Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA profiles from human genic regions suggest biogenic mechanisms and identify new Argonaute-associated species

ABSTRACT: Efforts to catalogue eukaryotic transcripts have uncovered a set of species derived from the termini and exon/intron boundaries of protein-coding loci. The biogenesis pathways of these small RNAs (sRNAs) are largely unknown, but a mechanism depending on backtracking of RNA polymerase II (RNAPII) has been suggested. Moreover, the functional relevance, if any, of these sRNAs remains elusive. By sequencing 12-100nt transcripts from cells depleted of major RNA degradation enzymes as well as RNAs associated with the effector-proteins Argonaute (AGO) 1/2, we provide mechanistic models for sRNA production and utilization. We suggest that neither splice site associated (SSa)- nor transcription start site associated (TSSa)-RNAs arise from RNAPII backtracking. Instead SSa-RNAs are largely degradation products of mRNA splicing intermediates, while TSSa-RNAs likely derive from nascent RNA protected by stalled RNAPII against nucleolysis. We also reveal new AGO1/2-associated RNAs, including such derived from 3'ends of introns (5'tailed miRtrons) and from mRNA 3'UTRs. Interestingly, both appear to draw from non-canonical microRNA (miRNA) biogenesis pathways.

ORGANISM(S): Homo sapiens

PROVIDER: GSE29116 | GEO | 2011/07/31

SECONDARY ACCESSION(S): PRJNA140385

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Small RNA profiles from human genic regions suggest biogenic mechanisms and identify new Argonaute-associated species

Project description:Efforts to catalogue eukaryotic transcripts have uncovered a set of species derived from the termini and exon/intron boundaries of protein-coding loci. The biogenesis pathways of these small RNAs (sRNAs) are largely unknown, but a mechanism depending on backtracking of RNA polymerase II (RNAPII) has been suggested. Moreover, the functional relevance, if any, of these sRNAs remains elusive. By sequencing 12-100nt transcripts from cells depleted of major RNA degradation enzymes as well as RNAs associated with the effector-proteins Argonaute (AGO) 1/2, we provide mechanistic models for sRNA production and utilization. We suggest that neither splice site associated (SSa)- nor transcription start site associated (TSSa)-RNAs arise from RNAPII backtracking. Instead SSa-RNAs are largely degradation products of mRNA splicing intermediates, while TSSa-RNAs likely derive from nascent RNA protected by stalled RNAPII against nucleolysis. We also reveal new AGO1/2-associated RNAs, including such derived from 3'ends of introns (5'tailed miRtrons) and from mRNA 3'UTRs. Interestingly, both appear to draw from non-canonical microRNA (miRNA) biogenesis pathways. 10 samples all from HeLa in three size ranges: 12-20, 18-30 and 30-100. 1 from 12-20: nuclear; 6 from 18-30: WT, nuclear, RRP40 knockdown, Ago1&2 IP, RRP40 knockdown and Ago1&2 IP, XRN1&2 knockdown; 3 from 30-100: WT, of RRP40 knockdown, XRN1&2 knockdown.

2011-07-31 | E-GEOD-29116 | biostudies-arrayexpress

The RNA Exosome Promotes Transcription Termination of backtracked RNA Polymerase II

Project description:Large fractions of genomes are expressed in most eukaryotic cells, generating a diverse repertoire of protein-coding and non-coding transcripts. With such complexity, and as the number of mRNA molecules per cell are often low, it is clear that errors anywhere in the gene expression process could have profound consequences on cellular functions. The exosome is a conserved RNA degradation machine that plays a fundamental role in monitoring the quality of gene expression in the nucleus. The current view is that the nuclear exosome constantly scrutinizes transcription and contributes to post-transcriptional turnover of faulty mRNAs. Yet, how nuclear RNA surveillance by the exosome is coordinated with transcription is still unknown. Here we show that the exosome can directly target the transcription machinery by terminating transcription events associated with paused and backtracked RNA polymerase II (RNAPII), contrary to the notion that the exosome acts exclusively on RNAs that have been released by RNAPII. Our data support a mechanism by which RNAPII backtracking provides a free RNA 3' end for the core exosome, resulting in transcription termination with the concomitant degradation of the associated transcript. These findings uncover a mechanism of co-transcriptional RNA surveillance whereby termination of transcription by the exosome prevents aberrant read-through RNAs and transcriptional interference at neighboring genes.

2014-09-20 | E-MTAB-2237 | biostudies-arrayexpress

Expression data from wild-type, Dgcr8 knockout and Dicer knockout ES cells

Project description:Dgcr8 and Dicer are both important components of the microRNA biogenesis pathway while Dicer is also implicated in biogenesis of other types of small RNAs such as siRNAs and mirtrons. Here we performed microarray analysis of WT, Dgcr8 and Dicer knockout ES cells to identify mRNAs differentially regulated upon loss of Dgcr8 and Dicer.

2009-09-23 | GSE16923 | GEO

Comprehensive Analysis of RDR1/2/6-independent Small RNAs in Arabidopsis thaliana

Project description:Plant small RNAs (sRNAs) regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren’t. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs (miRNAs) and other hairpin-derived sRNAs. In this study, we produced and analyzed sRNA-seq libraries produced from rdr1/rdr2/rdr6 triple mutant plants. We found 58 previously annotated MIRNA loci that were dependent on RDR function, casting doubt on their classification as MIRNAs. We also found 38 RDR-independent sRNA clusters that were not MIRNAs or otherwise hairpin-derived. These 38 sRNA loci have novel biogenesis mechanisms, and frequently arise from protein-coding genes. Altogether, our analysis suggests that these 38 sRNA loci represent one or more new types of sRNA loci in Arabidopsis thaliana.

2018-04-09 | GSE105262 | GEO

TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the S. pombe siRNA pathway

Project description:In the fission yeast Schizosaccharomyces pombe, the RNAi machinery is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic gene silencing. Efficient silencing also requires the TRAMP complex, which contains the non-canonical Cid14 polyA polymerase and targets aberrant RNAs for degradation. Here we use high-throughput sequencing to analyze Argonaute-associated small RNAs (sRNAs) in both the presence and absence of Cid14. Most sRNAs in fission yeast start with a 5’-uracil, largely because these are loaded most efficiently into Argonaute. In wild-type cells, most sRNAs match to repeated regions of the genome, whereas in cid14 cells, the sRNA profile changes to include major new classes of sRNAs originating from ribosomal RNAs and a tRNA. Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets.

2008-09-02 | GSE12416 | GEO

The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4

Project description:During the last decade several examples of coordination between gene transcription and mRNA degradation have been reported. mRNA imprinting by Rpb4 and 7 subunits of RNA polymerase II (RNAPII) and by the Ccr4-Not complex allows controlling its fate during transcription. Transcription regulation by mRNA degradation factors like Xrn1 constitutes a feedback loop that contributes to mRNA homeostasis. Mechanistic details of these phenomena are unclear. Most studies involve measurement of mRNA decay rates, usually by stressing procedures such as transcriptional shut-off or incorporation of modified nucleotides that can lead to biased results. In this work we have used the easily repressible yeast GAL1 gene to perform a genetic analysis of mRNA synthesis and degradation under physiological conditions. We combined this experimental approach with computational multi-agent modelling, testing different possibilities of Xrn1 and Ccr4-Not action in gene transcription. This double strategy brought us to conclude that Xrn1 regulates RNAPII backtracking in a Ccr4-independent manner. We validated this conclusion measuring TFIIS genome-wide recruitment to elongating RNAPII molecules. We found that xrn1∆ and ccr4∆ exhibited very different patterns of TFIIS/RNPAII which confirmed their differential role in controlling transcription elongation.

2019-07-17 | GSE127179 | GEO

Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals

Project description:A canonical pathway generates microRNAs (miRNAs) via stepwise cleavage of hairpin precursors by RNase III enzymes Drosha and Dicer, followed by loading of resultant ~22 nucleotide (nt) RNAs into an Argonaute (Ago) effector complex. In addition, non-canonical substrates can bypass either RNase III enzyme to yield functional small RNAs, including hundreds of intron-derived hairpins that comprise pre-miRNA mimics that bypass Drosha (i.e., mirtrons). Here, we show that mirtron breadth is much larger than currently appreciated, since hundreds of novel splicing-derived hairpins are detected in intermediate (~50-100 nt) but not small (20-30nt) RNA data. Since mirtrons were originally defined on the basis of small RNA duplexes, we term the larger set of loci as structured, splicing-derived RNAs (ssdRNAs). Although individual species generally accumulate modestly, these are broadly detected in Dicer and/or Ago complexes and can mediate repression in directed assays. Nevertheless, their extremely poor conservation suggests they do not generally benefit regulatory networks, and may instead contaminate the canonical miRNA pathway. In aggregate, ssdRNAs/mirtrons comprise the dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. We provide evidence that hairpin tailing is inhibitory for ssdRNA/mirtron biogenesis and/or function, and that this pathway has restricted the evolution of canonical pre-miRNAs that resemble splicing products. Overall, the rampant proliferation of evolutionary young mammalian mirtrons, coupled with an attendant molecular defense, comprises a Red Queen's race of intragenomic conflict.

2022-12-25 | GSE206186 | GEO

RNA-dependent RNA polymerases in the black-legged tick produce Argonaute-dependent small RNAs and regulate genes

Project description:Small regulatory RNAs (sRNAs) are involved in anti-viral defense and gene regulation. Although RNA-dependent RNA Polymerases (RdRPs) play essential roles in sRNA biogenesis in nematodes, plants and fungi, their involvement in other animals remains controversial. We identify abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs) expressed in the tick ISE6 cell line. The RdRP-dependent sRNAs are mainly derived from sense and antisense strands of RNA polymerase III-transcribed genes and repetitive elements. Knockdown of AGO/RdRP causes miregulation of protein-coding genes.These results demonstrate that arachnid RdRPs are important sRNA biogenesis factors, and the discovery of novel pathways underscores the importance of characterizing sRNA biogenesis in various organisms to understand virus-vector interactions and exploit RNAi for pest control.

2021-09-11 | GSE183810 | GEO

Argonaute proteins couple chromatin silencing to alternative splicing (RNA IP-Seq)

Project description:While Argonaute (AGO) proteins play a major role in transcriptional gene silencing (TGS) in many organisms, their role in the nucleus of somatic mammalian cells remains elusive. Here, we have purified AGO1 and AGO2 chromatin-embedded complexes, and found these proteins associated with previously described partners, but also with chromatin modifiers and, rather unexpectedly, with different splicing factors. Using the CD44 gene as a model for alternative splicing, we show that both AGO1 and AGO2 are required for Protein Kinase C (PKC)-dependent variant exon inclusion. AGO proteins facilitate the spliceosome recruitment and modulate the elongation rate of RNA polymerase II (RNAPII). The recruitment of AGO proteins to CD44 transcribed region is dependent on both the endonuclease Dicer and the chromodomain-containing protein HP1g, and results in locally increased levels of histone H3 lysine 9 (H3K9) methylation on variant exons. Genome wide analysis of splicing in either AGO2 or Dicer null cells showed that the two proteins have similar effects on many splicing events. Finally, sRNAs associated with nuclear AGO2 are mostly in sense orientation relative to protein-coding genes, supporting a role for intragenic antisense non-coding RNAs in the recruitment AGO and splicing factors. Together, our data demonstrate for the first time that the endogenous RNAi pathway is involved in alternative splicing decisions, unravelling a new model in which AGO proteins couple RNAPII elongation and chromatin modification. Deep sequencing of small RNAs (approx. 15-80 nucleotides) bound to either cytoplasmic or chromatin-associated AGO2 complex.

2012-09-10 | E-GEOD-39748 | biostudies-arrayexpress

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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