Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the cold treatment of tea leaves. Subsequently, aligning these sequencing date with plant known miRNAs, we characterized 112 C. sinensis conserved miRNAs. In addition, 215 potential candidate miRNAs were found; among them, 131 candidates with star sequence were chosen as novel miRNAs. There are both congruously and differently regulated miRNAs, and line-specific miRNAs were identified by microarray-based hybridization in response to cold stress. The miRNA chip included 3228 miRNA probes corresponding to miRNA transcripts listed in Sanger miRBase release 19.0 and 283 novel miRNAs probes founding in tea plant.
2015-05-14 | GSE53632 | GEO