Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic identification of long non-coding RNAs under allelopathic interference of PHBA in S. lycopersicum

ABSTRACT: Systematic identification of long non-coding RNAs under allelopathic interference of PHBA in S. lycopersicum

PROVIDER: PRJNA598162 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Systematic identification of long non-coding RNAs under allelopathic interference of PHBA in S. lycopersicum

Project description:In this study, we identifyed the LncRNAs expressed in S. lycopersicum leaves under different para-hydroxybenzoic acid concentration treatments.

2019-12-31 | GSE142733 | GEO

Intergenic non-coding transcription utilises an RNA-based mechanism to drive transcriptional interference

Project description:Recent studies have revealed that eukaryotic genomes are pervasively transcribed by RNA polymerase II, producing a plethora of non-coding RNAs which frequently overlap protein-coding genes. Despite the fact that overlapping transcription is well known to repress transcription initiation from downstream promoters, the mechanism behind this phenomenon has remained elusive. It was proposed that transcriptional interference relies on the act of transcription rather than the RNA itself to block access of the transcription machinery to downstream promoters. Here, we demonstrate that an RNA and chromatin-dependent mechanism is responsible for transcriptional interference in fission yeast. This relies on co-transcriptional recruitment of the histone deacetylase Clr3 to nascent non-coding RNA, leading to formation of hypoacetylated chromatin and repression of the downstream protein-coding gene. Our findings highlight the unexpected requirement for RNA as well as trans-acting protein factors in mediating the repressive effects imposed on gene expression through overlapping non-coding transcription.

2017-03-01 | GSE90155 | GEO

The dynamic landscape of coding and non-coding RNAs in the innate immune response to microbial pathogens

Project description:We performed a systematic analysis of the coding and non-coding transcriptomes of human macrophages after stimulation with ligands to TLR2/6 (FSL), TLR 1/2 (Pam3CSK4), and TLR4 (LPS)

2019-01-09 | GSE109084 | GEO

Systematic Analysis of Coding and Non-coding Elements in Developmental Pathways Implicated in Holoprosencephaly Pathogenesis

Project description:Systematic Analysis of Coding and Non-coding Elements in Developmental Pathways Implicated in Holoprosencephaly Pathogenesis

| PRJNA517545 | ENA

Systematic Analysis of Coding and Non-coding Elements in Developmental Pathways Implicated in Holoprosencephaly Pathogenesis

Project description:Systematic Analysis of Coding and Non-coding Elements in Developmental Pathways Implicated in Holoprosencephaly Pathogenesis

| PRJNA517546 | ENA

Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears

Project description:Systematic identification of aberrant non-coding RNAs and their mediated modules in rotator cuff tears

| PRJNA820273 | ENA

Seb1 is recruited co-transcriptionally to non-coding regions to drive transcriptional interference

Project description:Seb1 is recruited co-transcriptionally to non-coding regions to drive transcriptional interference

| PRJNA360639 | ENA

The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium

Project description:we found the expression levels of 76 known miRNAs were highly variable between the reciprocal hybrids through the high-throughput sequencing of small RNAs small RNA sequencing were performed in Solanum lycopersicum, S. pimpinellifolium and their reciprocal hybrids

2014-10-10 | E-GEOD-62196 | biostudies-arrayexpress

Comprehensive Identification of Soybean Long Non-coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts

Project description:Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-seq data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ~69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the current inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames (ORFs) from being regarded as protein-coding.

2020-01-09 | PXD014553 | Pride