Papers

A promoter level mammalian expression atlas.

Cap Analysis of Gene Expression (CAGE) across a large collection of primary cell types has revealed many mammalian promoters are composite entities composed of multiple closely-separated TSS, with independent cell-type-specific expression profiles. The FANTOM5 promoter centric expression atlas provides expression profiles for the majority of coding and non-coding transcripts in the human and mouse genomes.

Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans C. Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-sim, Ri-ichiroh Manabe, Jessica C. Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine L.Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, FumioNakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik vanNimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, TadasukeNozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D.Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B.Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, MizuhoSakai, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C.’t Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, TetsuroToyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, XiaobeiZhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki.
Nature 2014
DOI: 10.1038/nature13182

An atlas of active enhancers across human cell types and tissues.

Enhancers control the correct temporal and cell-type-specific activation of gene expression. We have made an atlas of active enhancers across the majority of human tissues and cell types. The atlas is used to compare regulatory programs between different cells, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers.

Robin Andersson, Claudia Gebhard, Irene Miguel-Escalada, Ilka Hoof, Jette Bornholdt, Mette Boyd, Yun Chen, Xiaobei Zhao, Christian Schmidl, Takahiro Suzuki, Evgenia Ntini, Erik Arner, Eivind Valen, Kang Li, Lucia Schwarzfischer, Dagmar Glatz, Johanna Raithel, Berit Lilje, Nicolas Rapin, Frederik Otzen Bagger, Mette Jørgensen, Peter Refsing Andersen, Nicolas Bertin, Owen Rackham, A. Maxwell Burroughs, J. Kenneth Baillie, Yuri Ishizu, Yuri Shimizu, Erina Furuhata, Shiori Maeda, Yutaka Negishi, Christopher J. Mungall, Terrence F. Meehan, Timo Lassmann, Masayoshi Itoh, Hideya Kawaji, Naoto Kondo, Jun Kawai, Andreas Lennartsson, Carsten O. Daub, Peter Heutink, David A. Hume, Torben Heick Jensen, Harukazu Suzuki, Yoshihide Hayashizaki, Ferenc Müller, The FANTOM Consortium, Alistair R. R. Forrest, Piero Carninci, Michael Rehli & Albin Sandelin
Nature 2014
DOI: 10.1038/nature12787

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Exploiting the fact that active promoters and enhancers are transcribed, we simultaneously measured their activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli. Our analysis suggests a highly generalizable model in which enhancer transcription is the earliest event in successive waves of transcriptional change during cellular differentiation or activation.

Erik Arner, Carsten O Daub, Kristoffer Vitting-Seerup, Robin Andersson, Berit Lilje, Finn Drablos, Andreas Lennartsson, Michelle Rönnerblad, Olga Hrydziuszko, Morana Vitezic, Tom C Freeman, Ahmad Alhendi, Peter Arner, Richard Axton, J Kenneth Baillie, Anthony Beckhouse, Beatrice Bodega, James Briggs, Frank Brombacher, Margaret Davis, Michael Detmar, Anna Ehrlund, Mitsuhiro Endoh, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Geoffrey J Faulkner, Carmelo Ferrai, Malcolm E Fisher, Lesley Forrester, Daniel Goldowitz, Reto Guler, Thomas Ha, Mitsuko Hara, Meenhard Herlyn, Tomokatsu Ikawa, Chieko Kai, Hiroshi Kawamoto, Levon Khachigian, Peter S Klinken, Soichi Kojima, Haruhiko Koseki, Sarah Klein, Niklas Mejhert, Ken Miyaguchi, Yosuke Mizuno, Mitsuru Morimoto, Kelly J Morris, Christine Mummery, Yutaka Nakachi, Soichi Ogishima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Xian-Yang Qin, Sugata Roy, Hiroki Sato, Suzana Savvi, Alka Saxena, Anita Schwegmann, Daisuke Sugiyama, Rolf Swoboda, Hiroshi Tanaka, Andru Tomoiu, Louise N Winteringham, Ernst Wolvetang, Chiyo Yanagi-Mizuochi, Misako Yoneda, Susan Zabierowski, Peter Zhang, Imad Abugessaisa, Nicolas Bertin, Alexander D. Diehl, Shiro Fukuda, Masaki Furuno, Jayson Harshbarger, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Yuri Ishizu, Masayoshi Itoh, Tsugumi Kawashima, Miki Kojima, Naoto Kondo, Marina Lizio, Terrence F. Meehan, Christopher J Mungall, Mitsuyoshi Murata, Hiromi Nishiyori-Sueki, Serkan Sahin, Sayako Sato-Nagao, Jessica Severin, Michiel JL de Hoon, Jun Kawai, Takeya Kasukawa, Timo Lassmann, Harukazu Suzuki, Hideya Kawaji, Kim M Summers, Christine Wells, FANTOM Consortium, David A Hume, Alistair RR Forrest, Albin Sandelin, Piero Carninci, Yoshihide Hayashizaki
Science 2015
DOI: 10.1126/science.1259418

An atlas of human long non-coding RNAs with accurate 5′ ends

There is a strong debate on whether the thousands of long non-coding RNAs transcribed from our genomes are functional or simply byproducts of a noisy transcriptional machinery. Scientists from the RIKEN-led FANTOM5 consortium used a technology known as Cap Analysis of Gene Expression (CAGE) to build an atlas of human long non-coding RNAs with accurate 5’ ends and summarized their expression patterns across the major cell types. In the work, published in Nature, they intersected this expression atlas with other genetic and genomic datasets and suggested many of these long non-coding RNAs might be functional.

Chung-Chau Hon, Jordan A. Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J. L. Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M. Poulsen, Jessica Severin, Marina Lizio, Hideya Kawaji, Takeya Kasukawa, Masayoshi Itoh, A. Maxwell Burroughs, Shohei Noma, Sarah Djebali, Tanvir Alam, Yulia A. Medvedeva, Alison C. Testa, Leonard Lipovich, Chi-Wai Yip, Imad Abugessaisa, Mickaël Mendez, Akira Hasegawa, Dave Tang, Timo Lassmann, Peter Heutink, Magda Babina, Christine A. Wells, Soichi Kojima, Yukio Nakamura, Harukazu Suzuki, Carsten O. Daub, Michiel J. L. de Hoon, Erik Arner, Yoshihide Hayashizaki, Piero Carninci & Alistair R. R. Forrest
Nature 2017
DOI: 10.1038/nature21374

An integrated expression atlas of miRNAs and their promoters in human and mouse

By applying short RNA-sequencing and Cap Analysis of Gene Expression (CAGE) we have generated expression profiles of mature miRNAs and their primary transcripts across a large collection of primary cell types. CAGE has also allowed us to map their promoters. We show that miRNA promoters are highly conserved, that the expression profiles of the mature and the primary transcript are correlated and that miRNAs originating from the same polycistron are highly correlated. We present the data as a web resource to the research community.

Derek de Rie, Imad Abugessaisa, Tanvir Alam, Erik Arner, Peter Arner, Haitham Ashoor, Gaby Åström, Magda Babina, Nicolas Bertin, A Maxwell Burroughs, Ailsa J Carlisle, Carsten O Daub, Michael Detmar, Ruslan Deviatiiarov, Alexandre Fort, Claudia Gebhard, Daniel Goldowitz, Sven Guhl, Thomas J Ha, Jayson Harshbarger, Akira Hasegawa, Kosuke Hashimoto, Meenhard Herlyn, Peter Heutink, Kelly J Hitchens, Chung Chau Hon, Edward Huang, Yuri Ishizu, Chieko Kai, Takeya Kasukawa, Peter Klinken, Timo Lassmann, Charles-Henri Lecellier, Weonju Lee, Marina Lizio, Vsevolod Makeev, Anthony Mathelier, Yulia A Medvedeva, Niklas Mejhert, Christopher J Mungall, Shohei Noma, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Helena Persson, Patrizia Rizzu, Filip Roudnicky, Pål Sætrom, Hiroki Sato, Jessica Severin, Jay W Shin, Rolf K Swoboda, Hiroshi Tarui, Hiroo Toyoda, Kristoffer Vitting-Seerup, Louise Winteringham, Yoko Yamaguchi, Kayoko Yasuzawa, Misako Yoneda, Noriko Yumoto, Susan Zabierowski, Peter G Zhang, Christine A Wells, Kim M Summers, Hideya Kawaji, Albin Sandelin, Michael Rehli, The FANTOM Consortium, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest & Michiel J L de Hoon
Nature Biotechnology 2017
DOI: 10.1038/nbt.3947

Comparative transcriptomics of primary cells in vertebrates

We compare transcriptome data from matching primary cell types in human, mouse, rat, dog, and chicken. While we found that the transcriptome measured by CAGE for the same cell type differed markedly between species, we identified a core regulatory network defining each cell type that is common between species. In general, the genes encoding products involved in RNA biology in the cell nucleus were found to be activated consistently in the same cell type regardless of the species.

Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S. Young, Robin Andersson, Erik Arner, Akira Hasegawa, Marina Lizio, Jordan A. Ramilowski, Imad Abugessaisa, Yuri Ishizu, Shohei Noma, Hiroshi Tarui, Martin S. Taylor, Timo Lassmann, Masayoshi Itoh, Takeya Kasukawa, Hideya Kawaji, Luigi Marchionni, Guojun Sheng, Alistair R.R. Forrest, Levon M. Khachigian, Yoshihide Hayashizaki, Piero Carninci and Michiel J.L. de Hoon
Genome Research 2020
DOI: 10.1101/gr.255679.119

Recounting the FANTOM CAGE-Associated Transcriptome

Eddie Luidy Imada, Diego Fernando Sanchez, Leonardo Collado-Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Aleksey Stupnikov, Francisco Lobo-Pereira, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, Michiel J.L. de Hoon, Jay W. Shin, Piero Carninci, Andrew E. Jaffe, Jeffrey T. Leek, Alexander Favorov, Gloria R. Franco, Ben Langmead and Luigi Marchionni
Genome Research 2020
DOI: 10.1101/gr.254656.119

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

Alexandre Fort, Kosuke Hashimoto, Daisuke Yamada, Md Salimullah, Chaman A Keya, Alka Saxena, Alessandro Bonetti, Irina Voineagu, Nicolas Bertin, Anton Kratz, Yukihiko Noro, Chee-Hong Wong, Michiel de Hoon, Robin Andersson, Albin Sandelin, Harukazu Suzuki, Chia-Lin Wei, Haruhiko Koseki, The FANTOM Consortium, Yuki Hasegawa, Alistair R R Forrest & Piero Carninci
Nature Genetics 2014
DOI: 10.1038/ng.2965

Systematic analysis of transcription start sites in avian development

Marina Lizio, Ruslan Deviatiiarov, Hiroki Nagai, Laura Galan, Erik Arner, Masayoshi Itoh, Timo Lassmann, Takeya Kasukawa, Akira Hasegawa, Marian A. Ros, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Hideya Kawaji, Oleg Gusev, Guojun Sheng
PLOS Biology 2017
DOI: 10.1371/journal.pbio.2002887

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

J. Kenneth Baillie, Andrew Bretherick, Christopher S. Haley, Sara Clohisey, Alan Gray, Lucile P. A. Neyton, Jeffrey Barrett, Eli A. Stahl, Albert Tenesa, Robin Andersson, J. Ben Brown, Geoffrey J. Faulkner, Marina Lizio, Ulf Schaefer, Carsten Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, IIBDGC Consortium, Damian Mole, Vladimir B. Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A. Wells, Nir Hacohen, Thomas C. Freeman, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, David A. Hume
PLOS Comput Biol 2018
DOI: 10.1371/journal.pcbi.1005934

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

J. Kenneth Baillie, Erik Arner, Carsten Daub, Michiel De Hoon, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, FANTOM Consortium , Geoffrey J. Faulkner, Christine A. Wells, Michael Rehli, Paul Pavli, Kim M. Summers, David A. Hume
PLOS Genetics 2017
DOI: 10.1371/journal.pgen.1006641

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli

Annalaura Vacca, Masayoshi Itoh, Hideya Kawaji, Erik Arner, Timo Lassmann, Carsten O. Daub, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, the FANTOM Consortium, Stuart Aitken, Colin A. Semple
Open Biology 2018
DOI: 10.1098/rsob.180011

Relatively frequent switching of transcription start sites during cerebellar development

Peter Zhang, Emmanuel Dimont, Thomas Ha, Douglas J. Swanson, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, the FANTOM Consortium, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Winston Hide and Dan Goldowitz
BMC Genomics 2018
DOI: 10.1186/s12864-017-4291-4

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

Sugata Roy, Sebastian Schmeier, Bogumil Kaczkowski, Erik Arner, Tanvir Alam, Mumin Ozturk, Ousman Tamgue, Suraj P. Parihar, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Reto Guler, Vladimir B. Bajic, Frank Brombacher & Harukazu Suzuki
Scientific Reports 2018
DOI: 10.1038/s41598-018-24509-6

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection

Peter G. Y. Zhang, Joanna Yeung, Ishita Gupta, Miguel Ramirez, Thomas Ha, Douglas J. Swanson, Sayaka Nagao-Sato, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Michiel de Hoon, the FANTOM consortium, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, Dan Goldowitz
Cerebellum 2018
DOI: 10.1007/s12311-017-0912-3

Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC

Masafumi Horie, Bogumil Kaczkowski, Mitsuhiro Ohshima, Hirotaka Matsuzaki, Satoshi Noguchi, Yu Mikami, Marina Lizio, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Daiya Takai, Yoko Yamaguchi, Patrick Micke, Akira Saito and Takahide Nagase
Mol Cancer Res 2017
DOI: 10.1158/1541-7786.MCR-17-0191

Comprehensive Characterization of Transcriptional Activity during Influenza A Virus Infection Reveals Biases in Cap-Snatching of Host RNA Sequences

Sara Clohisey, Nicholas Parkinson, Bo Wang, Nicolas Bertin, Helen Wise, Andru Tomoiu, FANTOM5 Consortium, Kim M. Summers, Ross W. Hendry, Piero Carninci, Alistair R.R. Forrest, Yoshihide Hayashizaki, Paul Digard, David A. Hume and J. Kenneth Baillie
Journal of Virology 2020
DOI: 10.1128/JVI.01720-19

Monitoring transcription initiation activities in rat and dog

Marina Lizio, Abdul Kadir Mukarram, Mizuho Ohno, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Chung Chau Hon, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest & Hideya Kawaji
Scientific Data 2017
DOI: 10.1038/sdata.2017.173

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system

Margherita Francescatto, Marina Lizio, Ingrid Philippens, Ronald Bontrop, Mizuho Sakai, Shoko Watanabe, Masayoshi Itoh, Akira Hasegawa, Timo Lassmann, Jessica Severin, Jayson Harshbarger, Imad Abugessaisa, Takeya Kasukawa, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Hideya Kawaji, Patrizia Rizzu & Peter Heutink
Scientific Data 2017
DOI: 10.1038/sdata.2017.163

Linking FANTOM5 CAGE peaks to annotations with CAGEscan

Nicolas Bertin, Mickaël Mendez, Akira Hasegawa, Marina Lizio, Imad Abugessaisa, Jessica Severin, Mizuho Sakai-Ohno, Timo Lassmann, Takeya Kasukawa, Hideya Kawaji, Yoshihide Hayashizaki, Alistair R. R. Forrest, Piero Carninci and Charles Plessy
Scientific Data 2017
DOI: 10.1038/sdata.2017.147

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes

Xian-Yang Qin, Mitsuko Hara, Erik Arner, Yoshikuni Kawaguchi, Ikuyo Inoue, Hideki Tatsukawa, Yutaka Furutani, Keisuke Nagatsuma, Tomokazu Matsuura, Feifei Wei, Jun Kikuchi, Hideko Sone, Carsten Daub, Hideya Kawaji, Timo Lassmann, Masayoshi Itoh, Harukazu Suzuki, Piero Carninci and Soichi Kojima
EBiomedicine 2017
DOI: 10.1016/j.ebiom.2017.09.008

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies

Imad Abugessaisa, Shuhei Noguchi, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Marina Lizio, Jessica Severin, Piero Carninci, Hideya Kawaji & Takeya Kasukawa
Scientific Data 2017
DOI: 10.1038/sdata.2017.107

FANTOM5 CAGE profiles of human and mouse samples

Shuhei Noguchi, Takahiro Arakawa, Shiro Fukuda, Masaaki Furuno, Akira Hasegawa, Fumi Hori, Sachi Ishikawa-Kato, Kaoru Kaida, Ai Kaiho, Mutsumi Kanamori-Katayama, Tsugumi Kawashima, Miki Kojima, Atsutaka Kubosaki, Ri-ichiroh Manabe, Mitsuyoshi Murata, Sayaka Nagao-Sato, Kenichi Nakazato, Noriko Ninomiya, Hiromi Nishiyori-Sueki, Shohei Noma, Eri Saijyo, Akiko Saka, Mizuho Sakai, Christophe Simon, Naoko Suzuki, Michihira Tagami, Shoko Watanabe, Shigehiro Yoshida, Peter Arner, Richard A. Axton, Magda Babina, J. Kenneth Baillie, Timothy C. Barnett, Anthony G. Beckhouse, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, Ailsa J. Carlisle, Hans C. Clevers, Carrie A. Davis, Michael Detmar, Taeko Dohi, Albert S.B. Edge, Matthias Edinger, Anna Ehrlund, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Afsaneh Eslami, Michela Fagiolini, Lynsey Fairbairn, Mary C. Farach-Carson, Geoffrey J. Faulkner, Carmelo Ferrai, Malcolm E. Fisher, Lesley M. Forrester, Rie Fujita, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Thomas Gingeras, Daniel Goldowitz, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Yuki Hasegawa, Meenhard Herlyn, Peter Heutink, Kelly J. Hitchens, David A. Hume, Tomokatsu Ikawa, Yuri Ishizu, Chieko Kai, Hiroshi Kawamoto, Yuki I. Kawamura, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, Sarah Klein, S. Peter Klinken, Alan J. Knox, Soichi Kojima, Haruhiko Koseki, Shigeo Koyasu, Weonju Lee, Andreas Lennartsson, Alan Mackay-sim, Niklas Mejhert, Yosuke Mizuno, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Kelly J. Morris, Hozumi Motohashi, Christine L. Mummery, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Robert Passier, Margaret Patrikakis, Ana Pombo, Swati Pradhan-Bhatt, Xian-Yang Qin, Michael Rehli, Patrizia Rizzu, Sugata Roy, Antti Sajantila, Shimon Sakaguchi, Hiroki Sato, Hironori Satoh, Suzana Savvi, Alka Saxena, Christian Schmidl, Claudio Schneider, Gundula G. Schulze-Tanzil, Anita Schwegmann, Guojun Sheng, Jay W. Shin, Daisuke Sugiyama, Takaaki Sugiyama, Kim M. Summers, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Andru Tomoiu, Hiroo Toyoda, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Yoko Yamaguchi, Masayuki Yamamoto, Chiyo Yanagi-Mizuochi, Misako Yoneda, Yohei Yonekura, Peter G. Zhang, Silvia Zucchelli, Imad Abugessaisa, Erik Arner, Jayson Harshbarger, Atsushi Kondo, Timo Lassmann, Marina Lizio, Serkan Sahin, Thierry Sengstag, Jessica Severin, Hisashi Shimoji, Masanori Suzuki, Harukazu Suzuki, Jun Kawai, Naoto Kondo, Masayoshi Itoh, Carsten O. Daub, Takeya Kasukawa, Hideya Kawaji, Piero Carninci, Alistair R.R. Forrest & Yoshihide Hayashizaki
Scientific Data 2017
DOI: 10.1038/sdata.2017.112

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

Hideya Kawaji, Takeya Kasukawa, Alistair Forrest, Piero Carninci & Yoshihide Hayashizaki
Scientific Data 2017
DOI: 10.1038/sdata.2017.113

The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers

Imad Abugessaisa, Shuhei Noguchi, Piero Carninci, and Takeya Kasukawa
Protein Function Prediction: Methods and Protocols 2017
DOI: 10.1007/978-1-4939-7015-5_15

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

Imad Abugessaisa, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci, The FANTOM consortium, Alistair Forrest, Takeya Kasukawa, and Hideya Kawaji
Database 2016
DOI: 10.1093/database/baw105

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

Imad Abugessaisa, Jordan A Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi, Michihira Tagami, Fumi Hori, Saumya Agrawal, Chung Chau Hon, Melissa Cardon, Shuya Ikeda, Hiromasa Ono, Hidemasa Bono, Masaki Kato, Kosuke Hashimoto, Alessandro Bonetti, Masaki Kato, Norio Kobayashi, Jay Shin, Michiel de Hoon, Yoshihide Hayashizaki, Piero Carninci, Hideya Kawaji and Takeya Kasukawa
Nucleic Acids Res 2021
DOI: 10.1093/nar/gkaa1054

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung Chau Hon, Michiel de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki, Piero Carninci, Takeya Kasukawa, Hideya Kawaji
Nucleic Acids Res 2019
DOI: 10.1093/nar/gky1099

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A. Ramilowski, Owen Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Takeya Kasukawa, Hideya Kawaji
Nucleic Acids Res 2017
DOI: 10.1093/nar/gkw995

refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites

Imad Abugessaisa, Shuhei Noguchi, Akira Hasegawa, Atsushi Kondo, Hideya Kawaji, Piero Carninci and Takeya Kasukawa
Journal of Molecular Biology 2019
DOI: 10.1016/j.jmb.2019.04.045

DeepCAGE transcriptomics identify HOXD10 as transcription factor regulating lymphatic endothelial responses to VEGF-C

Sarah Klein, Lothar C. Dieterich, Anthony Mathelier, Chloé Chong, Adriana Sliwa-Primorac, Young-Kwon Hong, Jay W. Shin, Marina Lizio, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, the FANTOM consortium, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Wyeth W. Wasserman, Michael Detmar
J Cell Sci 2016
DOI: 10.1242/jcs.186767

DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.

Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M.
Cell Rep. 2015
DOI: 10.1016/j.celrep.2015.10.002

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line.

Lizio M, Ishizu Y, Itoh M, Lassmann T, Hasegawa A, Kubosaki A, Severin J, Kawaji H, Nakamura Y; FANTOM consortium, Suzuki H, Hayashizaki Y, Carninci P, Forrest AR.
Front Genet. 2015
DOI: 10.3389/fgene.2015.00331

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

Yasuhiro Murakawa, Masahito Yoshihara, Hideya Kawaji, Miki Nishikawa, Hatem Zayed, Harukazu Suzuki, FANTOM Consortium, Yoshihide Hayashizaki
Trends in Genetics Volume 32, Issue 2, February 2016
DOI: 10.1016/j.tig.2015.11.004

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach

Georges St. Laurent, Yuri Vyatkin, Denis Antonets, Maxim Ri, Yao Qi, Olga Saik, Dmitry Shtokalo, Michiel J.L. de Hoon, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Erik Arner, Alistair R.R. Forrest, The FANTOM consortium, Estelle Nicolas, Timothy A. McCaffrey, Piero Carninci, Yoshihide Hayashizaki, Claes Wahlestedt, and Philipp Kapranov
Nucl. Acids Res. 20 April 2016
DOI: 10.1093/nar/gkw162

A predictive computational framework for direct reprogramming between human cell types

Owen J L Rackham, Jaber Firas, Hai Fang, Matt E Oates, Melissa L Holmes, Anja S Knaupp, The FANTOM Consortium, Harukazu Suzuki, Christian M Nefzger, Carsten O Daub, Jay W Shin, Enrico Petretto, Alistair R R Forrest, Yoshihide Hayashizaki, Jose M Polo, Julian Gough
Nature Genetics 2016
DOI: 10.1038/ng.3487

A draft network of ligand-receptor-mediated multicellular signalling in human

Jordan A Ramilowski, Tatyana Goldberg, Jayson Harshbarger, Edda Kloppman, Marina Lizio, Venkata P Satagopam, Masayoshi Itoh, Hideya Kawaji, Piero Carninci, Burkhard Rost, Alistair RR Forrest
Nature communications 2015
DOI: 10.1038/ncomms8866

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers

Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR; FANTOM5 Consortium.
Cancer Res. 2016
DOI: 10.1158/0008-5472.CAN-15-0484

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Laurence D. Hurst, Avazeh T. Ghanbarian, Alistair R. R. Forrest, FANTOM consortium, Lukasz Huminiecki
PLOS Bio. 2015
DOI: 10.1371/journal.pbio.1002315

Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage

Daniel Carbajo, Shigeyuki Magi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair R. R. Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub, FANTOM consortium, Mariko Okada-Hatakeyama
PLOS one 2015
DOI: 10.1371/journal.pone.0144176

The frequent evolutionary birth and death of functional promoters in mouse and human

Robert S Young, Yoshihide Hayashizaki, Robin Andersson, Albin Sandelin, Hideya Kawaji, Masayoshi Itoh, Timo Lassmann, Piero Carninci, Wendy A Bickmore, Alistair R Forrest, Martin S Taylor, FANTOM Consortium
Genome research
DOI: 10.1101/gr.190546.115

Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells

Marco Mina, Shigeyuki Magi, Giuseppe Jurman, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Erik Arner, Alistair RR Forrest, Piero Carninci, Yoshihide Hayashizaki, Carsten O Daub, Mariko Okada-Hatakeyama, Cesare Furlanello, FANTOM Consortium
Scientific reports
DOI: 10.1038/srep11999

EpiFactors: a comprehensive database of human epigenetic factors and complexes

Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, The FANTOM Consortium and Finn Drabløs
Database
DOI: 10.1093/database/bav067

Transcription factor, promoter, and enhancer utilization in human myeloid cells

Anagha Joshi, Christopher Pooley, Tom C. Freeman, Andreas Lennartsson, Magda Babina, Christian Schmidl, Teunis Geijtenbeek, the FANTOM Consortium, Tom Michoel, Jessica Severin, Masayoshi Itoh, Timo Lassmann, Hideya Kawaji, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Michael Rehli and David A. Hume
Journal of leukocyte biology
DOI: 10.1189/jlb.6TA1014-477RR

Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease

Claudia Carrieri, Alistair RR Forrest, Claudio Santoro, Francesca Persichetti, Piero Carninci, Silvia Zucchelli, Stefano Gustincich
Frontiers in Cellular Neuroscience
DOI: 10.3389/fncel.2015.00114

Paradigm shifts in genomics through the FANTOM projects

Michiel de Hoon, Jay W Shin, Piero Carninci
Mammalian Genome
DOI: 10.1007/s00335-015-9593-8

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses

Vanja Haberle, Alistair RR Forrest, Yoshihide Hayashizaki, Piero Carninci, Boris Lenhard
Nucleic acids research
DOI: 10.1093/nar/gkv054

CAGE-defined promoter regions of the genes implicated in Rett Syndrome

Morana Vitezic, Nicolas Bertin, Robin Andersson, Leonard Lipovich, Hideya Kawaji, Timo Lassmann, Albin Sandelin, Peter Heutink, Dan Goldowitz, Thomas Ha, Peter Zhang, Annarita Patrizi, Michela Fagiolini, Alistair RR Forrest, Piero Carninci, Alka Saxena
BMC genomics
DOI: 10.1186/1471-2164-15-1177

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

Nancy Yiu-Lin Yu, Björn M. Hallström, Linn Fagerberg, Fredrik Ponten, Hideya Kawaji, Piero Carninci, Alistair R. R. Forrest, The FANTOM Consortium, Yoshihide Hayashizaki, Mathias Uhlén and Carsten O. Daub
Nucleic Acids Research 2015
DOI: 10.1093/nar/gkv608

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics

Sugata Roy, Sebastian Schmeier, Erik Arner, Tanvir Alam, Suraj P. Parihar, Mumin Ozturk, Ousman Tamgue, Hideya Kawaji, Michiel J. L. de Hoon, Masayoshi Itoh1, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Vladimir B. Bajic, Reto Guler, FANTOM Consortium, Frank Brombacher, and Harukazu Suzuki
Nucleic Acids Research 2015
DOI: 10.1093/nar/gkv646

Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

Aitken S, Magi S, Alhendi AM, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Khachigian LM, Okada-Hatakeyama M, Semple CA.
PLoS Comput Biol.
DOI: 10.1371/journal.pcbi.1004217

Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body

Masahito Yoshihara, Hiroko Ohmiya, Susumu Hara, Satoshi Kawasaki, FANTOM consortium , Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji , Motokazu Tsujikawa, Kohji Nishida
PLoS ONE
DOI: 10.1371/journal.pone.0117581

Gateways to the FANTOM5 promoter level mammalian expression atlas

Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda1, Fumi Hori, Sachi Ishikawa-Kato, Christopher J Mungall, Erik Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D Diehl, Emmanuel Dimont, Tom C Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F Meehan, Koro Nishikata, Hiromasa Ono, Michael Rehli, Albin Sandelin, Erik A Schultes, Peter AC ‘t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W Wright, Carsten O Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Alistair RR Forrest, Hideya Kawaji and the FANTOM consortium
Genome Biology
DOI: 10.1186/s13059-014-0560-6

The Statistical Geometry of Transcriptome Divergence in Cell Type Evolution and Cancer

Cong Liang, the FANTOM Consortium, Alistair R. R. Forrest & Günter P. Wagner
Nature Communications 2015, 6:6066
DOI: 10.1038/ncomms7066

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators.

Laurence D Hurst, Oxana Sachenkova, Carsten Daub, Alistair R. R. Forrest and Lukasz Huminiecki
Genome Biology 2014, 15:413
DOI: 10.1186/s13059-014-0413-3

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules

Alice Grison, Silvia Zucchelli, Alice Urzì, Ilaria Zamparo, Dejan Lazarevic, Giovanni Pascarella, Paola Roncaglia, Alejandro Giorgetti, Paula Garcia-Esparcia, Christina Vlachouli, Roberto Simone, Francesca Persichetti, Alistair RR Forrest, Yoshihide Hayashizaki, Paolo Carloni, Isidro Ferrer, Claudia Lodovichi, Charles Plessy, the FANTOM Consortium, Piero Carninci and Stefano Gustincich
BMC Genomics 2014, 15:729
DOI: 10.1186/1471-2164-15-729

Deep sequencing blood transcriptomes

Alistair R.R. Forrest
Blood 123 (17)
DOI: 10.1182/blood-2014-03-563452

Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer

Roberto Verardo, Silvano Piazza, Enio Klaric, Yari Ciani, Giulio Bussadori, Stefania Marzinotto, Laura Mariuzzi, Daniela Cesselli, Antonio P. Beltrami, Miguel Mano, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, the FANTOM consortium, Carlo A. Beltrami and Claudio Schneider
Stem Cells
DOI: 10.1002/stem.1791

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

Yuki Hasegawa, Dave Tang, Naoko Takahashi, Yoshihide Hayashizaki, Alistair R. R. Forrest, the FANTOM consortium and Harukazu Suzuki
Scientific Reports
DOI: 10.1038/srep05228

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation

Yasuhiro Tomaru, Ryota Hasegawa, Takahiro Suzuki, Taiji Sato, Atsutaka Kubosaki, Masanori Suzuki, Hideya Kawaji, Alistair R.R. Forrest, Yoshihide Hayashizaki, FANTOM Consortium, Jay W. Shin, and Harukazu Suzuki
Nucleic Acids Research 2014
DOI: 10.1093/nar/gku567

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)

Hiroko Ohmiya, Morana Vitezic1, Martin C Frith, Masayoshi Itoh, Piero Carninci, Alistair RR Forrest, Yoshihide Hayashizaki, Timo Lassmann and The FANTOM Consortium
BMC Genomics 2014, 15:269
DOI: 10.1186/1471-2164-15-269

Redefinition of the human mast cell transcriptome by deep sequencing.

Using freshly isolated skin-derived Mast cells (MCs) FANTOM5 reveals a comprehensive view of the human MC transcriptome. Mast cells are unique in the hematopoietic lineage and are only distantly related to basophils. We also show that mast cells express BMP receptors and that BMPs can promote survival and recovery to stimulation of human MCs.

Efthymios Motakis, Sven Guhl, Yuri Ishizu, Masayoshi Itoh, Hideya Kawaji, Michiel de Hoon, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Torsten Zuberbier, Alistair R R Forrest, Magda Babina, and the FANTOM consortium
Blood
DOI: 10.1182/blood-2013-02-483792

Transcription and enhancer profiling in human monocyte subsets.

Complementary CAGE and epigenetic profiling dissects differences between the three major subpopulations of human monocytes. This FANTOM5 study highlights differential gene, transcription factor and enhancer usage and identifies previously unrecognized metabolic differences between subpopulations.

Christian Schmidl, Kathrin Renner, Katrin Peter, Ruediger Eder, Timo Lassmann, Piotr J. Balwierz, Masayoshi Itoh, Sayaka Nago-Sato, Hideya Kawaji, Piero Carninci, Harukazu Suzuki, Yoshihide Hayashizaki, Reinhard Andreesen, David A. Hume, Petra Hoffmann, Alistair R. R. Forrest, Marina P. Kreutz, Matthias Edinger, Michael Rehli for the FANTOM consortium
Blood
DOI: 10.1182/blood-2013-02-484188

The enhancer and promoter landscape of human regulatory and conventional T cell subpopulations.

Their ability to avert immune reactions makes regulatory T cells (Treg) highly interesting for clinical application. This FANTOM5 study investigates transcription factor networks in naïve and memory Treg and their conventional T cell (Tconv) counterparts both before and after in vitro expansion and shows that in vitro expanded Treg do not dramatically change their Treg-specific effector molecule repertoire.

Christian Schmid, Leo Hansmann, Timo Lassmann, Piotr J. Balwierz, Hideya Kawaji, Masayoshi Itoh, Jun Kawai, Sayaka Nagao-Sato, Harukazu Suzuki, Reinhard Andreesen, Yoshihide Hayashizaki, Alistair R. R. Forrest, Piero Carninci, Petra Hoffmann, Matthias Edinger, Michael Rehli, for the FANTOM consortium
Blood
DOI: 10.1182/blood-2013-02-486944

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

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. We show that methylation change at specific differentiation stages and overlap with the activity of key hematopoietic transcription factors. Also, differentially methylated sites were overrepresented in enhancer elements and enriched in enhancers that become active during differentiation.

Michelle Rönnerblad, Robin Andersson, Tor Olofsson, Iyadh Douag, Mohsen Karimi, Sören Lehmann, Ilka Hoof, Michiel de Hoon, Masayohi Itoh, Sayaka Nago-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Albin Sandelin, Karl Ekwall, Erik Arner, Andreas Lennartsson and the FANTOM consortium
Blood
DOI: 10.1182/blood-2013-02-482893

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis

Hematopoietic differentiation is governed by a complex regulatory program controlling the generation of different lineages of blood cells from multipotent hematopoietic stem cells. The transcriptional program that dictates hematopoietic cell fate and differentiation requires an epigenetic memory function provided by a network of epigenetic factors regulating DNA methylation, posttranslational histone modifications, and chromatin structure. To elucidate the contributions of different epigenetic factors in human hematopoiesis, high-throughput cap analysis of gene expression was used to build transcription profiles of 199 epigenetic factors in a wide range of blood cells.

Punit Prasad, Michelle Rönnerblad, Erik Arner, Masayohi Itoh, Hideya Kawaji, Timo Lassmann, Carsten Daub, Alistair R.R. Forrest, Andreas Lennartsson, Karl Ekwall, and the FANTOM consortium
Blood
DOI: 10.1182/blood-2013-02-483537

Comparison of CAGE and RNA-seq transcriptome profiling using a clonally amplified and single molecule next generation sequencing

We compared CAGE using both 2nd and 3rd generation sequencers and RNA-seq using a 2nd generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in discrimination of biological states, detection of differentially expressed genes, linearity of measurements as well as quantification reproducibility. The result provides a perspective on performance of these platforms, which will be a baseline to design further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.

Hideya Kawaji, Marina Lizio, Masayoshi Itoh, Mutsumi Kanamori-Katayama, Ai Kaiho, Hiromi Nishiyori-Sueki, Jay Shin, Miki Kojima-Ishiyama, Mitsuoki Kawano, Mitsuyoshi Murata, Noriko Ninomiya-Fukuda, Sachi Ishikawa-Kato, Sayaka Nagao-Sato, Shohei Noma, Yoshihide Hayashizaki, Alistair R.R. Forrest, Piero Carninci, and the FANTOM consortium
Genome Research
DOI: 10.1101/gr.156232.113

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Regulatory T (Treg) cells, which specifically express the transcription factor Foxp3, are engaged in the maintenance of immunological self-tolerance and homeostasis. Analysis of FANTOM5 CAGE data with epigenome data including DNA methylation and Transcription factor binding sites reveals that Treg specific demethylation and Foxp3 appear to play distinct but complementary roles in Treg specific gene regulation.

Hiromasa Morikawa, Naganari Ohkura, Alexis Vandenbon, Masayohi Itoh, Sayaka Nago-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R.R. Forrest, Daron Standley, Hiroshi Date, Shimon Sakaguchi, and the FANTOM consortium
Proc Natl Acad Sci USA.
DOI: 10.1073/pnas.1312717110

The Evolution of Human Cells in terms of Protein Innovation

Combining FANTOM5 CAGE data and protein domain annotation we are able to get a view on how different cell types have evolved. We are able to identify known evolutionary events as well highlight other novel events that until know have remained undetected.

Adam J. Sardar, Matt E. Oates, Hai Fang, Alistair R.R. Forrest, Hideya Kawaji, The FANTOM Consortium, Julian Gough, and Owen J.L. Rackham
Molecular Biology and Evolution
DOI: 10.1093/molbev/mst139

Interactive visualization and analysis of large-scale NGS data-sets using ZENBU.

Next generation sequencing protocols such as RNA-seq, ChIP-seq, DHS-seq and CAGE across large sample collections are generating a wealth of data to elucidate genomic function. To facilitate interactive comparison of results across 1000s of NGS experiments we present ZENBU, a web application combining data integration, and data analysis into a genome browser with enhanced gene expression and epigenomic visualization capabilities.

Jessica Severin, Marina Lizio, Jayson Harshbarger, Hideya Kawaji, Carsten O Daub, Yoshihide Hayashizaki, The FANTOM Consortium, Nicolas Bertin, Alistair R R Forrest
Nature Biotechnology 32, 217–219 (2014)
DOI: 10.1038/nbt.2840

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

The fibrillins and latent transforming growth factor binding proteins (LTBPs) form a superfamily of proteins involved in the structure of the extracellular matrix and in controlling the bioavailability of TGFβ family members. We present a study of transcription start sites, which suggests this important class of extracellular matrix proteins is subject to subtle regulatory variations that explain the differential roles of members of this gene family.

Margaret R Davis, Robin Andersson, Jessica Severin, Michiel de Hoon, Nicolas Bertin, J Kenneth Baillie, Hideya Kawaji, Albin Sandelin, Alistair RR Forrest, Kim M Summers
Molecular Genetics and Metabolism
DOI: 10.1016/j.ymgme.2013.12.006

Explaining the correlations among properties of mammalian promoters

Promoters have mysterious variation in CpG richness, TATA signals, evolutionary conservation, expression specificity, and chromosomal spread of transcription start sites. We warn of biases in measuring these properties, show that most promoters have rather non-specific expression, and provide simple explanations for the correlations among the properties.

Martin C. Frith and the FANTOM consortium
Nucleic Acids Research
DOI: 10.1093/nar/gku115

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

CAGExploreR is an R package that facilitates the detection and visualization of changes in the relative transcription from promoter regions in multi-promoter genes, all in the context of overall gene expression. Multiple samples can be compared simultaneously. Primarily based on the FANTOM5 promoter set definitions, however other regions such as MPromDb or user-supplied regions can also be used.

Emmanuel Dimont, Oliver Hofmann, Alistair R. R. Forrest, Hideya Kawaji, the FANTOM Consortium, and Winston Hide
Bioinformatics
DOI: 10.1093/bioinformatics/btu125

Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells

Obesity confers an increased risk of developing specific cancer forms. Increased fat cell secretion of adipokines may promote malignant tumors in obesity via tissue cross-talk. We found ceruloplasmin (CP) expression to be strongly enriched in obesity-associated cancer, and in adipose tissue of obese subjects. We demonstrate that CP is a novel adipokine, with increased production and secretion in obesity.

Erik Arner, Alistair R R Forrest, Anna Ehrlund, Niklas Mejhert, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Jurga Laurencikiene, Mikael Rydé, Peter Arner, and the FANTOM consortium.
PLOS ONE
DOI: 10.1371/journal.pone.0080274

Effects of cytosine methylation on transcription factor binding sites

Methylation of 16% of individual CpGs negatively correlates with neighboring TSS expression. We observed a selection against these CpGs within transcription factor binding sites (TFBSs), being stronger for repressors than for activators, as well as for core TFBS positions than for flanking ones. We suggested that selective methylation of TFBSs preventing transcription factor binding is restricted to special cases and cannot be a global mechanism for transcription regulation.

Yulia A Medvedeva, Abdullah Khamis, Ivan V Kulakovskiy, Wail Ba-Alawi, Md Shariful I Bhuyan, Hideya Kawaji, Timo Lassmann, Matthias Harbers, Alistair RR Forrest, Vladimir B Bajic and the FANTOM consortium
BMC genomics
DOI: 10.1186/1471-2164-15-119

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines

Deciphering the most common modes by which chromatin regulates transcription is an important task for improving our understanding of human cellular biology. Transcriptional data from FANTOM5 is integrated data from the ENCODE project to characterize chromatin features around expressed and repressed transcription start sites in four human cell lines.

Morten Rye, Geir K Sandve, Carsten O Daub, Hideya Kawaji, Piero Carninci, Alistair RR Forrest, Finn Drabløs
BMC Genomics
DOI: 10.1186/1471-2164-15-120

Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer

Masayoshi Itoh, Miki Kojima, Sayaka Nagao-Sato, Eri Saijo, Timo Lassmann, Mutsumi Kanamori-Katayama, Ai Kaiho, Marina Lizio, Hideya Kawaji, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki
PLoS One 7(1):e30809 (2012)
PUBMED: 22303458; DOI: 10.1371/journal.pone.0030809

Unamplified Cap Analysis of Gene Expression on a single molecule sequencer

Mutsumi Kanamori-Katayama, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Shintaro Katayama, Miki Kojima, Nicolas Bertin, Ai Kaiho, Noriko Ninomiya, Carsten O. Daub, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki.
Genome Research 21, 1150-9 (2011)
PUBMED: 21596820; DOI: 10.1101/gr.115469.110

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan

Charles Plessy, Nicolas Bertin, Hazuki Takahashi, Roberto Simone, Md Salimullah, Timo Lassmann, Morana Vitezic, Jessica Severin, Signe Olivarius, Dejan Lazarevic, Nadine Hornig, Valerio Orlando, Ian Bell, Hui Gao, Jacqueline Dumais, Philipp Kapranov, Huaien Wang, Carrie A Davis, Thomas R Gingeras, Jun Kawai, Carsten O Daub, Yoshihide Hayashizaki, Stefano Gustincich, Piero Carninci
Nature Methods 7, 528–34 (2010)
PUBMED: 20543846; DOI: 10.1038/nmeth.1470

NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes

Md Salimullah, Sakai Mizuho, Charles Plessy, Piero Carninci
Cold Spring Harbor Protocols, (2011)
PUBMED: 21205859; DOI: 10.1101/pdb.prot5559

Genome-wide analysis of mammalian promoter architecture and evolution

Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y.
Nature Genetics 38, 626-635 (2006)
PUBMED: 16645617, DOI: 10.1038/ng1789

The transcriptional landscape of the mammalian genome

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Science 309, 1559-1563 (2005)
PUBMED: 16141072, DOI: 10.1126/science.1112014

Antisense transcription in the mammalian transcriptome

Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engstrom PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt C.
Science 309, 1564-1566 (2005)
PUBMED: 16141073, DOI: 10.1126/science.1112009

Functional annotation of a full-length mouse cDNA collection

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Nature 409, 685-90 (2001)
PUBMED: 11217851, DOI: 10.1038/35055500