Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiple RNA recognition patterns during microRNA biogenesis in plants

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE46429 | GEO | 2013/06/12

SECONDARY ACCESSION(S): PRJNA200315

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Multiple RNA recognition patterns during microRNA biogenesis in plants

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

Specific Parallel Analysis of RNA Ends

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

Small RNA libraries

2018-09-11 | GSE116330 | GEO

A compendium of RNA-binding proteins that regulate microRNA biogenesis

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

Understanding the structure/sequence preference of plant miRNA biogenesis machinery

Project description:MicroRNAs (miRNAs) are ~21nt long endogenous non-coding RNAs that are involved in post-transcriptional silencing of target mRNAs. miRNAs are processed from precursors having a stem-loop structure that are recognized and cleaved by Dicer-like 1 (DCL1) with the help of dsRNA binding protein Hyponastic leaves 1 (HYL1) and a zinc finger protein named Serrate (SE). Plant miRNA stem-loops are very diverse in length and structure than animal miRNAs. Hence, mechanism of miRNA biogenesis from their precursors is poorly understood. Our bioinformatic analysis predicted that plant miRNAs have unique sequence signature. An artificial precursor with different predicted sequence signatures was constructed. This construct was expressed transiently in tobacco leaves and small RNAs were sequenced. Our analysis revealed that indeed the predicted sequence signature is prefered by plant miRNA biogenesis machinery.

2017-07-15 | GSE99094 | GEO

The helicase domain of Dicer ensures strict processing of evolutionarily optimized microRNAs

Project description:Ribonuclease Dicer generates small RNAs for RNA interference (RNAi) and microRNA (miRNA) pathways. Mammalian Dicer produces miRNAs but its tripartite N-terminal helicase domain inhibits processing of double-stranded RNA for RNAi. Mouse oocytes express Dicer, which enhances RNAi because it lacks the helicase’s proximal subdomain HEL1. Here we show that genetic removal of HEL1 in mice causes embryonic growth retardation, defects in the cardiopulmonary system, and perinatal lethality. HEL1 suppresses biogenesis of mirtrons, a non-canonical low-abundant class of miRNAs, and is required for high-fidelity cleavage and strand selection during biogenesis of canonical miRNAs. Essential is the HEL1 structure, not its helicase activity, because mutations of critical aminoacids do not affect viability or fertility and have minimal impact on miRNA biogenesis. Altogether, HEL1 is a critical structural component of Dicer in its role of a highly conserved structural “mold” that ensures high-fidelity processing and adaptive evolution of mammalian miRNA precursors.

2024-04-10 | GSE243016 | GEO

The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice

Project description:Dicer ribonucleases, which generate small RNAs for the RNA interference (RNAi) and microRNA (miRNA) pathways, often have an N-terminal DExD helicase subdomain (also called HEL1). In the mammalian Dicer, HEL1 inhibits RNAi while it appears unnecessary for miRNA biogenesis. To determine its functional significance, we genetically eliminated HEL1 from Dicer in mice. We observed embryonic growth retardation, defects in the cardiopulmonary system, and perinatal lethality. HEL1 suppresses biogenesis of mirtrons, a non-canonical low-abundant class of miRNAs, and is required for high-fidelity cleavage and strand selection during biogenesis of canonical miRNAs. The HEL1 domain itself is essential rather than its helicase activity, because mutations of critical catalytic amino acids do not affect mouse viability or fertility and have minimal impact on miRNA biogenesis. Therefore, HEL1 is a critical structural component of the mammalian Dicer, supporting its role of a conserved structural “mold” that ensures high-fidelity processing and adaptive evolution of mammalian miRNA precursors.

2022-11-03 | GSE196310 | GEO

The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice

2022-11-03 | GSE196309 | GEO

The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice

2022-11-03 | GSE196308 | GEO

The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice

2022-11-03 | GSE196306 | GEO