Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

Dupuy, Denis; Bertin, Nicolas; Venkatesan, Kavitha; Tu, Domena; Lee, David; Rosenberg, Jennifer; Svrzikapa, Nenad; Blanc, Aurelie; Carnec, Alain; Carvunis, Anne‐Ruxandra; Shingles, Jane; Reece‐Hoyes, John S.; Hunt-Newbury, Rebecca; Viveiros, Ryan; Mohler, William A.; Taşan, Murat; Roth, Frederick P.; Johnsen, Robert; Moerman, Donald G.; Baillie, David L.; Vidal, Marc

doi:10.1038/nbt1305

Cited by 275 publications

(209 citation statements)

References 42 publications

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“…The main functions of genes were determined by GO HMGB1 accelerates LPS-induced lung cell proliferation W Li et al analysis as described previously. [22][23][24] We used Fisher's exact test and χ 2 test results to classify the GO categories, and FDRs were calculated to correct P-values. Pathway analysis was used to identify the significantly changed pathways of the differential genes according to KEGG, Biocarta, and Reatome.…”

Section: Hmgb1 Accelerates Lps-induced Lung Cell Proliferation W LI Ementioning

confidence: 99%

High-mobility group box 1 accelerates lipopolysaccharide-induced lung fibroblast proliferation in vitro: involvement of the NF-κB signaling pathway

Deng

et al. 2015

Laboratory Investigation

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The mechanism underlying lipopolysaccharide (LPS)-induced aberrant proliferation of lung fibroblasts in Gram-negative bacilli-associated pulmonary fibrosis is unknown. High-mobility group box 1 (HMGB1) is a ubiquitous nuclear protein that is released from the nuclei of lung fibroblasts after LPS stimulation. It can exasperate LPS-induced inflammation and hasten cell proliferation. Thus, this study investigated the effects of LPS-and/or HMGB1-stimulating murine lung fibroblasts on gene expression using various assays in vitro. Thiazolyl-diphenyl-tetrazolium bromide (MTT) assay data showed that either LPS or HMGB1 could induce lung fibroblast proliferation. Endogenous HMGB1 secreted from lung fibroblasts was detected by enzyme-linked immunosorbent assay (ELISA) 48 h after LPS stimulation. Pretreatment with an anti-HMGB1 antibody inhibited the proliferative effects of LPS on lung fibroblasts. DNA microarray data showed that the NF-κB signaling genes were upregulated in cells after stimulated with LPS, HMGB1, or both. Secretion of matrix metalloproteinase (MMP)-2 and MMP-9, and tissue inhibitor of metalloproteinase 2 (TIMP-2) was significantly upregulated after treatment with LPS, HMGB1, or their combination. However, an NF-κB inhibitor was able to downregulate levels of these proteins. In addition, levels of Toll-like receptor 4 (TLR4), Toll-like receptor 2 (TLR2), and receptors for advanced glycation end products (RAGE) mRNA and proteins were also upregulated in these cells after LPS treatment and further upregulated by LPS plus HMGB1. In conclusion, the data from the current study demonstrate that LPS-induced lung fibroblast secretion of endogenous HMGB1 can augment the proproliferative effects of LPS and, therefore, may play a key role in exacerbation of pulmonary fibrosis. The underlying molecular mechanisms are related to the activation of the TLR4/NF-κB signaling pathway and its downstream targets.

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Section: Hmgb1 Accelerates Lps-induced Lung Cell Proliferation W LI Ementioning

confidence: 99%

High-mobility group box 1 accelerates lipopolysaccharide-induced lung fibroblast proliferation in vitro: involvement of the NF-κB signaling pathway

Deng

et al. 2015

Laboratory Investigation

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“…However, production of larger numbers of monoclonal capsules by means of high initial dilution is prohibitive as production volumes and processing times would rapidly become too high for large-scale laboratory applications. Therefore, we embedded cells under conditions of low dilution adapting the complex object parametric analyzer and sorter (COPAS) technology (31)(32)(33) featuring analyses rates of 30-40 compartments per second as a tool for the differentiation between monoclonal microcarriers and empty or polyclonal ones after cell cultivation.…”

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confidence: 99%

Isolation of monoclonal microcarriers colonized by fluorescent E. coli

et al. 2008

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Microencapsulation gains increasing importance for processing of bacterial libraries and especially in high-throughput (HT) environments where [10 6 samples per day are studied. As a rule, a one-to-one relationship between an individual cell and analytical results is of key importance. Ideally, each microcarrier would therefore contain exactly one cell or colony. However, synthesis of larger numbers of capsules containing exactly one cell is not feasible as cells are randomly distributed during carrier-production. The dilemma is that high dilution conditions will yield a satisfactory degree of monoclonality, but also a very large fraction of empty compartments, whereas distribution under low dilution generates unacceptable numbers of polyclonal compartments for whose removal no satisfactory technologies exist. Hydrogel carriers with a volume of 35 nL were used as growth compartments for individual microbial colonies. E. coli cells expressing green fluorescent protein (GFP) were encapsulated at low dilution thereby intentionally producing a considerable amount of polyclonal microcarrieres. Empty and polyclonal microcarriers were then removed from the desired monoclonal fraction by a COPAS Plus particle analyzer. The results were compared with model predictions in order to investigate possible limitations in the analysis and sorting of monoclonal microcarriers by COPAS. Fluorescent E. coli cells (GFP) distributed randomly throughout the microcarrier population. Cells were successfully propagated to colonies in the microcarriers and enriched to 95% monoclonality by a COAPS sorter. Enrichment-efficiency was found to mainly depend on the colony diameter. With increasing colony size two contrary effects were observed: First, improved sorting efficiency due to increased fluorescence intensity and therefore higher detection efficiency, and second, deterioration of sorting efficiency due to occlusion occurring in polyclonal carriers. The combination of microencapsulation under low dilution conditions followed by HT sorting procedures is an efficient way for isolating larger amount of monoclonal carriers from bacterial libraries while concomitantly keeping the amounts of empty carriers at a moderate level. ' International Society for Advancement of CytometryKey terms microencapsulation; monoclonality; microcarrier; in vitro compartmentalization (IVC); fluorescent E. coli; COPAS plus particle analyzer and sorter; ultrahigh throughput screening THE enormous complexity of living systems makes high-throughput (HT) experimenting and analyses an indispensable tool for research and development in the lifeand biosciences. Sample numbers exceeding 10 6 per day (1-4) require new technologies for sample miniaturization and highly parallelized processing (5). Naturally, most experimental strategies rely on formation of spatially separated monoclonal cell assemblies at the beginning. If microbial species are studied, an approach that is frequently employed for generating larger numbers of monoseptic compartments is to first ...

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“…Absolute value of fluorescence for individual worms are represented, and worms were only included if at least one fluorescence channel was above background. Individual worm profiles were then assembled into chronograms to visualize the ratio of fluorescence of each of the reporters along the animal body during the postembryonic development as previously described 50 . Each line of a chronogram represents the average profile of all the worms of the same exact size in the population analysed (see Supplementary Fig.…”

Section: Methodsmentioning

confidence: 99%

Backbone-independent nucleic acid binding by splicing factor SUP-12 reveals key aspects of molecular recognition

et al. 2014

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Cellular differentiation is frequently accompanied by alternative splicing, enabled by the expression of tissue-specific factors which bind to pre-mRNAs and regulate exon choice. During Caenorhabditis elegans development, muscle-specific expression of the splicing factor SUP-12, together with a member of the Fox-1 family of splicing proteins, generates a functionally distinct isoform of the fibroblast growth factor receptor EGL-15. Using a combination of NMR spectroscopy and isothermal titration calorimetry, we determined the mode of nucleic acid binding by the RNA recognition motif domain of SUP-12. The calculated structures provide the first atomic details of RNA and DNA binding by the family of proteins that include SUP-12, RBM24, RBM38/RNPC1, SEB-4 and XSeb4R. This information was further used to design strategic mutations to probe the interaction with ASD-1 and to quantitatively perturb splicing in vivo.

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Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

Cited by 275 publications

References 42 publications

High-mobility group box 1 accelerates lipopolysaccharide-induced lung fibroblast proliferation in vitro: involvement of the NF-κB signaling pathway

High-mobility group box 1 accelerates lipopolysaccharide-induced lung fibroblast proliferation in vitro: involvement of the NF-κB signaling pathway

Isolation of monoclonal microcarriers colonized by fluorescent E. coli

Backbone-independent nucleic acid binding by splicing factor SUP-12 reveals key aspects of molecular recognition

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