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FANTOM4: Systems biology of a leukemia transcriptome and its regulation. This special collection of articles are the companion papers for the three FANTOM4 papers published withNature Genetics. FANTOM4 has used genome-wide expression profiling to measure the expression dynamics of promoter usage, mRNAs, microRNAs and other small non-coding RNAs throughout a time course of differentiation in the acute myeloid leukemia cell line THP-1. Of particular interest was the extensive use of deepCAGE (a new deep sequencing application) to identify active promoters and their expression dynamics. Computational analysis, chromatin immunoprecipitation and perturbation experiments have then been used to build network models of the transcription factors and miRNAs, their targets and their role in differentiation and maintenance of the undifferentiated state.

  1. Research article

    Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

    Histone modifications play an important role in gene regulation. Acetylation of histone 3 lysine 9 (H3K9ac) is generally associated with transcription initiation and unfolded chromatin, thereby positively infl...

    Anton Kratz, Erik Arner, Rintaro Saito, Atsutaka Kubosaki, Jun Kawai, Harukazu Suzuki, Piero Carninci, Takahiro Arakawa, Masaru Tomita, Yoshihide Hayashizaki and Carsten O Daub

    BMC Genomics 2010 11:257

    Published on: 21 April 2010

  2. Research article

    Deciphering the transcriptional circuitry of microRNA genes expressed during human monocytic differentiation

    Macrophages are immune cells involved in various biological processes including host defence, homeostasis, differentiation, and organogenesis. Disruption of macrophage biology has been linked to increased path...

    Sebastian Schmeier, Cameron R MacPherson, Magbubah Essack, Mandeep Kaur, Ulf Schaefer, Harukazu Suzuki, Yoshihide Hayashizaki and Vladimir B Bajic

    BMC Genomics 2009 10:595

    Published on: 10 December 2009

  3. Research

    Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis

    With the move towards systems biology, we need sensitive and reliable ways to determine the relationships between transcription factors and their target genes. In this paper we analyze the regulatory relations...

    Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki and Masanori Suzuki

    Genome Biology 2009 10:R121

    Published on: 2 November 2009

  4. Methodology article

    Development of a high-throughput method for the systematic identification of human proteins nuclear translocation potential

    Important clues to the function of novel and uncharacterized proteins can be obtained by identifying their ability to translocate in the nucleus. In addition, a comprehensive definition of the nuclear proteome...

    Trinh Xuan Hoat, Nicolas Bertin, Noriko Ninomiya, Shiro Fukuda, Kengo Usui, Jun Kawai, Yoshihide Hayashizaki and Harukazu Suzuki

    BMC Cell Biology 2009 10:69

    Published on: 22 September 2009

  5. Method

    Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

    With the advent of ultra high-throughput sequencing technologies, increasingly researchers are turning to deep sequencing for gene expression studies. Here we present a set of rigorous methods for normalizatio...

    Piotr J Balwierz, Piero Carninci, Carsten O Daub, Jun Kawai, Yoshihide Hayashizaki, Werner Van Belle, Christian Beisel and Erik van Nimwegen

    Genome Biology 2009 10:R79

    Published on: 22 July 2009

  6. Method

    The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation

    In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differenti...

    Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine M Irvine, David A Hume, Alistair RR Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki and Carsten O Daub

    Genome Biology 2009 10:R40

    Published on: 19 April 2009

  7. Software

    Chromatin conformation signatures of cellular differentiation

    One of the major genomics challenges is to better understand how correct gene expression is orchestrated. Recent studies have shown how spatial chromatin organization is critical in the regulation of gene expr...

    James Fraser, Mathieu Rousseau, Solomon Shenker, Maria A Ferraiuolo, Yoshihide Hayashizaki, Mathieu Blanchette and Josée Dostie

    Genome Biology 2009 10:R37

    Published on: 19 April 2009

  8. Research

    Genome-wide investigation of in vivoEGR-1 binding sites in monocytic differentiation

    Immediate early genes are considered to play important roles in dynamic gene regulatory networks following exposure to appropriate stimuli. One of the immediate early genes, early growth response gene 1 (EGR-1), ...

    Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki and Yoshihide Hayashizaki

    Genome Biology 2009 10:R41

    Published on: 19 April 2009

  9. Software

    FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions

    EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new data types and sea...

    Jessica Severin, Andrew M Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr J Balwierz, Michiel JL de Hoon, David A Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten O Daub and Alistair RR Forrest

    Genome Biology 2009 10:R39

    Published on: 19 April 2009

  10. Methodology article

    Data-driven normalization strategies for high-throughput quantitative RT-PCR

    High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage tech...

    Jessica C Mar, Yasumasa Kimura, Kate Schroder, Katharine M Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume and John Quackenbush

    BMC Bioinformatics 2009 10:110

    Published on: 19 April 2009

  11. Research

    Transcriptional features of genomic regulatory blocks

    Genomic regulatory blocks (GRBs) are chromosomal regions spanned by highly conserved non-coding elements (HCNEs), most of which serve as regulatory inputs of one target gene in the region. The target genes are...

    Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Christian Bryne, Harukazu Suzuki, Carsten O Daub, Yoshihide Hayashizaki and Boris Lenhard

    Genome Biology 2009 10:R38

    Published on: 19 April 2009