Identification and characterization analysis of the Oriental River Prawn (Macrobrachium nipponense) microRNA response to hypoxia using a deep sequencing approach
Ontology highlight
ABSTRACT:
ORGANISM(S): Macrobrachium nipponense
SUBMITTER: sun shengming
PROVIDER: E-GEOD-72418 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs. In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.
2016-06-01 | E-GEOD-72416 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) function as regulators in a broad range of phenotypes. The Oriental River Prawn (Macrobrachium nipponense) is an important commercial species that is widely distributed in freshwater and low-salinity estuarine regions of China and other Asian countries. To date, there are no reports describing M. nipponense miRNAs. In this study, Solexa deep sequencing technology was used for high-throughput analysis of miRNAs in a small RNA library isolated from four M. nipponense tissues (gill, hepatopancreas, muscle and hemocytes). In total, 9,227,356 reads were obtained, 4,293,155 of which were related to 267 unique miRNAs, including 203 conserved and 64 prawn-specific miRNAs. Furthermore, miRNA features including length distribution and end variations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways regulated by M. nipponense miRNAs. In addition, 880 co-expressed and 39 specific (25 normoxia-specific and 14 hypoxia-specific) miRNAs of four combined tissues of prawns that may be involved in the response to hypoxia were confirmed using miRNA microarray analysis. Real-time quantitative PCR (qPCR) analysis of eight miRNAs in the normoxia and hypoxia groups showed good concordance between the sequencing and qPCR data. This study provides the first large-scale identification and characterization of M. nipponense miRNAs and their potential targets, and represents a foundation for further characterization of their roles in the regulation of the diversity of hypoxia processes.
2016-06-01 | E-GEOD-72417 | biostudies-arrayexpress
Project description:Background: The lack of obvious symptoms of early gastric cancer (GC) as well as the absence of sensitive and specific biomarkers results in poor clinical outcomes. Tubulin is currently emerging as important regulators of the microtubule cytoskeleton and thus have a strong potential to be implicated in a number of disorders, however, its mechanism of action in gastric cancer is still unclear. Tubulin alpha-1C(TUBA1C) is a subtype of α-tubulin, high TUBA1C expression has been shown to be closely related to a poor prognosis in in various cancers,this study, for the first time, revealed the mechanism of TUBA1C promotes malignant progression of gastric cancer in vitro and in vivo. Methods: The expression of lncRNA EGFR-AS1 was detected in human GC cell lines by qRT–PCR. Mass spectrometry experiments following RNA pulldown assays found that EGFR-AS1 directly binds to TUBA1C, the CCK8, EdU, transwell, wound-healing, cell cycle assays and animal experiments were conducted to investigate the function of TUBA1C in GC. Combined with bioinformatics analyses, reveal interaction between Ki-67, E2F1, PCNA and TUBA1C by western blot. Rescue experiments furtherly demonstrated the relationship of EGFR-AS1and TUBA1C. Results: TUBA1C was proved to be a direct target of EGFR-AS1, TUBA1C promotes gastric cancer proliferation, migration and invasion by accelerating the progression of the cell cycle from the G1 phase to the S phase and activating the expression of oncogenes: Ki-67,E2F1 and PCNA. Conclusions: TUBA1C is a new potential target of LncRNA EGFR-AS1 promotes gastric cancer progression and could be a novel biomarker and therapeutic target for GC.
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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
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Project description:Ras-related associated with diabetes (RRAD) is a small Ras-related GTPase that is frequently inactivated by DNA methylation of the CpG island in its promoter region in cancer tissues. However, the role of the methylation-induced RRAD inactivation in tumorigenesis remains unclear. In this study, the Ras regulated-transcriptome and epigenome were profiled by comparing T29H (a RasV12-transformed human ovarian epithelial cell line) with T29 (an immortalized but non-transformed cell line) through Reduced representation bisulfite sequencing (RRBS-seq) and Digital gene expression (DGE) . We found that RasV12-mediated oncogenic transformation was accompanied by RRAD promoter hypermethylation and a concomitant loss of RRAD expression. In addition, we found that the RRAD promoter was hypermethylated and its transcription was reduced in ovarian cancer versus normal ovarian tissues. Treatment with the DNA methyltransferase inhibitor 5-aza-2M-bM-^@M-2-deoxycytidine (5-aza-dC) resulted in demethylation in RRAD promoter and restored RRAD expression in T29H cells. By employing knockdown and overexpression techniques in T29 and T29H, respectively, we found that RRAD inhibited glucose uptake and lactate production by repressing the expression of glucose transporters. Finally, RRAD overexpression in T29H cells inhibited tumor formation in nude mice, suggesting RRAD is a tumor suppressor gene. Our results indicate that RasV12-mediated oncogenic transformation induces RRAD epigenetic inactivation, which in turn promotes glucose uptake and may contribute to ovarian cancer tumorigenesis Reduced representation bisulfite sequencing (MspI,~40-220bp size fraction) data for two cell lines (T29 and T29H) were generated by deep sequencing, in two replicates, using Illumina HiSeq 2000.
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2021-09-30 | E-MTAB-8845 | biostudies-arrayexpress
Project description:In a previous study, we found that H2S alleviates salinity stress in cucumber by maintaining the Na+/K+ balance and by regulating H2S metabolism and the oxidative stress response. However, little is known about the molecular mechanisms behind H2S-regulated salt-stress tolerance in cucumber. Here, an integrated transcriptomic and proteomic analysis based on RNA-seq and 2-DE was used to investigate the global mechanism underlying H2S-regulated salt-stress tolerance. In total, 11 761 differentially expressed genes (DEGs) and 61 differentially expressed proteins (DEPs) were identified. Analysis of the pathways associated with the DEGs showed that salt stress enriched expression of genes in primary and energy metabolism, such as photosynthesis, carbon metabolism and biosynthesis of amino acids. Application of H2S significantly decreased these DEGs but enriched DEGs related to plant-pathogen interaction, sulfur-containing metabolism, cell defense and signal transduction pathways. Notably, changes related to sulfur-containing metabolism and cell defense were also observed through proteome analysis, such as Cysteine synthase 1, Glutathione S-transferase U25-like, Protein disulfide-isomerase and Peroxidase 2. We present the first global analysis of the mechanism underlying H2S regulation of salt-stress tolerance in cucumber through tracking changes in the expression of specific proteins and genes.
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Project description:Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B 4-week maize plants were grown in the greenhouse in the absence of UV-B. Then, they were divided in two groups. One group was treated with UV-B lights provided once for 8 h, starting 3 h after the beginning of the light period, using fixtures mounted 30 cm above the plants (Phillips, F40UVB 40 W and TL 20 W/12) at a UV-B intensity of 2 W m-2, UV-A: 0.65 W m-2. The bulbs were covered with cellulose acetate to exclude wavelengths <280 nm. For the second control group, plants were exposed for 8 h under the same lamps covered with polyester film (no UV-B treatment, UV-B: 0.04 W m-2, UV-A: 0.4 W m-2). Lamp output was recorded using a UV-B/UV-A radiometer (UV203 A+B radiometer, Macam Photometrics, Ltd, Livingston, UK) to insure that both the bulbs and filters provided the designated UV dosage in all treatments. Leaf samples were collected immediately after irradiation. RNA was extracted immediately after the treatments, and used for the microRNA microarray experiments.
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