Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-throughput SOLEXA sequencing of endogenous small RNAs from Arabidopsis thaliana wild-type

ABSTRACT: The length of Arabidopsis microRNA genes and their precursors (pri-miRNAs) can very between several hundreds bp to several thousands bp. They may contain introns, precursors may undergo alternative splicing, and often there are more than one polyadenylation site. An intriguing question arise: why to transcribe thousands of base pairs to produce a small RNA molecule of about 21 nt in length? We decided to sequence small RNAs from 35-day-old rosette leaves and to map the obtained reads of 18-26 nt in length to Arabidopsis pri-miRNAs. Our analyses revealed the presence of sRNAs that can derive only from miRNA precursors. An example is the identification of a substantial number of miR319b.2 reads. This sRNA is a product of pri-miR319b processing. Our further experimental analyses show that it carries multiple signatures of a functional microRNA

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE35335 | GEO | 2014/01/25

SECONDARY ACCESSION(S): PRJNA152651

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

High-throughput SOLEXA sequencing of endogenous small RNAs from Arabidopsis thaliana wild-type

Project description:The length of Arabidopsis microRNA genes and their precursors (pri-miRNAs) can very between several hundreds bp to several thousands bp. They may contain introns, precursors may undergo alternative splicing, and often there are more than one polyadenylation site. An intriguing question arise: why to transcribe thousands of base pairs to produce a small RNA molecule of about 21 nt in length? We decided to sequence small RNAs from 35-day-old rosette leaves and to map the obtained reads of 18-26 nt in length to Arabidopsis pri-miRNAs. Our analyses revealed the presence of sRNAs that can derive only from miRNA precursors. An example is the identification of a substantial number of miR319b.2 reads. This sRNA is a product of pri-miR319b processing. Our further experimental analyses show that it carries multiple signatures of a functional microRNA 2 samples examined: wild type

2014-01-25 | E-GEOD-35335 | biostudies-arrayexpress

A quantitative map of human primary microRNA processing sites

Project description:Maturation of canonical microRNA (miRNA) is initiated by DROSHA that cleaves the primary transcript (pri-miRNA). Over 1,800 miRNA loci are annotated in humans, but it remains largely unknown if and at which sites the pri-miRNAs are cleaved by DROSHA. Here we performed in vitro processing on a full set of human pri-miRNAs (miRBase v21) followed by sequencing. This comprehensive profiling enabled us to classify miRNAs based on DROSHA-dependence and map their cleavage sites with respective processing efficiency measures. Only 758 pri-miRNAs are confidently processed by DROSHA, while the majority may be non-canonical or false entries. Analyses of the DROSHA-dependent pri-miRNAs show key cis-elements for processing. We observe widespread alternative processing as well as unproductive cleavage events such as “nick” or “inverse” processing. SRSF3 is a broad-acting auxiliary factor modulating alternative processing and suppressing unproductive processing. The profiling data and methods developed in this study will allow systematic analyses of miRNA regulation.

2021-07-28 | PXD025767 | Pride

RACK1 function in the miRNA pathway

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

Spliceosome disassembly factors ILP1 and NTR1 promote microRNA biogenesis in Arabidopsis

Project description:A battery of spliceosome-associated proteins has been identified in microRNA (miRNA) biogenesis; however, the underlying mechanisms remain elusive. The intron lariat spliceosome (ILS) complex is highly conserved among eukaryotes and its disassembly marks the end of a canonical splicing cycle. In this study, we show that two conserved disassembly factors of the ILS complex, ILP1 and NTR1, positively regulate microRNA biogenesis through facilitating transcriptional elongation in Arabidopsis. ILP1 and NTR1 form a stable complex and co-regulate alternative splicing of more than a hundred genes across the genome including the core circadian gene LHY and some pri-miRNAs. Dysfunction in either ILP1 or NTR1 result in reduced RNA polymerase II occupancy at elongated regions of MIR chromatins, without affecting MIR promoter activity, pri-miRNA decay and DCL1 processing. Our results provide insights into the molecular mechanisms of spliceosomal machineries in non-coding RNA regulation.

2019-11-12 | PXD011542 | Pride

Transcriptome-wide identification of small RNA targets in rice

Project description:MicroRNA (miRNA)-guided target RNA expression is vital for a wide variety of biological processes in eukaryotes. The integration of miRNAs in diverse biological networks relies upon the confirmation of their RNA targets. Most miRNA targets in Arabidopsis are validated, but those in rice are yet to be characterized. To identify transcriptome-wide small RNA targets in rice, we generated 20-nt small cDNA library and obtained nearly 40 million reads. Sequence analysis yielded 11,552,007 unique reads that can be perfectly mapped to the rice genome. Sequence analysis not only found homologous targets for conserved miRNAs but also many novel targets. Besides miRNA atregts, the rice degradome contained fragments derived from MIRNA precursors. A closer inspection of these fragments revealed a unique pattern distinct from siRNA producing loci. This attribute can serve as one of the ancillary criteria for separating miRNAs from siRNAs in plants. Keywords: high throughout sequencing of rice degradome Identify transcriptome-wide small RNA targets in rice

2010-05-03 | E-GEOD-17398 | biostudies-arrayexpress

Transcriptome-wide identification of small RNA targets in rice

2010-05-04 | GSE17398 | GEO

The high-throughput cleavage assays on 137 C.elegans pri-miRNAs

Project description:Microprocessor (MP), cleaving primary microRNAs (pri-miRNAs) to initiate the biogenesis of thousands of miRNAs, was discovered in animals in 2004. Understanding the molecular mechanism of MP is critical for interpreting the gene-silencing roles of miRNAs in various cellular processes and human diseases. Though the molecular mechanism of human MP (hMP) has been comprehensively investigated for nearly two decades and is well understood, that of Caenorhabditis elegans MP (cMP, cDrosha-Pasha complex) is still unknown. In this study, we revealed a comprehensive molecular mechanism of cMP, distinctively from that of hMP. In the proposed mechanism, cDrosha and Pasha (DGCR8 in humans) measure ~16 bp and ~25 bp of the pri-miRNA stem, respectively, and they are coordinated in determining cleavage sites of cMP in pri-miRNAs. In addition, we also demonstrated the molecular basis for their substrate measurement. Our findings illustrate an unknown molecular mechanism of cMP, clarify differences between the mechanism of hMP and cMP, and provide a foundation for understanding multiple mechanisms regulating miRNA expression acting on cMP.

2023-01-23 | GSE212229 | GEO

MicroRNA expression profile of bovine monocyte derived macrophages infected with Mycobacterium avium subsp. Paratuberculosis

Project description:In order to gain a better understanding of MAP infection in immature macrophages, high-throughput sequencing technology was used to perform an analysis of miRNAs profiles of bovine monocyte derived macrophages upon MAP infection.The total numbers of raw reads collected from the MAP-infected and control MDM cells were 14.3 and 17.0 million raw reads per library.The length distribution of the clean reads was focused on 21–24 nt in length and read counts of 22 nt were highest.A total of 510 mature miRNAs were identified, among these a total of 433 miRNAs were homologous to bovine, while 77 were predicted as novel miRNAs that not homologous to any species.The analyses of differential expression revealed 21 DE miRNAs in MDM challenged with MAP compared to the control MDM, Among the DE miRNAs, 14 were upregulated and 7 were downregulated.Furthermore, The GO and KEGG pathway enrichment of these miRNA targets were performed.

2019-04-16 | GSE129819 | GEO

SWI/SNF subunit CHR2 remodels pri-miRNAs via microprocessor component SE to inhibit miRNA production (miRNA-Seq)

Project description:We performed Illumina sequencing of sRNA libraries prepared from leaves of adult plants in Arabidopsis. Chromatin remodeling factor 2 (CHR2) positively regulates transcription of MIR loci whereas repressing microRNA (miRNA) accumulation in vivo. CHR2 can directly bind to and unwind primary miRNAs (pri-miRNAs) and inhibit their processing; and this inhibition entails its remodeling activity in vitro and in vivo.

2018-05-18 | GSE108858 | GEO

Construction and characterization of synthetic microRNA cluster for multiplex RNA interference in mammalian cells

Project description:RNA interference (RNAi) technology is widely used in basic and translational research. By mimicking natural primary microRNA (pri-miRNA) cluster, multiple engineered hairpins can be transcribed as a single transcript from the same Pol-II promoter, enabling multiplex RNAi in mammalian cells 1-5. However, constructing synthetic miRNA cluster is still time-consuming, and the processing and function of miRNA cluster are incompletely understood. Here, we identified a miRNA precursor architecture that allowed precise miRNA maturation. We established a hierarchical cloning method for efficient construction of synthetic miRNA cluster harboring up to 18 miRNA precursors. We demonstrated that maturation and function of individual miRNA precursors were independent on their positions in the cluster. We then analyzed the integration efficiency of miRNA clusters with varying number of miRNA precursors by using CRISPR/Cas9 mediated integration, piggyBac transposon system, and lentiviral system. This synthetic miRNA cluster system provides an important tool for multiplex RNAi in mammalian cells. Different kinds of synthetic miRNAs or miRNA clusters, including the same synthetic miRNA precursor embedded in a series of derivative backbones, 18 synthetic miRNA precursors, miRNA precursors with various stem lengths and miRNA clusters carrying different numbers of different pri-miRNA hairpins, were expressed in HEK293 cells. The microRNA maturation pattern of individual miRNA precursors was detected by small RNA sequencing.

2016-09-01 | E-GEOD-71088 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data