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Your search keyword '"Sayaka Nagao-Sato"' showing total 6 results
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6 results on '"Sayaka Nagao-Sato"'

1. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Author

Christine L. Mummery, Hiroshi Kawamoto, Mitsuru Morimoto, Hiroki Sato, Misako Yoneda, Kim M. Summers, Haruhiko Koseki, Carsten O. Daub, Imad Abugessaisa, Olga Hrydziuszko, Akira Hasegawa, Afsaneh Eslami, J Kenneth Baillie, Dan Goldowitz, Frank Brombacher, Piero Carninci, Thomas J. Ha, Tomokatsu Ikawa, Peter G. Zhang, Andru Tomoiu, Erik Arner, Robin Andersson, Soichi Kojima, Margaret Patrikakis, Andreas Lennartsson, Christine A. Wells, Valerio Orlando, Miki Kojima, Lesley M. Forrester, Peter Arner, Marina Lizio, Christopher J. Mungall, Geoffrey J. Faulkner, Berit Lilje, David A. Hume, Takeya Kasukawa, Hideya Kawaji, Louise N. Winteringham, Soichi Ogishima, Kristoffer Vitting-Seerup, Jayson Harshbarger, Michael Detmar, Anita Schwegmann, Yasushi Okazaki, Rolf Swoboda, Alka Saxena, Jun Kawai, Hiromi Nishiyori-Sueki, Mitsuko Hara, Yoshihide Hayashizaki, Ernst J. Wolvetang, Chieko Kai, Naoto Kondo, Richard A Axton, Albin Sandelin, James Briggs, Yutaka Nakachi, Dmitry A. Ovchinnikov, Carmelo Ferrai, Mitsuyoshi Murata, Masayoshi Itoh, Finn Drabløs, Anthony G Beckhouse, Lynsey Fairbairn, Meenhard Herlyn, Mariko Okada-Hatakeyama, Beatrice Bodega, Susan E. Zabierowski, Morana Vitezic, Michiel J. L. de Hoon, Masaaki Furuno, Ana Pombo, Reto Guler, Hiroshi Tanaka, Alistair R. R. Forrest, Serkan Sahin, Timo Lassmann, Robert Passier, S. Peter Klinken, Tom C. Freeman, Alexander D. Diehl, Niklas Mejhert, Anna Ehrlund, Ken Miyaguchi, Michela Fagiolini, Nicolas Bertin, Michelle Rönnerblad, Sayaka Nagao-Sato, Levon M. Khachigian, Mitsuhiro Endoh, Margaret B. Davis, Shiro Fukuda, Daisuke Sugiyama, Xian-Yang Qin, Malcolm E. Fisher, Yosuke Mizuno, Jessica Severin, Sarah Klein, Suzana Savvi, Kelly J. Morris, Terrence F. Meehan, Yuri Ishizu, Fumi Hori, Ahmad M. N. Alhendi, Sachi Ishikawa-Kato, Tsugumi Kawashima, Harukazu Suzuki, Sugata Roy, and Chiyo Yanagi-Mizuochi

Subjects
Transcription, Genetic, Cellular differentiation, Enhancer RNAs, Biology, Article, Mice, Dogs, Transcription (biology), Animals, RNA, Messenger, Enhancer, Gene, Transcription factor, Genetics, Regulation of gene expression, Multidisciplinary, Binding Sites, Stem Cells, Gene Expression Regulation, Developmental, Promoter, Cell Differentiation, Cell biology, Rats, Enhancer Elements, Genetic, Cattle, Transcription Factors
Abstract

Uncaging promoter and enhancer dynamics In order to understand cellular differentiation, it is important to understand the timing of the regulation of gene expression. Arner et al. used cap analysis of gene expression (CAGE) to analyze gene enhancer and promoter activities in a number of human and mouse cell types. The RNA of enhancers was transcribed first, followed by that of transcription factors, and finally by genes that are not transcription factors. Science , this issue p. 1010

Published
2015

2. Transcription and enhancer profiling in human monocyte subsets

Author

Petra Hoffmann, Piotr J. Balwierz, Timo Lassmann, Kathrin Renner, Sayaka Nagao-Sato, David A. Hume, Yoshihide Hayashizaki, Michael Rehli, Christian Schmidl, Katrin Peter, Reinhard Andreesen, Marina Kreutz, Alistair R. R. Forrest, Harukazu Suzuki, Matthias Edinger, Piero Carninci, Masayoshi Itoh, Hideya Kawaji, and Ruediger Eder

Subjects
Genetics, CD14, Immunology, Promoter, Regulome, Cell Biology, Hematology, Biology, Biochemistry, Cap analysis gene expression, Cell biology, Gene expression profiling, Enhancer, Downstream Enhancer, Transcription factor
Abstract

Human blood monocytes comprise at least 3 subpopulations that differ in phenotype and function. Here, we present the first in-depth regulome analysis of human classical (CD14(++)CD16(-)), intermediate (CD14(+)CD16(+)), and nonclassical (CD14(dim)CD16(+)) monocytes. Cap analysis of gene expression adapted to Helicos single-molecule sequencing was used to map transcription start sites throughout the genome in all 3 subsets. In addition, global maps of H3K4me1 and H3K27ac deposition were generated for classical and nonclassical monocytes defining enhanceosomes of the 2 major subsets. We identified differential regulatory elements (including promoters and putative enhancers) that were associated with subset-specific motif signatures corresponding to different transcription factor activities and exemplarily validated novel downstream enhancer elements at the CD14 locus. In addition to known subset-specific features, pathway analysis revealed marked differences in metabolic gene signatures. Whereas classical monocytes expressed higher levels of genes involved in carbohydrate metabolism, priming them for anaerobic energy production, nonclassical monocytes expressed higher levels of oxidative pathway components and showed a higher mitochondrial routine activity. Our findings describe promoter/enhancer landscapes and provide novel insights into the specific biology of human monocyte subsets.

Published
2014
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3. The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

Author

Michael Rehli, Petra Hoffmann, Masayoshi Itoh, Hideya Kawaji, Leo Hansmann, Reinhard Andreesen, Matthias Edinger, Yoshihide Hayashizaki, Timo Lassmann, Jun Kawai, Piero Carninci, Piotr J. Balwierz, Sayaka Nagao-Sato, Christian Schmidl, Harukazu Suzuki, and Alistair R. R. Forrest

Subjects
Genetics, Regulation of gene expression, Immunology, hemic and immune systems, chemical and pharmacologic phenomena, Promoter, Cell Biology, Hematology, Biology, Biochemistry, Cap analysis gene expression, Cell biology, Gene expression profiling, ETS1, Gene expression, Enhancer, Transcription factor
Abstract

CD4(+)CD25(+)FOXP3(+) human regulatory T cells (Tregs) are essential for self-tolerance and immune homeostasis. Here, we describe the promoterome of CD4(+)CD25(high)CD45RA(+) naive and CD4(+)CD25(high)CD45RA(-) memory Tregs and their CD25(-) conventional T-cell (Tconv) counterparts both before and after in vitro expansion by cap analysis of gene expression (CAGE) adapted to single-molecule sequencing (HeliScopeCAGE). We performed comprehensive comparative digital gene expression analyses and revealed novel transcription start sites, of which several were validated as alternative promoters of known genes. For all in vitro expanded subsets, we additionally generated global maps of poised and active enhancer elements marked by histone H3 lysine 4 monomethylation and histone H3 lysine 27 acetylation, describe their cell type-specific motif signatures, and evaluate the role of candidate transcription factors STAT5, FOXP3, RUNX1, and ETS1 in both Treg- and Tconv-specific enhancer architectures. Network analyses of gene expression data revealed additional candidate transcription factors contributing to cell type specificity and a transcription factor network in Tregs that is dominated by FOXP3 interaction partners and targets. In summary, we provide a comprehensive and easily accessible resource of gene expression and gene regulation in human Treg and Tconv subpopulations.

Published
2014
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4. Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation

Author

Erik Arner, Robin Andersson, Albin Sandelin, Mohsen Karimi, Tor Olofsson, Sören Lehmann, Ilka Hoof, Masayoshi Itoh, Alistair R. R. Forrest, Karl Ekwall, Yoshihide Hayashizaki, Timo Lassmann, Piero Carninci, Iyadh Douagi, Hideya Kawaji, Sayaka Nagao-Sato, Michiel J. L. de Hoon, Andreas Lennartsson, and Michelle Rönnerblad

Subjects
Genetics, Immunology, Cell Biology, Hematology, Methylation, Biology, Biochemistry, Granulopoiesis, Epigenetics of physical exercise, CpG site, DNA methylation, Epigenetics, Enhancer, Transcription factor
Abstract

In development, epigenetic mechanisms such as DNA methylation have been suggested to provide a cellular memory to maintain multipotency but also stabilize cell fate decisions and direct lineage restriction. In this study, we set out to characterize changes in DNA methylation and gene expression during granulopoiesis using 4 distinct cell populations ranging from the oligopotent common myeloid progenitor stage to terminally differentiated neutrophils. We observed that differentially methylated sites (DMSs) generally show decreased methylation during granulopoiesis. Methylation appears to change at specific differentiation stages and overlap with changes in transcription and activity of key hematopoietic transcription factors. DMSs were preferentially located in areas distal to CpG islands and shores. Also, DMSs were overrepresented in enhancer elements and enriched in enhancers that become active during differentiation. Overall, this study depicts in detail the epigenetic and transcriptional changes that occur during granulopoiesis and supports the role of DNA methylation as a regulatory mechanism in blood cell differentiation.

Published
2013
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5. Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer

Author

Eri Saijo, Miki Kojima, Hideya Kawaji, Masayoshi Itoh, Piero Carninci, Ai Kaiho, Yoshihide Hayashizaki, Timo Lassmann, Alistair R. R. Forrest, Sayaka Nagao-Sato, Mutsumi Kanamori-Katayama, and Marina Lizio

Subjects
DNA, Complementary, Science, Gene Expression, Computational biology, Biology, Genome, Workflow, Molecular Genetics, Automation, Mice, Genome Analysis Tools, Complementary DNA, Molecular Cell Biology, Genetics, Animals, Humans, Genomic library, Base sequence, Gene Library, Multidisciplinary, Base Sequence, cDNA library, Genome, Human, Reproducibility of Results, Computational Biology, Sequence Analysis, DNA, Genomics, Cap analysis gene expression, Gene Expression Regulation, Medicine, Human genome, Research Article
Abstract

BackgroundCap analysis of gene expression (CAGE) is a 5' sequence tag technology to globally determine transcriptional starting sites in the genome and their expression levels and has most recently been adapted to the HeliScope single molecule sequencer. Despite significant simplifications in the CAGE protocol, it has until now been a labour intensive protocol.MethodologyIn this study we set out to adapt the protocol to a robotic workflow, which would increase throughput and reduce handling. The automated CAGE cDNA preparation system we present here can prepare 96 'HeliScope ready' CAGE cDNA libraries in 8 days, as opposed to 6 weeks by a manual operator.We compare the results obtained using the same RNA in manual libraries and across multiple automation batches to assess reproducibility.ConclusionsWe show that the sequencing was highly reproducible and comparable to manual libraries with an 8 fold increase in productivity. The automated CAGE cDNA preparation system can prepare 96 CAGE sequencing samples simultaneously. Finally we discuss how the system could be used for CAGE on Illumina/SOLiD platforms, RNA-seq and full-length cDNA generation.

Published
2012

6. A promoter-level mammalian expression atlas

Author

Frank Brombacher, Wyeth W. Wasserman, Hiromasa Morikawa, Fumi Hori, Sayaka Nagao-Sato, Artem S. Kasianov, Mitsuhiro Endoh, Ilka Hoof, Hans Clevers, Hideki Tatsukawa, Anita Schwegmann, Kang Li, David A. de Lima Morais, Yoshihide Hayashizaki, Morana Vitezic, Judith A. Blake, Leonard Lipovich, Hozumi Motohashi, Timothy Ravasi, Meenhard Herlyn, Shuji Kawaguchi, Antti Sajantila, Haruhiko Koseki, Lukasz Huminiecki, Tsugumi Kawashima, Carrie A. Davis, Mamoon Rashid, Winston Hide, Alka Saxena, Mizuho Sakai, Carsten O. Daub, Kim M. Summers, Yuki Hasegawa, Hisashi Shimoji, Margaret Patrikakis, Efthymios Motakis, Morten Beck Rye, Dan Goldowitz, Masaaki Furuno, Lynsey Fairbairn, Alan Mackay-Sim, Andreas Lennartsson, John A.C. Archer, Mitsuru Morimoto, Harukazu Suzuki, Silvia Zucchelli, Weon Ju Lee, Hiroki Sato, Alan J. Knox, Margherita Francescatto, Xiaobei Zhao, Jay W. Shin, Thomas R. Gingeras, Soichi Ogishima, Jayson Harshbarger, Mark Thompson, Beatrice Bodega, Marco Chierici, Shintaro Katayama, Albin Sandelin, Sarah Rennie, Silvano Piazza, Tomokatsu Ikawa, Matthias Harbers, Magda Babina, Peter G. Zhang, Gabriel M. Altschule, Lenhard Vladimir B. Bajic, Andrew P. Gibson, Malcolm E. Fisher, Karl Ekwall, Yukio Nakamura, Arnab Pain, Michiel J. L. de Hoon, Toshio Kitamura, Anthony G Beckhouse, Ai Kaiho, Julian Gough, James Briggs, Jordan A. Ramilowski, Miki Kojima, Alistair R. R. Forrest, Erik Anthony Schultes, Jessica C. Mar, Dipti Vijayan, Peter Arner, S. Peter Klinken, Michael Rehli, Kazuhiro Kajiyama, Christophe Simon, Piero Carninci, Marco Roncador, Shigeo Koyasu, Mary C. Farach-Carson, Shigehiro Yoshida, Swati Pradhan-Bhatt, Zuotian Tatum, Masanori Suzuki, Mette C. Jørgensen, Benoit Marchand, Misako Yoneda, James Prendergast, Noriko Ninomiya, Tom C. Freeman, Yulia A. Medvedeva, Niklas Mejhert, Jun Takai, Alexander D. Diehl, Akiko Saka, Marc van de Wetering, Takehiro Hashimoto, Naoto Kondo, Martin S. Taylor, Albert S.B. Edge, Mutsumi Kanamori-Katayama, Colin A. Semple, Alexander V. Favorov, Giuseppe Jurman, Toshiyuki Nakamura, Thomas J. Ha, Yuri Ishizu, Shannan J. Ho Sui, David A. Hume, Owen J. L. Rackham, Michela Fagiolini, Daisuke Sugiyama, Helena Persson, Hironori Satoh, Robert Young, Emily J. Wood, Akira Hasegawa, Yosuke Mizuno, Juha Kere, Hiroshi Tanaka, Michihira Tagami, A. Maxwell Burroughs, Sugata Roy, Sachi Kato, Taeko Dohi, Hai Fang, Chieko Kai, Fumio Nakahara, Christian Schmidl, Hiromi Nishiyori, Thierry Sengstag, Sven Guhl, Kei Iida, Antje Blumenthal, Boris Lenhard, Sarah Krampitz, Peter A C 't Hoen, Piotr J. Balwierz, Masayuki Yamamoto, Eri Saijyo, Suzana Savvi, Intikhab Alam Altschuler, Marina Lizio, Alison M. Meynert, Kazuyo Moro, Kenichi Nakazato, Sebastian Schmeier, Carlo Vittorio Cannistraci, Yasushi Okazaki, Yishai Shimoni, Kelly J Hitchens, Hideki Enomoto, Jeroen F. J. Laros, Naganari Ohkura, Ilya E. Vorontsov, Davide Albanese, Hiroshi Ohno, Yun Chen, Terrence F. Meehan, Mitsuhiro Ohshima, Mitsuko Hara, Emiliano Dalla, Roberto Verardo, Claudio Schneider, Takahiro Arakawa, Oliver Hofmann, Matthias Edinger, Mariko Okada-Hatakeyama, Susan E. Zabierowski, Shohei Noma, Yutaka Nakachi, Shoko Watanabe, Kaoru Kaida, Mitsuyoshi Murata, Takaaki Sugiyama, Hui Jia, Tetsuro Toyoda, Naoko Suzuki, Vsevolod J. Makeev, Naoko Takahashi Tagami, Hiroko Ohmiya, Christine L. Mummery, Emmanuel Dimont, Shiro Fukuda, Jun Kawai, Ivan V. Kulakovskiy, Anthony Mathelier, Nicolas Bertin, Hiroshi Kawamoto, Vanja Haberle, Robert Passier, Levon M. Khachigian, Yuki I. Kawamura, Jessica Severin, Valerio Orlando, Takeya Kasukawa, Teunis B. H. Geijtenbeek, Charles Plessy, Ernst J. Wolvetang, Stefano Gustincich, Shimon Sakaguchi, Erik van Nimwegen, Reto Guler, Martin C. Frith, Andrea Califano, Timo Lassmann, Peter Heutink, Boris R. Jankovic, Ri Ichiroh Manabe, Berit Lilje, Yari Ciani, Erik Arner, Rie Fujita, Robin Andersson, J Kenneth Baillie, Andrew T. Kwon, Atsutaka Kubosaki, Jun Ichi Furusawa, Soichi Kojima, Daniel Carbajo, Christine A. Wells, Tadasuke Nozaki, Rolf Swoboda, Hiroo Toyoda, Tony J. Kenna, Yoko Yamaguchi, Hideya Kawaji, Louise N. Winteringham, Cesare Furlanello, Michael Detmar, Judith S. Kempfle, Bogumil Kaczkowski, Gundula G. Schulze-Tanzil, Linda M. van den Berg, Alessandro Bonetti, Eivind Valen, Masayoshi Itoh, Yohei Yonekura, Guojun Sheng, Ulf Schaefer, Masahide Hamaguchi, Patrizia Rizzu, Anagha Joshi, Dmitry A. Ovchinnikov, Finn Drabløs, Christopher J. Mungall, Geoffrey J. Faulkner, Hubrecht Institute for Developmental Biology and Stem Cell Research, AII - Amsterdam institute for Infection and Immunity, Infectious diseases, Experimental Immunology, Human genetics, and NCA - Brain mechanisms in health and disease

Subjects
Transcription, Genetic, Cells, Messenger, Gene regulatory network, Mammalian promoter database, Biology, Article, Cell Line, Promoter Regions, Mice, Open Reading Frames, Essential, Atlases as Topic, Genetic, Animals, Cluster Analysis, Humans, Gene Regulatory Networks, RNA, Messenger, Promoter Regions, Genetic, Gene, Transcription factor, Cells, Cultured, Conserved Sequence, Genetics, Regulation of gene expression, Cultured, Multidisciplinary, Genes, Essential, Genome, Promoter, Molecular Sequence Annotation, Cap analysis gene expression, Genes, Gene Expression Regulation, Organ Specificity, Transcription Factors, Transcription Initiation Site, Transcriptome, RNA, Human genome, Transcription
Abstract

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body. We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles. TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved. Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs. The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses. The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research.

Published
2014
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