Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Full-length RNA-seq of short RNAs from Cuscuta campestris

ABSTRACT: Cuscuta campestris is an obligate parasitic plant that attaches to the stems of host plants to obtain water and nutrients. C. campestris produces a specialized set of microRNAs specifically at the host-parasite interface. Many of these interface-induced microRNAs target mRNAs from the host. This experiment was designed to capture full-length primary transcripts that give rise to C. campestris interface-induced microRNAs. C. campestris shoot tips were stimulated to produce haustoria, then harvested to extract total RNA. RNA was then treated with various enzymes to modify 5' ends. Libraries were then made and sequenced. Importantly the library method only captures RNAs with a 5'-monophosphate. Therefore the specific enzymatic treatments can reveal the native 5' ends of the sequenced RNAs. Data were used to identify the primary transcripts for many of the known C. campestris primary microRNA transcripts. The data were also interrogated to tally specific snRNAs (U1, U2, U4, and U5) that are known to have a 2,2,7mGppp cap, and the tally pre-tRNAs, which are known to have a ppp 5' end. The analyzed results indicated that C. campestris interface-induced microRNA primary transcripts likely have a 5' ppp, not a cap, consistent with transcription by RNA polymerase III. The analysis also demonstrated that C. campestris interface-induced microRNA primary transcripts mostly terminate within stretches of polyT and lack polyA tails, also features consistent with Pol III transcription. Finally, the analysis indicated that the transcriptional start sites were located ~ 55 bp downstream of a common ten-base pair promoter element (the upstream sequence element). The 55bp spacing is also consistent with Pol III transcription.

ORGANISM(S): Cuscuta campestris

PROVIDER: GSE221347 | GEO | 2023/01/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

microRNA accumulation from Cuscuta campestris in vitro haustoria

Project description:The parasitic plant Cuscuta campestris produces specialized microRNAs that are specifically expressed at the haustorial interface. Some of these "Interface-Induced MicroRNAs" function to target host mRNAs. C. campestris haustoria can be induced in the absence of any host tissues using a combination of light and physical pressure. This experiment tested with such in vitro, host-free haustoria produced interface-induced microRNAs. Small RNA-seq was performed from three different treatments: Shoot tips of C. campestris without any haustoria formation, in vitro haustoria formed in the presence of host tissue (detached leaves of Arabidopsis thaliana) and in vitro haustoria formed in the absence of any host tissue.

2022-07-06 | GSE205256 | GEO

Proteomics of U1810 cells upon treatment with microRNAs with an AAGUGC seed motif.

Project description:microRNA dysregulation is a common feature of cancer cells, but the complex roles of microRNAs in cancer are not fully elucidated. Here we used functional genomics to identify oncogenic microRNAs in non-small cell lung cancer and to evaluate their impact on response to EGFR targeting therapy. Our data demonstrate that microRNAs with an AAGUGC-motif in their seed-sequence increase both cancer cell proliferation and sensitivity to EGFR inhibitors. Global transcriptomics, proteomics and target prediction resulted in the identification of several tumor suppressors involved in the G1/S transition as targets of AAGUGC-microRNAs. The clinical implications of our findings were evaluated by analysis of public domain data supporting the link between this microRNA seed-family, their tumor suppressor targets and cancer cell proliferation. In conclusion we propose that AAGUGC-microRNAs are an integral part of an oncogenic signaling network, and that these findings have potential therapeutic implications, especially in selecting patients for EGFR-targeting therapy.

2017-03-31 | MSV000080829 | MassIVE

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

Project description:In this study transcriptional start sites (TSS) for H. pylori 26695 were determined To detect the complement of transcripts expressed from H. pylori, we collected three independent biological replicates (B1 – B3) from 26695 wild type strain grown to mid-exponential (OD 600 ~0.6) phase under microaerophilic conditions at 37°C in BHI medium. For all three samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5’ terminator exonuclease (+TEX samples), which degrades RNAs containing a 5’-monophosphate (5’-P) and, thus, enriches for primary transcripts containing 5’-triphosphates (5’-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5’-PPP) and processed RNAs (5’-P).

2015-07-01 | E-GEOD-67564 | biostudies-arrayexpress

Systematic analysis of intronic microRNAs reveals cooperativity within the multi-component FTX locus to promote colon cancer development

Project description:Approximately half of all microRNAs reside within intronic regions and are often co-transcribed with their host genes. However, most studies on intronic microRNAs focus on individual microRNAs, and conversely most studies on protein-coding and non-coding genes frequently ignore any intron-derived microRNAs. We hypothesize that the individual components of such multi-genic loci may play cooperative or competing roles in driving disease progression, and that examining the combinatorial effect of these components would uncover deeper insights into their functional importance. To address this, we perform systematic analyses of intronic microRNA:host loci in colon cancer. We observe that the FTX locus, comprising of a long non-coding RNA FTX and multiple intronic microRNAs, is highly upregulated in cancer and demonstrate that cooperativity within this multi-component locus promotes cancer growth. In addition, we show that FTX interacts with DHX9 and DICER and delineate its novel roles in regulating A-to-I RNA editing and microRNA expression. These results show for the first time that a long non-coding RNA can regulate A-to-I RNA editing, further expanding the functional repertoire of long non-coding RNAs. We further demonstrate the inhibitory effects of intronic miR-374b and -545 on the tumor suppressors PTEN and RIG-I to enhance the proto-oncogenic PI3K-AKT signaling. Finally, we show that intronic miR-421 may exert an autoregulatory effect on miR-374b and -545. Taken together, our data unveil the intricate interplay between intronic microRNAs and their host transcripts in the modulation of key signaling pathways and disease progression, adding new perspectives to the functional landscape of multi-genic loci.

2021-01-05 | PXD021823 | Pride

Lack of associations of microRNAs with severe NAFLD in people living with HIV: Discovery case-control study

Project description:The aim of this discovery case-control study was to identify patterns of differential expression of microRNAs in people living with HIV (PLWH) and assess their diagnostic value for non-alcoholic fatty liver disease (NALFD). Cases were defined as patients with severe NAFLD and controls as patients without NAFLD, characterized using the controlled attenuation parameter (CAP). Cases and controls were matched 1:1 for age, sex, body mass index, CD4+ lymphocyte count, active HCV infection, and ART regimen. Serum 2,083 simultaneous microRNA transcripts were analyzed using HTG technology and compared between cases and controls. Forty-five patients, 23 cases, and 22 controls were included in the study. In the analysis of the expression pattern of the 2,083 microRNAs, no differential expression patterns were found between both groups of patients included in the study. Analysis of the microRNA transcriptome profile of nonobese PLWH with severe NAFLD did not appear to differ from that of patients without NAFLD. Thus, microRNA might not serve as a proper biomarker for predicting severe NALFD in this population.

2023-05-03 | E-MTAB-12974 | biostudies-arrayexpress

Identification and validation of antisense RNAs in Escherichia coli

Project description:In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions To detect the complement of transcripts expressed from E. coli, we collected two independent biological replicates (B1 and B2 samples) from MG1655 wild type strain grown to exponential (OD 600 ~0.4) or stationary phase (OD 600 ~2.0) in LB medium (samples LB 0.4 and LB 2.0, respectively) as well as grown to exponential phase (OD 600 ~0.4) in M63 minimal glucose medium (sample M63 0.4). For all six samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5M-bM-^@M-^Y terminator exonuclease (+TEX samples), which degrades RNAs containing a 5M-bM-^@M-^Y-mono-phosphate (5M-bM-^@M-^Y-P) and, thus, enriching enriches for primary transcripts containing 5M-bM-^@M-^Y-tri-phosphates (5M-bM-^@M-^Y-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5M-bM-^@M-^Y-PPP) and processed RNAs (5M-bM-^@M-^Y-P).

2014-10-18 | E-GEOD-55199 | biostudies-arrayexpress

microRNA-like off-target transcript regulation by siRNAs

Project description:siRNAs mediate sequence-specific gene silencing in cultured mammalian cells but also silence unintended transcripts. Many siRNA off-target transcripts match the guide-strand ‘‘seed region,’’ similar to the way microRNAs match their target sites. The extent to which this seed-matched, microRNA-like, off-target silencing affects the specificity of therapeutic siRNAs in vivo is currently unknown. Here, we compare microRNA-like off-target regulations in mouse liver in vivo with those seen in cell culture for a series of therapeutic candidate siRNAs targeting Apolipoprotein B (APOB). Each siRNA triggered regulation of consistent microRNA-like off-target transcripts in mouse livers and in cultured mouse liver tumor cells. In contrast, there was only random overlap between microRNA-like off-target transcripts from cultured human and mouse liver tumor cells. Therefore, siRNA therapeutics may trigger microRNA-like silencing of many unintended targets in vivo, and the potential toxicities caused by these off-target gene regulations cannot be accurately assessed in rodent models.

2009-02-01 | GSE14073 | GEO

Effects of Ars2 or DGCR8 siRNA on microRNA expression

Project description:Ars2 is a component of the nuclear cap-binding complex that is required for cellular proliferation and contributes to microRNA biogenesis. Arrays were performed to determine the repertoire of microRNAs that change following knock-down of Ars2. Knock-down of DGCR8 was also performed to determine which microRNAs were expressed and had half-lives short enough to significantly decrease over the duration of the experiment.

2012-02-01 | GSE34680 | GEO

Proteomics of U1810 cells upon treatment with microRNAs with an AAGUGC seed motif.

2016-06-28 | PXD004163 | Pride

Small RNAs from Cuscuta campestris parasitizing Arabidopsis thaliana

Project description:Dodders (Cuscuta spp.) are obligate parasitic plants that obtain water and nutrients from the stems of host plants via specialized feeding structures called haustoria. Dodder haustoria facilitate bi-directional movement of viruses, proteins, and mRNAs between host and parasite, but the functional effects of these movements are not clear. Here we show that C. campestris haustoria accumulate high levels of many novel microRNAs (miRNAs) while parasitizing Arabidopsis thaliana hosts. Many of these miRNAs are 22 nts long, a usually rare size of plant miRNA associated with amplification of target silencing through secondary small interfering RNA (siRNA) production. Several A. thaliana mRNAs are targeted by C. campestris 22 nt miRNAs during parasitism, resulting in high levels of secondary siRNA production. The targeted mRNAs function in hormone perception, pathogen-defense signaling, phloem function, and stem-cell identity. Homologs of these target mRNAs from diverse plants also have high-confidence complementary sites to C. campestris miRNAs, suggesting that homologous mRNAs are targeted by C. campestris across its very broad host range. These data show that C. campestris miRNAs act as trans-species regulators of host gene expression, and suggest that they may act as virulence factors during parasitism.

2017-12-18 | GSE84955 | GEO

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