Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA115477 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR029054.fastq.gz | Fastqsanger.gz |
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Project description:Vault particles are conserved organelles that have been implicated in multidrug resistance and intracellular transport. They are formed by three different proteins and the non-coding vault RNAs (vRNAs). Here we show that human vRNAs produce several small RNAs (svRNAs) by mechanisms different from the canonical microRNA (miRNA) pathway. At least one of these svRNAs, we named svRNAb, associates with Argonaute proteins to guide sequence-specific cleavage and regulate gene expression in a manner similar to miRNAs. We demonstrate that svRNAb downregulates CYP3A4, a key enzyme in drug metabolism. Our findings expand the repertoire of small regulatory RNAs and assign, for the first time, a function to vRNAs that may help explain the observed association between vaults and drug resistance. Keywords: Transcriptome analysis Small RNAs 18-35 nt were isolated from MCF7 cell total RNA and sequenced on the Illumina Genome Analyzer
2009-09-07 | E-GEOD-16060 | biostudies-arrayexpress
Project description:Vault particles are conserved organelles that have been implicated in multidrug resistance and intracellular transport. They are formed by three different proteins and the non-coding vault RNAs (vRNAs). Here we show that human vRNAs produce several small RNAs (svRNAs) by mechanisms different from the canonical microRNA (miRNA) pathway. At least one of these svRNAs, we named svRNAb, associates with Argonaute proteins to guide sequence-specific cleavage and regulate gene expression in a manner similar to miRNAs. We demonstrate that svRNAb downregulates CYP3A4, a key enzyme in drug metabolism. Our findings expand the repertoire of small regulatory RNAs and assign, for the first time, a function to vRNAs that may help explain the observed association between vaults and drug resistance. Keywords: Transcriptome analysis
2009-09-08 | GSE16060 | GEO
Project description:Vault RNAs (vRNAs) are evolutionarily conserved small non-coding RNAs transcribed by RNA polymerase lll. Initially described as components of the vault particle, they have since also been described as noncanonical miRNA precursors and as riboregulators of autophagy. As central molecules in these processes, vRNAs have been attributed numerous biological roles including regulation of cell proliferation and survival, response to viral infections, drug resistance, and animal development. Yet, their impact to mammalian physiology remains largely unexplored. To study vault RNAs in vivo, we generated a mouse line with a conditional Vaultrc5 loss of function allele. Because Vaultrc5 is the sole murine vRNA, this allele enables the characterization of the physiological requirements of this conserved class of small regulatory RNAs in mammals. Using this strain, we show that mice constitutively null for Vaultrc5 are viable and histologically normal but have a slight reduction in platelet counts pointing to a potential role for vRNAs in hematopoiesis. This work paves the way for further in vivo characterizations of this abundant but mysterious RNA molecule. Specifically, it enables the study of the biological consequences of constitutive or lineage-specific Vaultrc5 deletion and of the physiological requirements for an intact Vaultrc5 during normal hematopoiesis or in response to cellular stresses such as oncogene expression, viral infection, or drug resistance.
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Project description:Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we adapted the individual-nucleotide resolution UV cross-linking and immunoprecipitation method (iCLIP) to identify NSun2-mediated methylation in RNA transcriptome. We confirm site-specific methylation in tRNA and identify messenger and non-coding RNAs as potential methylation targets for NSun2. Using RNA bisulfite sequencing we establish Vault non-coding RNAs as novel substrates for NSun2 and identified six cytosine-5 methylated sites. Furthermore, we show that loss of cytosine-5 methylation in Vault RNAs causes aberrant processing into argonaute-associating small RNA fragments (svRNA). Thus, impaired Vault non-coding RNA processing may be an important contributor to the etiology of NSUN2-deficieny human disorders. mRNA-seq in Embryonic kidney (HEK293) cells transfected with siRNA against Nsun2 vs control
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Project description:Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we adapted the individual-nucleotide resolution UV cross-linking and immunoprecipitation method (iCLIP) to identify NSun2-mediated methylation in RNA transcriptome. We confirm site-specific methylation in tRNA and identify messenger and non-coding RNAs as potential methylation targets for NSun2. Using RNA bisulfite sequencing we establish Vault non-coding RNAs as novel substrates for NSun2 and identified six cytosine-5 methylated sites. Furthermore, we show that loss of cytosine-5 methylation in Vault RNAs causes aberrant processing into argonaute-associating small RNA fragments (svRNA). Thus, impaired Vault non-coding RNA processing may be an important contributor to the etiology of NSUN2-deficieny human disorders.
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Project description:Autosomal-recessive loss of the NSUN2 gene has been recently identified as a causative link to intellectual disability disorders in humans. NSun2 is an RNA methyltransferase modifying cytosine-5 in transfer RNAs (tRNA). Whether NSun2 methylates additional RNA species is currently debated. Here, we adapted the individual-nucleotide resolution UV cross-linking and immunoprecipitation method (iCLIP) to identify NSun2-mediated methylation in RNA transcriptome. We confirm site-specific methylation in tRNA and identify messenger and non-coding RNAs as potential methylation targets for NSun2. Using RNA bisulfite sequencing we establish Vault non-coding RNAs as novel substrates for NSun2 and identified six cytosine-5 methylated sites. Furthermore, we show that loss of cytosine-5 methylation in Vault RNAs causes aberrant processing into argonaute-associating small RNA fragments (svRNA). Thus, impaired Vault non-coding RNA processing may be an important contributor to the etiology of NSUN2-deficieny human disorders.
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2008-10-15 | E-GEOD-12527 | biostudies-arrayexpress
Project description:Human genome encodes a multitude of different non-coding transcripts that have been traditionally separated based on their lengths into long or small non-coding RNAs. The vast majority of both long and short non-coding transcripts are not annotated and their functions, mechanisms of action and biological relevance remain unknown. However, based on the functional understanding of the known classes of long and small non-coding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Still, direct evidence of functionality is lacking for most non-coding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we have developed a high-throughput assay to test functionality of sncRNAs based on overexpressing them in human cells. Surprisingly, we found that a significant fraction (> 40%) unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small non-coding transcriptome can harbor multiple functional transcripts that warrant future studies.
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Project description:Human genome encodes a multitude of different non-coding transcripts that have been traditionally separated based on their lengths into long or small non-coding RNAs. The vast majority of both long and short non-coding transcripts are not annotated and their functions, mechanisms of action and biological relevance remain unknown. However, based on the functional understanding of the known classes of long and small non-coding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Still, direct evidence of functionality is lacking for most non-coding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we have developed a high-throughput assay to test functionality of sncRNAs based on overexpressing them in human cells. Surprisingly, we found that a significant fraction (> 40%) unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small non-coding transcriptome can harbor multiple functional transcripts that warrant future studies.
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