Project description:This SuperSeries is composed of the following subset Series: GSE32898: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq] GSE32899: Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [ChIP_Seq] Refer to individual Series
Project description:Recent advances in next generation sequencing have improved human genome annotations and revealed thousands of previosly unknown long non-coding RNA loci. Here, we characterized immune-responsive long non-coding RNAs (lncRNAs) and determined their subcellular localization and co-sedimentation with protein complexes in primary human macrophages. To this end, we profiled LPS-responsive lncRNAs, isolated cytoplasmic and nuclear RNA fractions from mock- and LPS-treated cells and seperated cell lysates on 10-60 % glycerol gradients, followed by gradient fractionation. All samples were subjected to RNA-Seq analysis. LPS-responsive lncRNAs were found to be mostly cytoplasmic. Glycerol gradient datasets revealed that a substantial fraction of LPS-responsive lncRNAs, similar to mRNAs, co-sediments with ribosomal RNAs and also ribosomal proteins, as confirmed by mass-spectrometry analysis. LncRNAs not co-sedimenting with ribosomes displayed a highly heterogenous gradient distriubtion. Among these truly non-coding RNAs we identified lncRNA MaIL1 as a novel element of the macrophage TLR-TRIF signaling pathway contributing to antibacterial defense.
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.
Project description:strand specific sequencing of RNAs from MAoECs to determine the endothelial-specific expression profile of protein-coding and long non-coding RNAs
Project description:Previous studies have documented that long non-coding RNAs participate in a wide-spectrum of biological processes. We hypothesized that long non-coding RNAs may promote glycolysis and tumorigenesis in colorectal cancer by manipulating of target genes. To test this hypothesis, we performed a global non-coding RNA expression profiling in 10 CRC tissues.
Project description:Cortical neural progenitor cells (NPCs) change their competency over time during development, giving rise to distinct cell types sequentially. Many genes that govern cortical development are now known, but it remains elusive how their temporal expression is controlled. Recently, long non-coding RNAs are found to be essential for cell-fate specification and precise gene regulation in many developmental events. In this study, strand-specific RNA sequencing studies unveil large amount of long non-coding RNAs are actively and differentially expressed across mouse cortical development. Integration of RNA sequencing data from key stages of developing mouse cortex enables us to cluster coding and non-coding transcripts into co-expression “modules” to infer functional relationships. Intriguingly, the cortical transcriptome undergoes significant changes in early mouse neurogenesis. Cortical long non-coding RNAs tends to be transcribed from genomic loci adjacent to protein-coding genes related to neural development. Finally, we found large amount of predicted enhancer regions are able to transcribe RNAs. This study will help us better understand molecularly how cortical NPCs specify their fates during development, especially roles of lncRNAs in this process.
