In angiosperms, stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about genes that regulate these processes in rice. Here we generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array. In total, we identified 665 probe sets (550 genes) to be expressed specifically or predominantly in the stigma papillar cells of rice. Real-Time quantitative RT-PCR analysis of 34 selected genes confirmed their stigma-specific expression. The expression of five selected genes was further validated by RNA in situ hybridization. Gene annotation shows that several auxin-signaling components, transporters and stress-related genes are significantly overrepresented in the rice stigma gene set. We also found that genes involved in cell wall metabolism and cellular communication appear to be conserved in the stigma between rice and Arabidopsis. Our results indicate that the stigmas appear to have conserved and novel molecular functions between rice and Arabidopsis.
Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice.
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Activation of the STING (Stimulator of Interferon Genes) pathway by microbial or self-DNA, as well as cyclic di nucleotides (CDN), results in the induction of numerous genes that suppress pathogen replication and facilitate adaptive immunity. However, sustained gene transcription is rigidly prevented to avoid lethal STING-dependent pro-inflammatory disease by mechanisms that remain unknown. We demonstrate here that after autophagy-dependent STING delivery of TBK1 (TANK-binding kinase 1) to endosomal/lysosomal compartments and activation of transcription factors IRF3 (interferon regulatory factors 3) and NF-B (nuclear factor kappa beta), that STING is subsequently phosphorylated by serine/threonine UNC-51-like kinase (ULK1/ATG1) and IRF3 function is suppressed. ULK1 activation occurred following disassociation from its repressor adenine monophosphate activated protein kinase (AMPK), and was elicited by CDNS generated by the cGAMP synthase, cGAS. Thus, while CDNs may initially facilitate STING function, they subsequently trigger negative-feedback control of STING activity, thus preventing the persistent transcription of innate immune genes.
Cyclic dinucleotides trigger ULK1 (ATG1) phosphorylation of STING to prevent sustained innate immune signaling.
Age, Specimen part, TreatmentView Samples
WRKY6-overexpressing line 35S:WRKY6-9, knockout mutant wrky6-1 and wild-type seedlings were used to analyze genes whose expression are controlled under WRKY6.
The WRKY6 transcription factor modulates PHOSPHATE1 expression in response to low Pi stress in Arabidopsis.
Age, Specimen partView Samples
Despite the role of the estrogen receptor alpha (ERalpha) pathway as a key growth driver for breast cells, the phenotypic consequence of exogenous introduction of ERalpha into ERalpha-negative cells paradoxically has been growth inhibition. We map the binding profiles of ERalpha and its interacting transcription factors (TFs), FOXA1 and GATA3 in MCF-7 breast carcinoma cells. We observe that these three TFs form a functional enhanceosome and cooperatively modulate the transcriptional networks previously ascribed to ERalpha alone. We demonstrate that these enhanceosome occupied sites are associated with optimal enhancer characteristics with highest p300 coactivator recruitment, RNA Pol II occupancy, and chromatin opening. The enhancesome binding sites appear to regulate the genes driving core ERalpha function. Most importantly, we show that the transfection of all three TFs was necessary to reprogramme the ERalpha-negative MDA-MB-231 and BT-459 cells to restore the estrogen responsive growth and to transcriptionally resemble the estrogen treated ERalpha-positive MCF-7 cells. Cumulatively, these results suggest that all the enhanceosome components comprising ERalpha, FOXA1 and GATA3 are necessary for the full repertoire of cancer associated effects of the ERalpha.
Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state.
Specimen part, Cell lineView Samples
Compatibility between high-density oligonucleotide arrays is significantly affected by probe-level sequence information. With a careful filtering of the probes based on their sequence overlaps, data from different generations of microarrays can be combined more effectively. The dataset of 14 human muscle biopsy samples from patients with inflammatory myopathies that were hybridized on both HG-U95Av2 and HG-U133A human arrays for this purpose. Signal values from GCOS 1.2 with Detection call and p-value are provided here, and CEL files are also available for download.
Combining gene expression data from different generations of oligonucleotide arrays.
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roX RNAs are involved in the chromosome-wide gene regulation that occurs during dosage compensation in Drosophila. Dosage compensation equalizes expression of X-linked and autosomal genes. Drosophila males increase transcription two-fold from their single X chromosome. This is mediated by the MSL complex, which is composed of the male-specific lethal (MSL) proteins and two noncoding roX RNAs, roX1 and roX2. Upon elimination of both roX transcripts, a global decrease of X-linked gene expression is observed in males. Expression of the genes on the entire 4th chromosome also decreased in the absence of both roX transcripts. roX1 RNA also presents in females in the early stages. To investigate the effect of loss of roX transcripts on gene expression in females, gene expression was analyzed by microarrays in roX1-roX2- female flies. To eliminate inconsistency caused by differences in genetic background, expression of roX1-roX2- females with females of virtually identical genetic background but carrying the [hsp83-roX1+] transgene were compared. Expression of any chromosome did not change in roX1-roX2- females. It was concluded that roX RNAs only effect in males .
Coordinated regulation of heterochromatic genes in Drosophila melanogaster males.
We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta. Overall design: Examination of three root types of maize under salt treatment for understanding the different responding mechenism to salt stress.
Comparative transcriptome profiling of the maize primary, crown and seminal root in response to salinity stress.
Specimen part, SubjectView Samples
Expression profiling of isoflavone and 3,3-diindolylmethane treated C4-2B prostate cancer cells was conducted using Affymetrix Human Genome U133 Plus 2.0. Array
Targeting bone remodeling by isoflavone and 3,3'-diindolylmethane in the context of prostate cancer bone metastasis.
Cell line, TimeView Samples
The challenge of predicting which patients with breast cancer will develop metastases leads to the overtreatment of patients with benign disease and to the inadequate treatment of the aggressive cancers. Here, we report the development and testing of a microfluidic assay that quantifies the abundance and proliferation of migratory cells in breast-cancer specimens, for the assessment of their metastatic propensity and for the rapid screening of potential antimetastatic therapeutics. On the basis of the key roles of cell motility and proliferation in cancer metastasis, the device accurately predicts the metastatic potential of breast-cancer cell lines and of patient-derived xenografts. Compared to unsorted cancer cells, highly motile cells isolated by the device exhibited similar tumourigenic potential but markedly increased metastatic propensity in vivo. RNA sequencing of the highly motile cells revealed an enrichment of motility-related and survival-related genes. The approach might be developed into a companion assay for the prediction of metastasis in patients and for the selection of effective therapeutic regimens. Overall design: RNA was isolated from samples of 1000Â migratory or unsorted cells in triplicate
A microfluidic assay for the quantification of the metastatic propensity of breast cancer specimens.
Specimen part, Cell line, SubjectView Samples