Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells.

ABSTRACT: Germline stem cells are germ cells at an early developmental stage, so their development is key to ensuring human reproduction. There is increasing evidence that long noncoding RNA (lncRNA) and circular RNA (circRNA) play important roles in the development of germ cells. This data descriptor provides unique lncRNA and circRNA transcriptomic information for mouse germline stem cells. Using the Illumina HiSeqx 2000 system, a total of 511,836,732 raw reads were generated. High-quality transcripts, lncRNAs, and circRNAs were identificated and quantified using the reads, and more precise annotations of lncRNAs (especially 9357 novel lncRNAs) and circRNAs were performed in the germline stem cells. We then analyzed the transcript structures, genetic variants, and the interaction between circRNA and microRNA to provide the basis for subsequent functional experiments. This comprehensive dataset will help advance data sharing and deepen our understanding of mouse germline stem cells, providing a theoretical foundation for research on germ cell development and human reproduction, among others.

SUBMITTER: Li X

PROVIDER: S-EPMC6437644 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide identification, characterization and evolutionary analysis of long intergenic noncoding RNAs in cucumber.

Project description:Long intergenic noncoding RNAs (lincRNAs) are intergenic transcripts with a length of at least 200 nt that lack coding potential. Emerging evidence suggests that lincRNAs from animals participate in many fundamental biological processes. However, the systemic identification of lincRNAs has been undertaken in only a few plants. We chose to use cucumber (Cucumis sativus) as a model to analyze lincRNAs due to its importance as a model plant for studying sex differentiation and fruit development and the rich genomic and transcriptome data available. The application of a bioinformatics pipeline to multiple types of gene expression data resulted in the identification and characterization of 3,274 lincRNAs. Next, 10 lincRNAs targeted by 17 miRNAs were also explored. Based on co-expression analysis between lincRNAs and mRNAs, 94 lincRNAs were annotated, which may be involved in response to stimuli, multi-organism processes, reproduction, reproductive processes, and growth. Finally, examination of the evolution of lincRNAs showed that most lincRNAs are under purifying selection, while 16 lincRNAs are under natural selection. Our results provide a rich resource for further validation of cucumber lincRNAs and their function. The identification of lincRNAs targeted by miRNAs offers new clues for investigations into the role of lincRNAs in regulating gene expression. Finally, evaluation of the lincRNAs suggested that some lincRNAs are under positive and balancing selection.

| S-EPMC4370693 | biostudies-literature

Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening.

Project description:LncRNAs represent a class of RNA transcripts of more than 200 nucleotides (nt) in length without discernible protein-coding potential. The expression levels of lncRNAs are significantly affected by stress or developmental cues. Recent studies have shown that lncRNAs participate in fruit development and ripening processes in tomato and strawberry; however, in other fleshy fruits, the association between lncRNAs and fruit ripening remains largely elusive. Here, we constructed 9 ssRNA-Seq libraries from three different peach (Prunus persica) fruit developmental stages comprising the first and second exponential stages and the fruit-ripening stage. In total, 1500 confident lncRNAs from 887 loci were obtained according to the bioinformatics analysis. The lncRNAs identified in peach fruits showed distinct characteristics compared with protein-coding mRNAs, including lower expression levels, lower complexity of alternative splicing, shorter isoforms and smaller numbers of exons. Expression analysis identified 575 differentially expressed lncRNAs (DELs) classified into 6 clusters, among which members of Clusters 1, 2, 4 and 5 were putatively associated with fruit development and ripening processes. Quantitative real-time PCR revealed that the DELs indeed had stage-specific expression patterns in peach fruits. GO and KEGG enrichment analysis revealed that DELs might be associated with fruit-ripening-related physiological and metabolic changes, such as flavonoid biosynthesis, fruit texture softening, chlorophyll breakdown and aroma compound accumulation. Finally, the similarity analysis of lncRNAs within different plant species indicated the low sequence conservation of lncRNAs. Our study reports a large number of fruit-expressed lncRNAs and identifies fruit development phase-specific expressed lncRNA members, which highlights their potential functions in fruit development and ripening processes and lays the foundations for future functional research.

| S-EPMC9247041 | biostudies-literature

Genome-Wide Identification and Characterization of Long Noncoding RNAs of Brown to White Adipose Tissue Transformation in Goats.

Project description:Long noncoding RNAs (lncRNAs) play an important role in the thermogenesis and energy storage of brown adipose tissue (BAT). However, knowledge of the cellular transition from BAT to white adipose tissue (WAT) and the potential role of lncRNAs in goat adipose tissue remains largely unknown. In this study, we analyzed the transformation from BAT to WAT using histological and uncoupling protein 1 (UCP1) gene analyses. Brown adipose tissue mainly existed within the goat perirenal fat at 1 day and there was obviously a transition from BAT to WAT from 1 day to 1 year. The RNA libraries constructed from the perirenal adipose tissues of 1 day, 30 days, and 1 year goats were sequenced. A total number of 21,232 lncRNAs from perirenal fat were identified, including 5393 intronic-lncRNAs and 3546 antisense-lncRNAs. Furthermore, a total of 548 differentially expressed lncRNAs were detected across three stages (fold change ≥ 2.0, false discovery rate (FDR) < 0.05), and six lncRNAs were validated by qPCR. Furthermore, trans analysis found lncRNAs that were transcribed close to 890 protein-coding genes. Additionally, a coexpression network suggested that 4519 lncRNAs and 5212 mRNAs were potentially in trans-regulatory relationships (r > 0.95 or r < -0.95). In addition, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the targeted genes were involved in the biosynthesis of unsaturated fatty acids, fatty acid elongation and metabolism, the citrate cycle, oxidative phosphorylation, the mitochondrial respiratory chain complex, and AMP-activated protein kinase (AMPK) signaling pathways. The present study provides a comprehensive catalog of lncRNAs involved in the transformation from BAT to WAT and provides insight into understanding the role of lncRNAs in goat brown adipogenesis.

| S-EPMC6721666 | biostudies-literature

Long Noncoding RNAs and Circular RNAs in Autoimmune Diseases.

Project description:Immune responses are essential for the clearance of pathogens and the repair of injured tissues; however, if these responses are not properly controlled, autoimmune diseases can occur. Autoimmune diseases (ADs) are a family of disorders characterized by the body's immune response being directed against its own tissues, with consequent chronic inflammation and tissue damage. Despite enormous efforts to identify new drug targets and develop new therapies to prevent and ameliorate AD symptoms, no definitive solutions are available today. Additionally, while substantial progress has been made in drug development for some ADs, most treatments only ameliorate symptoms and, in general, ADs are still incurable. Hundreds of genetic loci have been identified and associated with ADs by genome-wide association studies. However, the whole list of molecular factors that contribute to AD pathogenesis is still unknown. Noncoding (nc)RNAs, such as microRNAs, circular (circ)RNAs, and long noncoding (lnc)RNAs, regulate gene expression at different levels in various diseases, including ADs, and serve as potential drug targets as well as biomarkers for disease progression and response to therapy. In this review, we will focus on the potential roles and genetic regulation of ncRNA in four autoimmune diseases-systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, and type 1 diabetes mellitus.

| S-EPMC7407480 | biostudies-literature

Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia.

Project description:Notch signaling is a key developmental pathway that is subject to frequent genetic and epigenetic perturbations in many different human tumors. Here we investigate whether long noncoding RNA (lncRNA) genes, in addition to mRNAs, are key downstream targets of oncogenic Notch1 in human T cell acute lymphoblastic leukemia (T-ALL). By integrating transcriptome profiles with chromatin state maps, we have uncovered many previously unreported T-ALL-specific lncRNA genes, a fraction of which are directly controlled by the Notch1/Rpbjκ activator complex. Finally we have shown that one specific Notch-regulated lncRNA, LUNAR1, is required for efficient T-ALL growth in vitro and in vivo due to its ability to enhance IGF1R mRNA expression and sustain IGF1 signaling. These results confirm that lncRNAs are important downstream targets of the Notch signaling pathway, and additionally they are key regulators of the oncogenic state in T-ALL.

| S-EPMC4131209 | biostudies-literature

Genome-wide identification and developmental expression profiling of long noncoding RNAs during Drosophila metamorphosis.

Project description:An increasing number of long noncoding RNAs (lncRNAs) have been discovered with the recent advances in RNA-sequencing technologies. lncRNAs play key roles across diverse biological processes, and are involved in developmental regulation. However, knowledge about how the genome-wide expression of lncRNAs is developmentally regulated is still limited. We here performed a whole-genome identification of lncRNAs followed by a global expression profiling of these lncRNAs during development in Drosophila melanogaster. We combined bioinformatic prediction of lncRNAs with stringent filtering of protein-coding transcripts and experimental validation to define a high-confidence set of Drosophila lncRNAs. We identified 1,077 lncRNAs in the given transcriptomes that contain 43,967 transcripts; among these, 646 lncRNAs are novel. In vivo expression profiling of these lncRNAs in 27 developmental processes revealed that the expression of lncRNAs is highly temporally restricted relative to that of protein-coding genes. Remarkably, 21% and 42% lncRNAs were significantly upregulated at late embryonic and larval stage, the critical time for developmental transition. The results highlight the developmental specificity of lncRNA expression, and reflect the regulatory significance of a large subclass of lncRNAs for the onset of metamorphosis. The systematic annotation and expression analysis of lncRNAs during Drosophila development form the foundation for future functional exploration.

| S-EPMC4800424 | biostudies-literature

Genome-wide identification of Arabidopsis long noncoding RNAs in response to the blue light.

Project description:Long non-coding RNAs (lncRNAs) have been shown in animals to play roles in a wide range of biological processes. In plant, light modulates the growth and development as a key external signal. However, little is known about the role of plant lncRNA in response to light. In this study, we sequenced the messenger RNAs (mRNAs), lncRNAs and microRNAs (miRNAs) in Arabidopsis seedlings under blue light for 2 h and 8 h. Compared to dark, we identified 4197 mRNAs, 375 miRNAs and 481 lncRNAs, or 5207 mRNAs, 286 miRNAs and 545 lncRNAs of differential expressions under blue light treatments for 2 h or 8 h respectively. Subsequently, a total of 407 competing endogenous RNA (ceRNA) pairs (lncRNA-mRNA-miRNA) were constructed. We identified a blue light-induced lncRNA which plays roles in blue light-directed plant photomorphogenesis and response to mannitol stress by serving as a ceRNA to sequester miR167 in a type of target mimicry. These results revealed previously unknown roles of the lncRNA in blue light signaling and mannitol stress, and provided useful resources of lncRNAs associated with miRNAs in response to blue light.

| S-EPMC7148362 | biostudies-literature

Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana.

Project description:Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.

| S-EPMC8002735 | biostudies-literature

Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean.

Project description:Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3' and 5' ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean. A total of 5,372 circRNAs were identified, approximately 80% of which were paralogous circRNAs generated from paralogous genes. Despite high sequence homology, the paralogous genes could produce different paralogous circRNAs with different expression patterns. Two thousand and one hundred thirty four circRNAs were predicted to be 92 miRNAs target mimicry. CircRNAs and circRNA isoforms exhibited tissue-specific expression patterns in soybean. Based on the function of circRNA-host genes, the soybean circRNAs may participate in many biological processes such as developmental process, multi-organism process, and metabolic process. Our study not only provided a basis for research into the function of circRNAs in soybean but also new insights into the plant circRNA kingdom.

| S-EPMC5514102 | biostudies-literature

Roles of Long Noncoding RNAs and Circular RNAs in Translation.

Project description:Most of the eukaryotic genome is pervasively transcribed, yielding hundreds to thousands of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), some of which are well conserved during evolution. Functions have been described for a few lncRNAs and circRNAs but remain elusive for most. Both classes of RNAs play regulatory roles in translation by interacting with messenger RNAs (mRNAs), microRNAs (miRNAs), or mRNA-binding proteins (RBPs), thereby modulating translation in trans Moreover, although initially defined as noncoding, a number of lncRNAs and circRNAs have recently been reported to contain functional open reading frames (ORFs). Here, we review current understanding of the roles played by lncRNAs and circRNAs in protein synthesis and discuss challenges and open questions in the field.

| S-EPMC6546045 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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