29 results match your criteria: "Omics Science Center (OSC)[Affiliation]"
Genome Res
September 2022
RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
In eukaryotes, capped RNAs include long transcripts such as messenger RNAs and long noncoding RNAs, as well as shorter transcripts such as spliceosomal RNAs, small nucleolar RNAs, and enhancer RNAs. Long capped transcripts can be profiled using cap analysis gene expression (CAGE) sequencing and other methods. Here, we describe a sequencing library preparation protocol for short capped RNAs, apply it to a differentiation time course of the human cell line THP-1, and systematically compare the landscape of short capped RNAs to that of long capped RNAs.
View Article and Find Full Text PDFBMC Genomics
September 2019
Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
Background: The work of the FANTOM5 Consortium has brought forth a new level of understanding of the regulation of gene transcription and the cellular processes involved in creating diversity of cell types. In this study, we extended the analysis of the FANTOM5 Cap Analysis of Gene Expression (CAGE) transcriptome data to focus on understanding the genetic regulators involved in mouse cerebellar development.
Results: We used the HeliScopeCAGE library sequencing on cerebellar samples over 8 embryonic and 4 early postnatal times.
Nucleic Acids Res
December 2018
Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.
MicroRNAs (miRNAs) modulate the post-transcriptional regulation of target genes and are related to biology of complex human traits, but genetic landscape of miRNAs remains largely unknown. Given the strikingly tissue-specific miRNA expression profiles, we here expand a previous method to quantitatively evaluate enrichment of genome-wide association study (GWAS) signals on miRNA-target gene networks (MIGWAS) to further estimate tissue-specific enrichment. Our approach integrates tissue-specific expression profiles of miRNAs (∼1800 miRNAs in 179 cells) with GWAS to test whether polygenic signals enrich in miRNA-target gene networks and whether they fall within specific tissues.
View Article and Find Full Text PDFSci Rep
September 2018
Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, 2052, Australia.
Smooth muscle cells (SMC) in blood vessels are normally growth quiescent and transcriptionally inactive. Our objective was to understand promoter usage and dynamics in SMC acutely exposed to a prototypic growth factor or pro-inflammatory cytokine. Using cap analysis gene expression (FANTOM5 project) we report differences in promoter dynamics for immediate-early genes (IEG) and other genes when SMC are exposed to fibroblast growth factor-2 or interleukin-1β.
View Article and Find Full Text PDFCerebellum
June 2018
Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.
Laser-capture microdissection was used to isolate external germinal layer tissue from three developmental periods of mouse cerebellar development: embryonic days 13, 15, and 18. The cerebellar granule cell-enriched mRNA library was generated with next-generation sequencing using the Helicos technology. Our objective was to discover transcriptional regulators that could be important for the development of cerebellar granule cells-the most numerous neuron in the central nervous system.
View Article and Find Full Text PDFEBioMedicine
October 2017
Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 3510198, Japan; Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo 1058461, Japan. Electronic address:
PLoS Biol
September 2017
International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period.
View Article and Find Full Text PDFNat Biotechnol
September 2017
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.
MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libraries, with matching Cap Analysis Gene Expression (CAGE) data, from 396 human and 47 mouse RNA samples. Promoters were identified for 1,357 human and 804 mouse miRNAs and showed strong sequence conservation between species.
View Article and Find Full Text PDFMethods Mol Biol
June 2018
Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.
Cap analysis of gene expression (CAGE) is a convenient approach for genome-wide identification of promoter regions at single base-pair resolution level and accurate expression estimation of the corresponding transcripts. Depending on the initial biomaterial amount and sequencing technology, different computational pipelines for data processing are available, as well as variations of the CAGE protocol that improve sensitivity and accuracy. Therefore, this chapter elucidates the key steps of sample preparation, sequencing, and data analysis via an example of a promoter expression estimation study in chicken development.
View Article and Find Full Text PDFMethods Mol Biol
January 2017
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Methods Mol Biol
February 2018
Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
Transcripts in all eukaryotes are characterized by the 5'-end specific cap structure in mRNAs. Cap Analysis Gene Expression or CAGE makes use of these caps to specifically obtain cDNA fragments from the 5'-end of RNA and sequences those at high throughput for transcript identification and genome-wide mapping of transcription start sites for coding and noncoding genes. Here, we provide an improved version of our nanoCAGE protocol that has been developed for preparing CAGE libraries from as little as 50 ng of total RNA within three standard working days.
View Article and Find Full Text PDFPLoS Genet
March 2017
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom.
The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria.
View Article and Find Full Text PDFNature
March 2017
RIKEN Center for Life Science Technologies (Division of Genomic Technologies), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045 Japan.
Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters.
View Article and Find Full Text PDFDatabase (Oxford)
November 2017
Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Kanagawa 230-0045, Japan
The Functional Annotation of the Mammalian Genome project (FANTOM5) mapped transcription start sites (TSSs) and measured their activities in a diverse range of biological samples. The FANTOM5 project generated a large data set; including detailed information about the profiled samples, the uncovered TSSs at high base-pair resolution on the genome, their transcriptional initiation activities, and further information of transcriptional regulation. Data sets to explore transcriptome in individual cellular states encoded in the mammalian genomes have been enriched by a series of additional analysis, based on the raw experimental data, along with the progress of the research activities.
View Article and Find Full Text PDFNucleic Acids Res
April 2016
Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA
Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs.
View Article and Find Full Text PDFNat Commun
September 2015
Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan.
Modulation of epigenetic patterns has promising efficacy for treating cancer. 5-Hydroxymethylated cytosine (5-hmC) is an epigenetic mark potentially important in cancer. Here we report that 5-hmC is an epigenetic hallmark of prostate cancer (PCa) progression.
View Article and Find Full Text PDFSci Rep
July 2015
Fondazione Bruno Kessler, Via Sommarive 18, I-38123 Povo, Trento, Italy.
The analysis of CAGE (Cap Analysis of Gene Expression) time-course has been proposed by the FANTOM5 Consortium to extend the understanding of the sequence of events facilitating cell state transition at the level of promoter regulation. To identify the most prominent transcriptional regulations induced by growth factors in human breast cancer, we apply here the Complexity Invariant Dynamic Time Warping motif EnRichment (CIDER) analysis approach to the CAGE time-course datasets of MCF-7 cells stimulated by epidermal growth factor (EGF) or heregulin (HRG). We identify a multi-level cascade of regulations rooted by the Serum Response Factor (SRF) transcription factor, connecting the MAPK-mediated transduction of the HRG stimulus to the negative regulation of the MAPK pathway by the members of the DUSP family phosphatases.
View Article and Find Full Text PDFBMC Genomics
December 2014
Omics Science Center, RIKEN Yokohama Institute, Omics Science Center (OSC), 1-17-22 Suehiro cho, Tsurumi ku, Yokohama, Japan.
Background: Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been studied individually, not much is known about their relation to each other with respect to expression levels and regulatory regions. Here we analyzed data from hundreds of mouse and human samples included in the FANTOM5 project, to identify transcript initiation sites, expression levels, expression correlations and regulatory regions of the three genes.
View Article and Find Full Text PDFNat Biotechnol
March 2014
1] RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Suehiro-cho, Tsurumi-ku, Yokohama, Japan. [2] RIKEN Omics Science Center (OSC), Yokohama, Japan.
Exp Cell Res
February 2013
Omics Science Center (OSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan.
Adipogenesis is the process of cell differentiation by which mesenchymal stem cells (MSC) become adipocytes. Investigating the transcriptional regulatory process during adipogenesis may provide strategies to prevent obesity and other metabolic disorders. In recent years, numerous zinc finger proteins (ZFPs) have been implicated in regulating differentiation and cell fate determination.
View Article and Find Full Text PDFBiochemistry
August 2012
RIKEN Omics Science Center (OSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Yokohama, Kanagawa 230-0045, Japan.
Nucleic acid oligonucleotides are widely used in hybridization experiments for specific detection of complementary nucleic acid sequences. For design and application of oligonucleotides, an understanding of their thermodynamic properties is essential. Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotides (ECHOs) were developed as uniquely labeled DNA oligomers containing commonly one thymidine having two covalently linked thiazole orange dye moieties.
View Article and Find Full Text PDFMethods Mol Biol
July 2012
Omics Science Center (OSC), RIKEN Yokohama Institute, Kanagawa, Japan.
Since its discovery over three decades ago, it has become abundantly clear that the ubiquitin (Ub) system is a quintessential feature of all aspects of eukaryotic biology. At the heart of the system lies the conjugation and deconjugation of Ub and Ub-like (Ubls) proteins to proteins or lipids drastically altering the biochemistry of the targeted molecules. In particular, it represents the primary mechanism by which protein stability is regulated in eukaryotes.
View Article and Find Full Text PDFFront Biosci (Landmark Ed)
January 2012
Omics Science Center (OSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, 230-0045 Kanagawa, Japan.
The ubiquitin (Ub) system is centered on conjugation and deconjugation of Ub and Ub-like (Ubls) proteins by a system of ligases and peptidases, respectively. Ub/Ubls contain the beta-grasp fold, also found in numerous proteins with biochemically distinct roles unrelated to the conventional Ub-system. The beta-GF underwent an early radiation spawning at least seven clades prior to the divergence of extant organisms from their last universal common ancestor, first emerging in the context of translation-related RNA-interactions and subsequently exploding to occupy various functional niches.
View Article and Find Full Text PDFNucleic Acids Res
May 2011
RIKEN Omics Science Center (OSC), RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan.
The application of isothermal amplification technologies is rapidly expanding and currently covers different areas such as infectious disease, genetic disorder and drug dosage adjustment. Meanwhile, many of such technologies have complex reaction processes and often require a fine-tuned primer set where existing primer design tools are not sufficient. We have developed a primer selection system for one important primer, the turn-back primer (TP), which is commonly used in loop-mediated amplification (LAMP) and smart amplification process (SmartAmp).
View Article and Find Full Text PDFBiotechniques
December 2010
RIKEN Omics Science Center (OSC), RIKEN Yokohama Institute, Yokohama, Japan.
In DNA amplification, the initial step of copying a target sequence from the template DNA--the so-called intermediate product generation step--is very important. In examining the turn-back primer (TP)-dependent isothermal DNA amplification (TIA) method, we determined the actual time point of intermediate product generation by extrapolating dsDNA amplification curves. Our results indicate that intermediate product creation is the rate-limiting step in TIA, and good TP design is advantageous for improving the intermediate production process.
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