Ago-bound miRNAs and pre-miRNAs
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR566485.fastq.gz | Fastqsanger.gz | |||
| ERR566486.fastq.gz | Fastqsanger.gz | |||
| ERR566487.fastq.gz | Fastqsanger.gz |
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Project description:MicroRNA precursors (pre-miRNAs) are short hairpin RNAs that are rapidly processed into mature microRNAs (miRNAs) in the cytoplasm. Due to their low abundance in cells, sequencing-based studies of pre-miRNAs have been limited. We successfully enriched for and deep sequenced pre-miRNAs in human cells by capturing these RNAs during their interaction with Argonaute (AGO) proteins. Using this approach, we detected > 350 pre-miRNAs in human cells and > 250 pre-miRNAs in a reanalysis of a similar study in mouse cells. We uncovered widespread trimming and non-templated additions to 3’ ends of pre-miRNAs and mature miRNAs. Additionally, we identified novel AGO2-cleaved pre-miRNAs and created an index for microRNA precursor processing efficiency. This analysis revealed a subset of pre-miRNAs that produce low levels of mature miRNAs despite abundant precursors, including an annotated miRNA in the 5’ UTR of the DiGeorge syndrome critical region 8 (Dgcr8) mRNA transcript. This led us to search for other AGO-associated stem-loops originating from other mRNA species, which identified hundreds of putative pre-miRNAs derived from mRNA sequences in both the mouse and human transcriptomes. Intriguingly, we found that iron responsive elements in ferritin heavy and light chain mRNAs are processed into AGO-associated stem-loops in both mouse and humans but do not produce functional small RNAs. In summary, we provide a wealth of information on mammalian pre-miRNAs, and identify novel microRNA and microRNA-like elements localized in mRNAs.
2016-07-30 | GSE71710 | GEO
Project description:MicroRNA precursors (pre-miRNAs) are short hairpin RNAs that are rapidly processed into mature microRNAs (miRNAs) in the cytoplasm. Due to their low abundance in cells, sequencing-based studies of pre-miRNAs have been limited. We successfully enriched for and deep sequenced pre-miRNAs in human cells by capturing these RNAs during their interaction with Argonaute (AGO) proteins. Using this approach, we detected > 350 pre-miRNAs in human cells and > 250 pre-miRNAs in a reanalysis of a similar study in mouse cells. We uncovered widespread trimming and non-templated additions to 3â?? ends of pre-miRNAs and mature miRNAs. Additionally, we identified novel AGO2-cleaved pre-miRNAs and created an index for microRNA precursor processing efficiency. This analysis revealed a subset of pre-miRNAs that produce low levels of mature miRNAs despite abundant precursors, including an annotated miRNA in the 5â?? UTR of the DiGeorge syndrome critical region 8 (Dgcr8) mRNA transcript. This led us to search for other AGO-associated stem-loops originating from other mRNA species, which identified hundreds of putative pre-miRNAs derived from mRNA sequences in both the mouse and human transcriptomes. Intriguingly, we found that iron responsive elements in ferritin heavy and light chain mRNAs are processed into AGO-associated stem-loops in both mouse and humans but do not produce functional small RNAs. In summary, we provide a wealth of information on mammalian pre-miRNAs, and identify novel microRNA and microRNA-like elements localized in mRNAs. pre-miRNA-seq and miRNA-seq from HEK293T cells. Reanalysis of HEK293T smRNA-seq, MEF pre-miRNA and MEF smRNA-seq (processed data for these Samples are linked below). The reanalyzed HEK293T Samples are from Series GSE66224 and consists of Samples GSM1617437 and GSM1617438. The reanalyzed MEF pre-miRNA and MEF smRNA-seq Samples were downloaded from European Nucleotide Archive (http://www.ebi.ac.uk/ena/) under the accession number PRJEB6756 (ERX525474 and ERX525475). RNA-seq analysis of HEK293T cells following knockdown of DGCR8, DROSHA or Luciferase.
2016-07-30 | E-GEOD-71710 | biostudies-arrayexpress
Project description:microRNAs (miRNAs) associating with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3' ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3' binding are sufficient to trigger extensive miRNA 3’ modifications in HEK293T cells and in cancer patients. Comparing these modifications in TUT4, TUT7 and DIS3L2 knockout cells, we find that TUT7 is more robust than TUT4 in oligo-uridylating mature miRNAs, which in turn leads to their degradation by the DIS3L2 exonuclease. Our findings indicate a decay machinery removing AGO-associated miRNAs with an exposed 3' end. A set of endogenous miRNAs including miR-7 are targeted by this machinery presumably due to target-directed miRNA degradation.
2020-04-17 | GSE139567 | GEO
Project description:we resolved precusor let7 (pre-let-7) and human Dicer-TRBP complex bound precusor let7 (hDicer-TRBP-pre-let-7) secondary structure based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We found the free pre-let-7 RNA is more flexible comparing with hDicer-TRBP-pre-7 in the double strand region [10-20nt and 50- 60 nt].
2018-02-14 | GSE110516 | GEO
Project description:MicroRNAs (miRNAs) associated with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3' ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3' binding are sufficient to trigger extensive miRNA 3' modifications in HEK293T cells and in cancer patients. Comparing these modifications in TUT4, TUT7 and DIS3L2 knockout cells, we find that TUT7 is more robust than TUT4 in oligouridylating mature miRNAs, which in turn leads to their degradation by the DIS3L2 exonuclease. Our findings indicate a decay machinery removing AGO-associated miRNAs with an exposed 3' end. A set of endogenous miRNAs including miR-7, miR-222 and miR-769 are targeted by this machinery presumably due to target-directed miRNA degradation.
| S-EPMC7265490 | biostudies-literature
Project description:RNAi is a conserved mechanism in which small RNAs induce silencing of complementary targets. How Argonaute-bound small RNAs are targeted for degradation is not well understood. We show here that the adenyl-transferase Cid14, a member of the TRAMP complex, and the uridyl-transferase Cid16 add non-templated nucleotides to Argonaute-bound small RNAs in fission yeast. The tailing of Argonaute-bound small RNAs in vitro recruits the 3’-5’ exonuclease Rrp6 to degrade small RNAs. Failure in degradation of Argonaute-bound small RNAs results in accumulation of “noise” small RNAs on Argonaute and targeting of diverse euchromatic genes by RNAi. To protect themselves from uncontrolled RNAi, cid14Δ cells exploit the RNAi machinery and silence genes essential for RNAi itself, which is required for their viability. Our data indicate that surveillance of Argonaute-bound small RNAs by Cid14/Cid16 and the exosome protects the genome from uncontrolled RNAi and reveal a rapid RNAi-based adaptation to stress conditions.
2017-05-09 | GSE95821 | GEO
Project description:As a key member of the grass-specific subclade of argonaute proteins, AGO18b protein has been proposed to bind 24-nt meiotic phasiRNAs based on their co-expression in tapetal and meiotic cells. Here we show that expression of in maize tassels is strictly induced by developmental stages. Interestingly, reduced expression of AGO18b in both Mutator-mediated (ago18b::mum) and RNAi mutants leads to an increase in plant height and tassel length, suggesting its non-meiotic function as a negative regulator of SAM/IM maintenance. During the premiotic stage, AGO18b primarily binds to 21-nt phasiRNAs with 5’-uridine and less binds to 24-nt phasiRNAs with 5’-adenosine, coincident with its enrichment of miR2275 required for the 24-nt phasiRNA production. MiR166a, the negative regulator of SAM, is mostly enriched among AGO18b-bound miRNAs, implicating a novel negative regulator of IM. We suggest that AGO18b regulates maize tassel development via both phasiRNAs and miRNA pathways.
2019-08-07 | GSE93983 | GEO
Project description:MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate protein gene expression post-transcriptionally. By base pairing with target mRNAs, miRNAs triggers mRNA degradation or translational suppression[1-4]. Abnormal miRNAs levels are associated with cancers, diabetes, neurological and other diseases[5-8]. RNA polymerase II transcribes primary miRNA (pri-miR) in the nucleus and pri-miRs are subsequently processed by Microprocessor, which is composed of Drosha and DiGeorge syndrome critical region 8 (DGCR8) proteins, to generate precursor miRNAs (pre-miRs). Pre-miRs are exported from the nucleus to the cytoplasm in a GTP-dependent manner by Exportin-5. In the cytoplasm, a pre-miRs are further processed by Dicer to generate 21-22 nt mature miRNA[4, 9]. Argonaute (Ago) protein loads one of mature miRNAs into protein and forms miRNA-induced silencing complex, which is responsible for mRNA degradation or translational suppression[2, 4].
2023-04-24 | GSE230167 | GEO
Project description:secondary structure based on icSHAPE of pre-let-7 and hDicer-TRBP bound pre-let-7
| PRJNA433923 | ENA
Project description:Drosophila Dicer-1 produces microRNAs (miRNAs) from pre-miRNA, whereas Dicer-2 generates small interfering RNAs (siRNAs) from long dsRNA. loquacious (loqs) encodes three Dicer partner proteins, Loqs-PA, Loqs-PB, and, Loqs-PD, generated by alternative splicing. To understand the function of each Loqs isoform, we constructed loqs isoform-specific rescue flies. Loqs-PD promotes siRNA production in vivo by Dicer-2. Loqs-PA or Loqs-PB is required for viability, but the proteins are not fully redundant: Loqs-PB is required to produce a specific subset of miRNAs. Surprisingly, Loqs-PB tunes the product size cleaved by Dicer-1 from pre-miR-307a, generating a longer miRNA isoform with a distinct seed sequence and target specificity. The mouse and human Dicer-binding partner TRBP, a homolog of Loqs-PB, similarly tunes the site of pre-miR-132 cleavage by mammalian Dicer. Thus, Dicer-binding partner proteins can change the choice of cleavage site by Dicer, producing miRNAs with different target specificities than those that would be made by Dicer alone. Examination of Dicer-binding proteins on small RNA profiles of female fly heads, fly ovaries, mouse embryonic fibroblasts, and mouse tail fibroblasts.
2012-12-07 | E-GEOD-37443 | biostudies-arrayexpress