RIKEN Integrated Sequence Analysis (RISA) System---384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

Shibata, Kazuhiro

doi:10.1101/gr.152600

Cited by 53 publications

(32 citation statements)

References 15 publications

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“…This analysis also revealed six potential sites of N-glycosylation (Asn-Xaa-Thr or Asn-Xaa-Ser) at positions 127, 175, 329, 424, 444, and 509. All of these structural features are also conserved in the amino acid sequence deduced from a mouse cDNA isolated as part of a large scale cDNA sequencing project (42). The protein encoded by this mouse cDNA (accession numbers AK004939 and BAB23684) likely corresponds to the mouse ortholog of the human serine proteinase identified in this work (Fig.…”

Section: Identification and Characterization Of A Human Fetal Liver Cmentioning

confidence: 63%

“…The amino acid sequence of human matriptase-2 identified in this work is shown in bold. The sequences for human and mouse matriptase were extracted from the SwissProt data base, whereas the sequence BAB23684 corresponding to the putative mouse matriptase-2 was deduced from a cDNA sequence reported in (42). The multiple alignment was performed with the PILEUP program of the GCG package.…”

Section: Production Of Recombinant Matriptase-2 In E Coli and Analysmentioning

confidence: 99%

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Matriptase-2, a Membrane-bound Mosaic Serine Proteinase Predominantly Expressed in Human Liver and Showing Degrading Activity against Extracellular Matrix Proteins

Velasco¹,

Cal²,

Quesada

et al. 2002

Journal of Biological Chemistry

154

233

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We have identified and cloned a fetal liver cDNA encoding a new serine proteinase that has been called matriptase-2. This protein exhibits a domain organization similar to other members of an emerging family of membrane-bound serine proteinases known as type II transmembrane serine proteinases. Matriptase-2 contains a short cytoplasmic domain, a type II transmembrane sequence, a central region with several modular structural domains including two CUB (complement factor C1s/C1r, urchin embryonic growth factor, bone morphogenetic protein) domains and three low density lipoprotein receptor tandem repeats, and finally, a Cterminal catalytic domain with all typical features of serine proteinases. The human matriptase-2 gene maps to 22q12-q13, a location that differs from all type II transmembrane serine proteinase genes mapped to date. Immunofluorescence and Western blot analysis of COS-7 cells transfected with the isolated cDNA confirmed that matriptase-2 is anchored to the cell surface. Matriptase-2 was expressed in Escherichia coli, and the purified recombinant protein hydrolyzed synthetic substrates used for assaying serine proteinases and endogenous proteins such as type I collagen, fibronectin, and fibrinogen. Matriptase-2 could also activate single-chain urokinase plasminogen activator, albeit with low efficiency. These activities were abolished by inhibitors of serine proteinases but not by inhibitors of other classes of proteolytic enzymes. Northern blot analysis demonstrated that matriptase-2 transcripts are only detected at significant levels in both fetal and adult liver, suggesting that this novel serine proteinase may play a specialized role in matrix remodeling processes taking place in this tissue during development or in adult tissues.

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Section: Identification and Characterization Of A Human Fetal Liver Cmentioning

confidence: 63%

Section: Production Of Recombinant Matriptase-2 In E Coli and Analysmentioning

confidence: 99%

Matriptase-2, a Membrane-bound Mosaic Serine Proteinase Predominantly Expressed in Human Liver and Showing Degrading Activity against Extracellular Matrix Proteins

Velasco¹,

Cal²,

Quesada

et al. 2002

Journal of Biological Chemistry

154

233

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“…Other glycopeptides from extracellular glycoproteins are commonly modified with high mannose oligosaccharides with between five and nine mannose residues in a distinct, microheterogeneic manner. In this study, two functionally unknown proteins were also identified, RIKEN cDNA 1100001H23 (44) and RIKEN cDNA 2310020A21 (45), as high mannose type oligosaccharide-carrying proteins. The N-glycosylation microheterogeneity analysis revealed that the former is modified with Man 5 GlcNAc 2 , Man 6 GlcNAc 2 , Man 7 GlcNAc 2 , and Man 8 GlcNAc 2 , whereas the latter is predominantly modified with M3 and M3F.…”

Section: Table I Observed Signals Of Aowr-labeled Oligosaccharides Rementioning

confidence: 99%

High Throughput Quantitative Glycomics and Glycoform-focused Proteomics of Murine Dermis and Epidermis

Uematsu

Furukawa

Nakagawa

et al. 2005

Molecular & Cellular Proteomics

111

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Despite recent advances in our understanding of the significance of the protein glycosylation, the throughput of protein glycosylation analysis is still too low to be applied to the exhaustive glycoproteomic analysis. Aiming to elucidate the N-glycosylation of murine epidermis and dermis glycoproteins, here we used a novel approach for focused proteomics. A gross N-glycan profiling (glycomics) of epidermis and dermis was first elucidated both qualitatively and quantitatively upon N-glycan derivatization with novel, stable isotope-coded derivatization reagents followed by MALDI-TOF(/TOF) analysis. This analysis revealed distinct features of the N-glycosylation profile of epidermis and dermis for the first time. A high abundance of high mannose type oligosaccharides was found to be characteristic of murine epidermis glycoproteins. Based on this observation, we performed high mannose type glycoform-focused proteomics by direct tryptic digestion of protein mixtures and affinity enrichment. We The rapid progress in the sequence analysis of genomes of a variety of living organisms is accelerating the investigation of various related proteins involved in biological processes and disorders. Carbohydrate modifications can profoundly affect protein function. Their importance in disease is evident from a growing number of embryonic lethal phenotypes seen in knock-out mice with defects in glycoconjugate assembly or processing (1), and hence a large scale protein glycosylation analysis has become important.The accurate identification of protein glycosylation is challenging because of the complex structures, labile nature, and microheterogeneity of glycoproteins. The presence of nonglycopeptides in a sample also limits the sensitivity for analysis of glycopeptides on mass spectrometry due to ion suppression. Although several new techniques enabling the large scale identification of glycoproteins have recently been developed (2-4), they cannot provide information about oligosaccharide moieties because the analysis is performed on peptides of which such moieties are enzymatically removed prior to the analysis. It is also well known that glycosylation is cell type-specific, so a single glycoprotein can have a different spectrum of glycan structures when expressed in different cells. Recent progress in mass spectrometry (e.g. electron capture-induced dissociation using Fourier transform mass spectrometry (5, 6) and MALDI-LIFT-TOF/TOF (7)) has demonstrated the ability to provide information both on peptide sequence and glycan structure for the analysis of glycopeptides. However, the throughput of these techniques is not high enough to apply to large scale protein glycosylation analyses. Therefore, unveiling the significance of protein glycosylation in an efficient manner requires further thought. One solution is to develop a focused approach based on function and information content.In this study, we describe a glycomic approach to rationalize the focusing process using murine dermis and epidermis as models. A gross N-glycan profi...

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“…mRNA was prepared by standard methods (11). The cDNA synthesis was carried out by using a 25-g mRNA and first-strand cDNA primer (oligo dT [12][13][14][15][16][17][18] ) with SuperScript II RT in the presence of trehalose and sorbitol (13). Subsequently, full-length cDNA was selected with biotinylated cap-trapper Abbreviations: CAGE, cap analysis gene expression; TSP, transcriptional starting point; SAGE, serial analysis of gene expression; TU, transcriptional unit; RefSeq, Reference Sequence database.…”

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confidence: 99%

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

Shiraki

Kondo

Katayama

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

666

517

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We introduce cap analysis gene expression (CAGE), which is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5 end mRNAs. CAGE allows high-throughout gene expression analysis and the profiling of transcriptional start points (TSP), including promoter usage analysis. By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), we redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit. The frequency of CAGE tags correlates well with results from other analyses, such as serial analysis of gene expression, and furthermore maps the TSPs more accurately, including in tissue-specific cases. The highthroughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression.full-length cDNA ͉ transcriptome ͉ sequencing ͉ cap-trapping E ven the comparison of mammalian genome draft sequences (1) has left many unanswered questions with regard to the exact identification of expressed genes, their promoter elements, and the network of promoter͞transcriptional factor usage that underlies gene expression. Partial identification of the promoter sites has been provided by gene discovery programs based on the sequencing of full-length cDNA libraries (2-4); these have been instrumental in identifying the sequence of promoter regions, including potentially different promoters (5). Several thousand promoters can be determined by sequencing 5Ј ends from full-length cDNA libraries and mapping the sequences to the genome, thus determining which correspond to coding and regulatory regions, respectively. These analyses can produce statistics on transcriptional start sites derived from large numbers of 5Ј end sequences. However, these methods lack the throughput to provide significantly abundant data for intermediately͞lowly expressed genes, chiefly because the comprehensive sequencing of cDNA libraries is prohibitively expensive. On the other hand, microarrays for high-throughput tissue expression analysis do exist (6), but these cannot determine transcription starting points and therefore cannot be used to accurately identify the cis regulatory elements that will be essential for computing gene networks. Another limitation of microarrays is that the only genes͞transcripts that can be studied are those that have already been identified by the sequencing, which is far from completion (2). Serial analysis of gene expression (SAGE) allows partial sequence information of short tags at the 3Ј ends of mRNAs (7) to be obtained. Although the information is partial, it is amenable to relatively cheap high-throughput digital data collection, because it is based on the cloning and subsequent sequencing of concatamers of short DNA fragments derived from 3Ј ends of multiple mRNAs (http:͞͞cgap.nci.nih.gov͞ SAGE). This method was further improved on by Long-SAGE, which allows for the cloning of 20-nt SAGE tags (8), which mainly identify single loci on the ge...

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RIKEN Integrated Sequence Analysis (RISA) System---384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

Cited by 53 publications

References 15 publications

Matriptase-2, a Membrane-bound Mosaic Serine Proteinase Predominantly Expressed in Human Liver and Showing Degrading Activity against Extracellular Matrix Proteins

Matriptase-2, a Membrane-bound Mosaic Serine Proteinase Predominantly Expressed in Human Liver and Showing Degrading Activity against Extracellular Matrix Proteins

High Throughput Quantitative Glycomics and Glycoform-focused Proteomics of Murine Dermis and Epidermis

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

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