Long non-coding RNAs discriminate the stages and gene regulatory states of the human humoral immune response (RNA-Seq)
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ABSTRACT:
PROVIDER: PRJNA472759 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7207680_1.fastq.gz | Fastqsanger.gz | |||
| SRR7207680_2.fastq.gz | Fastqsanger.gz | |||
| SRR7207690_1.fastq.gz | Fastqsanger.gz | |||
| SRR7207690_2.fastq.gz | Fastqsanger.gz | |||
| SRR7207700_1.fastq.gz | Fastqsanger.gz |
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Project description:Long non-coding RNAs discriminate the stages and gene regulatory states of the human humoral immune response
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Project description:Long non-coding RNAs (lncRNAs) make up a vast majority of the human transcriptome and have key regulatory functions. We performed unbiased de novo annotation of transcripts expressed during the humoral immune response in humans. Remarkably, 30% of the total human genome is transcribed during this process, and yet 58% of these transcripts manifest striking differential expression indicating phylogenetic relationships among cell types that is even more robust than coding genes. We provide a regulatory atlas of lncRNAs in naïve B and GC B-cells that indicates their partition into ten functionally distinct categories based on chromatin features including H3K4me1, H3K4me2, H3K4me3, H3K27ac, H3K27me3, DNase hypersensitivity, CTCF, EP300, CREBBP, MED1, BRD4, FOXO1 and FOXP1 localization. This procedure defined lncRNAs classes such as enhancer RNA (eRNA), bivalent lncRNA, and CTCF associated, among others. eRNAs are transcribed in 8.6% of regular enhancers and 36.5% of super enhancers, associated with coding genes that participate in critical immune regulatory pathways. Plasma cells uniquely featured high levels of circular RNAs accounted for by and reflecting the combinatorial clonal state of the Immunoglobulin loci.
2019-01-15 | GSE114816 | GEO
Project description:lncRNAs make up a majority of the human transcriptome and have key regulatory functions. Here we perform unbiased de novo annotation of transcripts expressed during the human humoral immune response to find 30% of the human genome transcribed during this process, yet 58% of these transcripts manifest striking differential expression, indicating an lncRNA phylogenetic relationship among cell types that is more robust than that of coding genes. We provide an atlas of lncRNAs in naive and GC B-cells that indicates their partition into ten functionally categories based on chromatin features, DNase hypersensitivity and transcription factor localization, defining lncRNAs classes such as enhancer-RNAs (eRNA), bivalent-lncRNAs, and CTCF-associated, among others. Specifically, eRNAs are transcribed in 8.6% of regular enhancers and 36.5% of super enhancers, and are associated with coding genes that participate in critical immune regulatory pathways, while plasma cells have uniquely high levels of circular-RNAs accounted for by and reflecting the combinatorial clonal state of the Immunoglobulin loci.
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Project description:Liver is the major organ of lipid biosynthesis in chicken. In laying hens, the liver synthesizes most of yolk precursors and transports to the developing follicles to produce eggs. However, a systematic and comprehensive investigation of long non-coding RNAs (lncRNAs) and mRNAs transcriptome in chicken liver across different developmental stages remain clearly unknown. Here, we constructed 12 RNA libraries from liver tissue during four developmental stages, including juvenile period (JP, day 60), sexual maturity period (SM, day 133), peak laying period (PL, day 220) and broodiness period (BP, day 400). A total of 16,930 putative lncRNAs and 18,260 mRNAs were identified among these samples. More than half of identified lncRNAs were intergenic lncRNAs (lincRNAs), accounting for 53.70%. The temporal expression pattern showed that lncRNAs were more restricted than mRNAs. We identified numerous differentially expressed lncRNAs (DE lncRNA) and mRNAs (DEGs) by pairwise comparisons between the four developmental stages and found that vitellogenin 2 (VTG2), riboflavin binding protein (RBP), and a novel protein-coding gene were differentially expressed in all stages. Time-series analysis showed that the module with up-regulated genes were enriched in related to lipid metabolism process. Co-expression networks suggested the functional relatedness between mRNAs and lncRNAs and the results showed the DE-lncRNAs also mainly involve in lipid biosynthesis and metabolism process. These results suggest the transcriptome variation of liver in different developmental stages and improve the comparative understandings of molecular mechanisms of liver development in chickens.
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Project description:Background: Chronic spinal cord injury (SCI) remains one of the most debilitating neurological disorders and the majority of SCI patients are in the chronic phase. Previous studies of SCI that were limited by resources and technology have usually focused on few genes and pathways at a time. Thus, a comprehensive view of the complex molecular changes underlying SCI pathophysiology is needed. In particular, the biological roles of long non-coding RNAs (lncRNAs), a class of regulatory RNAs, have never been characterized systemically in SCI. Results: This study is the first to investigate alterations in the expression of both coding and long non-coding genes in the sub-chronic and chronic stages of SCI using RNA-Sequencing. Our data revealed differentially expressed genes, canonical pathways, and networks unique to particular time points or common to multiple time points in the progression of SCI. For example, a network of multiple critical genes responsible for astrogliosis and fibrosis was identified among differentially expressed genes common to three time points (1month, 3months, and 6 months after SCI). Moreover, the potential functions of rat lncRNAs in SCI were extensively analyzed. First, a comprehensive annotation database was compiled for rat lncRNAs that revealed several interesting characteristics of lncRNAs in the rat genome. Then, by correlating the temporal expression patterns of lncRNAs with those of protein-coding genes, we identified lncRNAs that are associated with functional categories such as signaling pathways, immune response, epigenetic modification, nervous system, and extracellular matrix. The expression patterns of some lncRNAs are highly correlated with those of their most proximal protein-coding genes, so it is possible that these lncRNAs regulate the expression of their protein-coding neighbors. Finally, we searched for transcription factor motifs enriched in the upstream regulatory regions of differentially expressed lncRNAs, and identified differentially expressed lncRNAs that are homologous to human genomic regions harboring molecular variants associated with human neurological diseases. Conclusions: Overall, our study provides an unprecedented resource for the study of sub-chronic and chronic SCI that will help the research community identify new molecular targets for future functional investigation.
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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.
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Project description:In summary, we present a systematic in silico screen for the conserved non-coding RNA structures by comparing the P. falciparum genome with seven other malaria species and describe 668 candidate RNA secondary structures. By combining microarray and northern data, we provide evidence for expression of 28 novel ncRNA candidates at the transcript level in the blood stages of P. falciparum, a subset of which show intra-erythrocytic stage-specificity for expression. Few of the expressed novel candidates appear to have similarity to functionally known ncRNAs characterised to-date. The ncRNA candidates that show a narrow phylogenetic distribution, such as the internal var-associated ncRNAs, may be involved in species-specific function. At present, we can not assign specific function to these novel ncRNAs, however, our study highlights the abundance of these novel ncRNA structures in P. falciparum and suggests important roles for these ncRNAs in cellular processes. Although the control of gene expression by mechanisms such as epigenetics, post-transcriptional gene regulation and transcript stability has been recently shown in Plasmodium, all the key cellular players in such types of non-conventional gene regulation in Plasmodium are yet to be identified. Taking cues from the functionally characterized components of the higher eukaryotic non-coding RNA populations, it is tempting to speculate that ncRNAs may, at least in part, be instrumental in gene regulation in P. falciparum. However, in contrast to the higher eukaryotes, the absence of a conventional RNAi pathway and its associated components in malaria suggests that these malaria-specific novel ncRNAs, where functional, must exert their role using novel pathways or mechanisms, possibly unique to malaria. It remains to be determined what fraction of the ncRNAs described here are involved in modulating expression of one or more genes or gene families in malaria and also the precise cellular function for them not only in the blood stages but also in the other life-cycle stages of P. falciparum.
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Project description:Long non-coding RNAs and mRNAs profiling of liver tissue during four developmental stages in chickens
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