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ABSTRACT:
PROVIDER: PRJNA760952 | ENA |
REPOSITORIES: ENA
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Project description:siRNA-mediated inhibition compared to untreated cells and cells transfected with nonsense siRNA Together with far upstream element binding protein (FBP), the FBP-interacting repressor (FIR) represents a molecular tool for the transcriptional fine tune regulation of target genes. Previous evidence indicates that strong overexpression of FBP in human hepatocellular carcinoma (HCC) supports tumor growth and correlates with poor patient prognosis. However, the role of the transcriptional repressor FIR in hepatocarcinogenesis remains poorly delineated. We show that overexpression of FIR correlates with tumor dedifferentiation and tumor cell proliferation in about 60% of primary HCCs. Elevated FIR levels are associated with genomic gains of the fir gene locus at chromosome 8q24.3 in human HCC specimens. In vitro, nuclear enrichment of FIR supports HCC cell proliferation and migration. Expression profiling of HCC cells after siRNA-mediated silencing of FIR identified the transcription factor DP-1 (TFDP1) as a transcriptional target of FIR. Surprisingly, FIR stimulates the expression of FBP in a TFDP1/E2F-dependent manner. FIR splice variants lacking or containing exon 2 and/or exon 5 are expressed in the majority of HCCs. Specific inhibition of FIR isoforms with and without exon 2 revealed that all FIR splice variants facilitate tumor-supporting effects. This finding was confirmed in xenograft transplantation experiments with lentiviral-infected shRNA targeting all FIR variants as well as FIR with and without exon 2. In summary, high-level nuclear FIR does not facilitate repressor properties but supports tumor growth in HCC cells. Thus, the pharmacological inhibition of FIR might represent a promising therapeutic strategy for HCC patients.
2014-09-03 | GSE55692 | GEO
Project description:Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability particularly of oak heartwood and, hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies in the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. We investigated the feasibility of such studies using heartwood samples core-drilled from the trunks of standing oak trees spanning the AD 1776-2014. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. We sequenced whole-genome and DNA methylome libraries for oak heartwood up to 100 and 50 years of age, respectively. However, only 56 genomic regions with sufficient coverage for quantitative methylation analysis were identified, suggesting that the high-throughput sequencing of DNA will be in principal feasible for wood formed <100 years ago is impeded by the reduction in library complexity caused by the bisulfite treatment used to generate the oak methylome.
2020-01-07 | GSE143201 | GEO
Project description:siRNA-mediated inhibition compared to untreated cells and cells transfected with nonsense siRNA Together with far upstream element binding protein (FBP), the FBP-interacting repressor (FIR) represents a molecular tool for the transcriptional fine tune regulation of target genes. Previous evidence indicates that strong overexpression of FBP in human hepatocellular carcinoma (HCC) supports tumor growth and correlates with poor patient prognosis. However, the role of the transcriptional repressor FIR in hepatocarcinogenesis remains poorly delineated. We show that overexpression of FIR correlates with tumor dedifferentiation and tumor cell proliferation in about 60% of primary HCCs. Elevated FIR levels are associated with genomic gains of the fir gene locus at chromosome 8q24.3 in human HCC specimens. In vitro, nuclear enrichment of FIR supports HCC cell proliferation and migration. Expression profiling of HCC cells after siRNA-mediated silencing of FIR identified the transcription factor DP-1 (TFDP1) as a transcriptional target of FIR. Surprisingly, FIR stimulates the expression of FBP in a TFDP1/E2F-dependent manner. FIR splice variants lacking or containing exon 2 and/or exon 5 are expressed in the majority of HCCs. Specific inhibition of FIR isoforms with and without exon 2 revealed that all FIR splice variants facilitate tumor-supporting effects. This finding was confirmed in xenograft transplantation experiments with lentiviral-infected shRNA targeting all FIR variants as well as FIR with and without exon 2. In summary, high-level nuclear FIR does not facilitate repressor properties but supports tumor growth in HCC cells. Thus, the pharmacological inhibition of FIR might represent a promising therapeutic strategy for HCC patients. Expression profiling of cells transfected with scrambled/nonsense siRNA (control), and after siRNA-mediated FIR inhibition.
2014-09-03 | E-GEOD-55692 | biostudies-arrayexpress
Project description:Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated. We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution.
2012-06-28 | GSE24226 | GEO
Project description:Objective: In order to study the change law of Chinese fir gene expression caused by fertilization, it provides scientific basis for Chinese fir fertilization theory and practice. Method: Using Illumina HiSeq4000 high-throughput sequencing technology, sequencing sequences of four different fertilizer treatment materials (control CK1, nitrogen treatment N1, phosphorous treatment P1, and phosphorous and nitrogen mixture treatment NP1, each with three biological repeats) were obtained, and a series of comparative analysis of the differences were conducted. The experimental material was the 1-year clone cuttings of Chinese fir K62. At the end of 2017year, sand culture experiment was carried out in the plastic greenhouse of research institute of subtropical forestry,CAF. Because it was transcriptome sequencing without reference genome , sequencing reads need to be spliced into de novo, unigene and transcripts are assembled, and then functional annotation, differential expression and other project analysis are conducted. Result: In 12 samples, transcriptome sequencing produced clean reads5.0E+07nt to 7.1E+07nt, and the total splicing length was 724,341,090nt. BLASTX analysis was performed on clean reads in six databases (Nr, Swiss-prot,eggNOG, ,KEGG, Pfam, GO), and 74,288 genes were generated；The Venn diagram reveals the general overview of the gene response of different fertilization treatments: in the N1-VS-CK1 comparison group, NH4NO3 stimulation induced the opening expression of 3,295 genes, and CK1 produced 2,944 genes resistant to nitrogen; Similar results were obtained for other comparison groups. Chinese fir fertilization turns on and up-regulates the expression of some genes while shutting down or down regulating some genes of expression; Analysis of gene differential expression revealed that :720 differentially expressed genes were screened out in the N1-VS-CK1 comparison group, and 3,694 genes were found to be silenced by nitrogen application. Similar results were obtained in the other five groups: a number of differentially expressed genes were screened out, and a number of genes were silenced by nitrogen and phosphorus fertilizer; The results of the heatmap clustering graph of the six comparison groups were revealed that the genes between the same treatment and the same comparison group are basically distributed in blocks: either high expression or low expression, and vice versa. The gene distribution between different treatments in the same comparison group was complementary. To fertilize Chinese fir, it is better to mix fertilizer with different types of fertilizers; The GO enrichment and functional classification has three major categories, namely, biological process BP, cell component CC and molecular function MF, with 50 small categories; Fertilization, whether single fertilizer or multiple fertilizers, has the greatest impact on the GO terms of Chinese fir: chloroplasts, cytoskeleton, cell membrane, nucleus and cytoplasm. secondly molecular function, protein binding and biological process are affected. These results revealed that nitrogen and phosphorus can promote the absorption and metabolism of themselves and each other; KEGG enrichment analysis was performed in 6 comparison groups, and the most significant first 5 Pathway KEGG terms were selected in each comparison group, the comprehensive analysis results showed that after fertilizing Chinese fir, the most significant KEGG term was photosynthesis, nitrogen metabolism, carbon fixation and carbon metabolism, plant hormone signal transduction, plant-pathogen interaction, phenylpropanoid biosynthesis, pentose-phosphate pathway, porphyrin and chlorophyll metabolism, arginine biosynthesis and ect. Based on the above studies, the significantly up-regulated or down-regulated genes in important terms obtained by GO enrichment and classification and KEEG enrichment can be studied, and the results can guide the diagnosis of Chinese fir fertilization. Conclusion: Illumina HiSeq4000 transcriptome sequencing is a quick and cheap way to study the molecular mechanisms of non-model plants, including coniferous trees with large genomes. Chinese fir fertilization can not only turn on some genes, but also turn off some genes. The growth and development of Chinese fir will be regulated in a way that is favorable for its adaptation to the environment, competitive resources and growth and development.
2019-01-12 | GSE121245 | GEO
Project description:Far infrared radiation (FIR), a subdivision of the electromagnetic spectrum, has been proved to be beneficial for long-term effects of tissue healing, anti-inflammation, promoting growth, modulating sleep, acceleration of microcirculation, and pain relief. We attempt to study whether FIR would be beneficial for renal proximal tubule cell (RPTC) cultivation and renal tissue engineering. We observed the FIR effects on RPTCs, including cell viability, functional characteristics, immunofluorescence presentations, and subcellular findings. And the FIR protective effects would be further examined with HK-2 cell (Human proximal tubule cell line) against cisplatin, a nephrotoxic agent. Our study showed that daily exposure to FIR for 30 minutes could significantly increase rabbit RPTC viability in vitro assessed by MTT assay. FIR is not only beneficial in RPTC cell viability. RPTCs with FIR exposure presented higher expression of Na-K ATPase and GLUT1 (Glucose Transporter 1). The finding was documented with western blot analysis with statistical significance. With Q-PCR, CDK5R1, GNAS, NPPB, and TEK expressions were significantly enhanced. With HK-2 cell, the proximal tubule cell line, FIR had protective effects against cisplatin nephrotoxicity through reducing apoptosis. FIR is a potential photomodulation therapy to facilitate RPTC cultivation with higher cell viability and better functional chanacteristics and would possibly be applied in further nephrotoxicity protection and other cisplatin-sensitive cell protection.
2017-09-05 | GSE98096 | GEO
Project description:High glucose impairs the angiogenic activities of late endothelial precursor cells (EPC). We found that far infrared (FIR) treatment restored partially the activity of late EPC. However, the mechanisms are unclear. We applied microRNA expression microarrays to assess the microRNA expression profiles of high glucose-treated late EPC with or without FIR treatment.
2014-04-03 | GSE37043 | GEO
Project description:High glucose impairs the angiogenic activities of late endothelial precursor cells (EPC). We found that far infrared (FIR) treatment restored partially the activity of late EPC. However, the mechanisms are unclear. We performed gene expression microarray analysis to assess the expression profiles of high glucose-treated late EPC with or without FIR treatment.
2014-04-03 | GSE37044 | GEO