Transcriptional kinetics and molecular functions of long non-coding RNAs
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ABSTRACT:
PROVIDER: PRJEB48214 | ENA |
REPOSITORIES: ENA
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Project description:An increasing number of long non-coding RNAs (lncRNAs) have confirmed important functions, yet little is known about their transcriptional dynamics and it remains challenging to determine their regulatory functions. Here, allele-sensitive single-cell RNA-seq was used to demonstrate that lncRNAs have lower burst frequencies compared to mRNAs. We observed an increased cell-to-cell variability in lncRNA expression that was due to more sporadic bursting (lower frequency) with larger numbers of RNA molecules being produced. Exploiting heterogeneity in asynchronously growing cells, we identified and experimentally validated lncRNAs with cell-state specific functions involved in cell cycle progression and apoptosis. Finally, we identified cis-functioning lncRNAs and knockdown of these lncRNAs modulated either transcriptional burst frequency or size of the nearby protein-coding gene. Collectively, we identify distinct transcriptional regulation of lncRNAs and we demonstrate a role for lncRNAs in the regulation of transcriptional bursting of mRNAs.
2021-11-19 | E-MTAB-11054 | biostudies-arrayexpress
Project description:Long non-coding RNAs in B cells
| PRJNA292725 | ENA
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
Project description:Long non-coding RNAs (lncRNAs) are an emerging class of regulatory molecules with a potentially broad-range of epigenomic regulatory functions. These functions are likely mediated by lncRNA-chromatin interactions either directly or indirectly through protein intermediates. Thus, comprehensive genomic mapping of all lncRNA targets describing the ‘RNA-chromatin interactome’ are critical for inferring lncRNA functions. Current methodologies for investigating lncRNA-chromatin interaction are one-RNA-at-a-time, and most inferred lncRNA functions were based on indirect “guilt-by-association”. To address these limitations, we devised an unbiased genome-wide strategy to identify all RNA interactions with chromatin by paired-end-tag sequencing (RICh-PET). We comprehensively characterized a human RNA-chromatin interactome and uncovered complex RNA-chromatin networks with many showing long-distance interactions predominantly at gene promoters. Further analysis revealed both global and specific transcriptional regulation by lncRNAs to genes involved in cancer biology, demonstrating the capacity of RICh-PET to concomitantly identify thousands of lncRNAs and chromatin targets in the human genome, thus significantly advancing the understanding of lncRNA functions.
2023-04-30 | GSE53052 | GEO
Project description:Leishmania major is a kinetoplastid protozoan parasite which causes the debilitating infectious disease cutaneous leishmaniasis (CL). This disease results in scars and disfiguration of the infected individuals. The L. major genome was the first leishmanial genome to be sequenced in 2005 and this study resulted in the identification of 8,300 protein coding genes. This landmark study paved the way for further sequencing of other leishmanial parasites (L. infantum, L. braziliensis and L. donovani). A recent study provided the glimpse of the global transcriptome of L. major promastigotes. This study identified 1,884 uniquely expressed non-coding RNAs (ncRNA) in L. major. Additionally, we had previously mapped the global proteome of L. major promastigote using a proteogenomic approach which resulted in identification of 3,613 proteins in L. major promastigotes which covered 43% of its proteome. In the present study, we have carried out extensive analysis of the 1,884 novel ncRNAs using a proteogenomic approach to identify their protein coding potential. Our analysis resulted in identification of 10 novel protein coding genes based on peptide data and additional hundreds of proteins coding genes based on homology searches of previously classified ncRNA genes. We have analyzed each of these novel protein coding genes and in the process have improved the genome annotation of L. major on the basis of mass spectrometry derived peptide data and also based on homology.
2016-05-11 | PXD002465 | Pride
Project description:Interventions: Case series:Nil
Primary outcome(s): intestinal microecological disorders;blood non-coding RNAs and immune status
Study Design: Randomized parallel controlled trial
| 2681498 | ecrin-mdr-crc
Project description:Keloid is a dermal fibroproliferative disease with various etiologies and unclear pathogenesis. Recent studies have revealed that circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) exerted regulatory functions through a competing endogenous RNA (ceRNA) pathway in keloid progression. However, the expression profiles of circRNAs and lncRNAs in keloid dermal tissues (KDTs) remain unknown. This study aimed to identify differentially expressed circRNAs, lncRNAs and genes in KDTs.
2023-09-07 | GSE212954 | GEO
Project description:Using RNA CaptureSeq we annotated non-coding RNAs transcribed from genome intervals surrounding breast cancer risk signals in a range of mammary-derived tissue and cell lines.
| EGAS00001003353 | EGA
Project description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts, while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1,133 non-coding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than protein-coding genes and are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first comprehensive identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic and evolutionary studies. RNA-Seq for 8 zebrafish developmental stages, 2 lanes for each stage (3 for shield).
2011-11-17 | E-GEOD-32898 | biostudies-arrayexpress
Project description:Long non-coding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time series of RNA-Seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts, while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1,133 non-coding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than protein-coding genes and are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first comprehensive identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic and evolutionary studies. ChIP-Seq for H3K4me3 and H3K27me3 at zebrafish shield stage.
2011-11-17 | E-GEOD-32899 | biostudies-arrayexpress