Comparative transcript profiling of gene expression between seedless Ponkan mandarin (Citrus reticulata Blanco) and its seedy wild type during floral organ development
ABSTRACT: Seedlessness is an important agronomic trait for citrus, and male sterility (MS) is one main cause of seedless citrus fruit. However, the molecular mechanism of citrus seedlessness remained not well explored. An integrative strategy combining SSH (suppression subtractive hybridization) library with cDNA microarray was employed to study the underlying mechanism of seedlessness of a Ponkan mandarin seedless mutant (Citrus reticulate Blanco). Screening with custom microarray, a total of 279 differentially expressed clones were identified, and 133 unigenes (43 contigs and 90 singletons) were obtained after sequencing. Gene Ontology (GO) distribution showed that the majority of differential genes involved in metabolic process, responded to stimulus and functioned as DNA/RNA binding, catalytic activity and oxidoreductase activity. Expression dynamics of some candidate clones revealed a gene encoding male sterility protein 2 was highly up-regulated, while several transcription factors (TFs) such as AP2/EREBP, MYB, WRKY, NAC and C2C2-GATA zinc-finger domain TFs were specifically down-regulated in the seedless mutant compared with the wild type. Our research highlighted some candidate pathways that participated in the citrus male gametophyte development and could be beneficial for seedless citrus breeding in the future. Flower buds from the seedless citrus mutant and its wild type were collected at four developmental stages: quaring stage (SF, about 20 DBF), medium bud stage (MF, about 10 DBF), flowers at full bloom stage (BF) and young ovaries of 2-3 days after flowering (OV). Total RNA extracted from the mutant and the wild type was hybridized to the array. The hybridization was performed in duplicate by dye swap.
Project description:High-throughput small RNA and degradome sequencing were performed to identify a large number of miRNAs and their targets. Differential expression of several miRNAs reveals that miRNA regulatory network was closely linked to gametophyte development and male sterility in Ponkan mandarin. The expression profiles of miR156 and miR167 as well as their targets demonstrated their contribution in male sterility in the Ponkan seedless type. This study provides valuable information for better understanding of miRNAs network in plant anther development and lays a foundation to future research on male sterility in citrus and even other species. small RNA and degradome sequencing of seedy ‘Egan No.1’ and its male sterile and seedless mutant ‘Qianyang seedless’
2014-12-08 | E-GEOD-53389 | ArrayExpress
Project description:male sterility in seedless citrus Raw sequence reads
Project description:We studied genome-wide miRNA expression in THP-1 cells treated with/without AGEs. Significant upregulation of miR-214 was observed in THP-1 cells treated with/without AGEs. Two samples, one treated with AGE-BSA and one without AGEs.
Project description:Bud mutations arise often in citrus. The selection of mutants is one of the most important breeding methods in citrus. However, the molecular bases of bud mutation have rarely been studied. To identify the potential important or novel genes involved in bud mutation, different transcriptomic techniques combing suppression subtractive hybridization (SSH) and microarray were performed between a lycopene accumulated mutant, ‘Hong Anliu’ sweet orange (Citrus sinensis L. Osbeck), and its wild-type during fruit maturation. Microarray analysis revealed that differentially expressed clones are extensively coordinated with the initiation of lycopene accumulation. After sequencing of the differentially expressed clones, a total of 267 non-redundant transcripts were obtained, 182 (68.2%) of which share homology (E-value ≤ 1×10-10) with known gene products or known protein domains. A list of candidate genes which involved in cellular metabolic process, primary metabolic process, localization, macromolecular metabolic process was obtained. Out of these genes, 12 share homology with previously described signal transduction or transcription factors, suggesting complex regulatory control. These results demonstrate profound effect on gene expression of bud mutation in citrus fruits and provide new insights into the molecular basis of bud mutation. Keywords: bud mutation, candidate genes, Citrus, cNDA microarray, suppression subtractive hybridization (SSH) Fruits from the mutant and its wild type were collected at five time points from August to December. Total RNA extracted from the mutant was hybridized to the array together with RNA from the wild type. Each hybridization was performed in duplicate by dye swap.
Project description:Expression of a panel of miRNAs was analyzed in three different cell lines comparing stable knock down of ZEB1 (shZEB) to control transfected cell lines. The analyzed cell lines derived of mammary (MDA MB 231) or colon cancer (SW480, HCT116).
Project description:The microarray test aims to find the miRNAs involved in somatic embryogenesis in Arabidopsis. The plant microRNA array V2.0 (CapitalBio Corp., Beijing, China) contained 426 non-reduplicated plant miRNA probes, including 188 in Arabidopsis. Finally, 75 plant miRNAs expressed differentially, 36 increased and 39 decreased included. Two critical period samples of somatic embryogenesis were chosen for the microarray test: the edge of embryonic calli in embryonic callus-inducing medium (ECIM) for 14 days and the secondary somatic embryos protuberances in somatic embryo-inducing medium (SEIM) for 2 days (marked as “14D” and “J2D” accordingly) . Three chip were test in each sample.
Project description:Pak1 as a serine/threonine kinase, has been implicated in cytoskeletal remodelling, cell motility, apoptosis and transformation. Pak1 plays important roles in multiple signal pathways. Pak1 protects cells from apoptosis through at least three different pathways including forkhead box O1 (FOXO1), B-cell CLL/lymphoma 2 (Bcl-2) and DLC1. Pak1 also regulates activity of Raf and Aurora kinases to affect cellular proliferation. Overexpression of Pak1 is involved in the regulation of actin assembly and disassembly through phosphorylations of LIM Kinase and cytoskeletal associated proteins such as Filamin A, Paxillin, Caldesmon, Cortactin and Arp2/3. Pak1 also regulates microtubule dynamics via activation of tubulin cofactor B (TCoB) and DLC1, and inhibition of stathmin. In spite of a large body of work about the mechanism of Pak1 action in cancer, it remains unknown whether Pak1 signaling could potentially regulate the biology of regulatory miRNAs. This is particularly relevant for gastric cancer because Pak1 can activate many regulators of miRNAs expression in gastric cancer cells including NF-kappaB and ERK, and Pak1 signaling has profound phenotypic effects on the biology of gastric cancer cells. We constructed Pak1 knockdown stable cell lines. The stable Pak1 knockdown gastric cancer BGC823 cells and control cells were performed miRNA chip analysis by CapitalBio company. Gastric cancer BGC823 cells with stable Pak1 knockdown and BGC-823 gastric cancer cells transfected with U6 were used in this experiment. Total RNA was extracted by trizol,Here we use a Capitalbio mammal microRNA V3.0(CapitalBio, Beijing, China) containing 509 well-characterized human, mouse and rat miRNAs and various controls to profile the expression levels of miRNA in 16 and conU6 group.three chip were test in each group, and the procedure was repeated twice.
Project description:Since the expression profile of miRNAs is specific in different tissues or under different physiological conditions, the correlations between miRNAs and mRNAs could vary under different biological circumstances. This is a study also used expression profiles of miRNA and mRNA during monocytic differentiation to explore the correlations between the expression levels of miRNAs and mRNA, either negative or positive. After treatment of TPA, U937 cells present functional differentiation markers as well as specific cell morphology, which were confirmed by flow cytometric analysis and Wright-Giemsa staining.Here we use a miRNA microarray (CapitalBio, Beijing, China) containing 509 well-characterized human, mouse and rat miRNAs and various controls to profile the expression levels of miRNA in normal U937 cells and differentiated U937 cells. Three independent biological experiments were performed, and for each differentiated and control sample, two hybridizations were performed by using a reversal fluorescent strategy.
Project description:MicroRNAs are important cellular components and their dysfunctions are associated with various disease.Small-cell lung cancer (SCLC) is an aggressive disease with a poor prognosis, but little is know about the underlying machinery that leads to rapid tumor growth and early metastases.In this study, clinical outcome prediction miRNAs were successfully found through expression profiling of a total of 924 miRNA genes in 42 SCLC cases. 42 patients with respectable very limited disease (training set) were enrolled. All the patients underwent surgical resection followed by adjuvant chemotherapy according to the standard of care. Total RNA was extracted from formalin-fixed paraffin-embedded （FFPE）specimens, low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V3 biochip representing about 924 microRNA . three chip were test in each group, and the procedure was repeated twice.