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FANTOM findings boost for biologists

Genomic regulatory blocks have unique features that may explain their ability to respond to regulatory inputs from very long distances, according to a special thematic series of companion articles from the FANTOM4 consortium. This research, to be published across a number of BioMed Central's open access journals, including Genome Biology and BMC Bioinformatics, provide further insight into HCNE (highly conserved non-coding element) mediated long-range gene regulation at the core of animal multicellularity regulation.

Now at its fourth stage, FANTOM4, prominently led by OSC's Yoshihide Hayashizaki, has culminated after over three years of research. The center joined forces with scientists from research centers and universities in Australia, Switzerland, Norway, South Africa, Sweden, Canada, Denmark, Italy, Germany, Singapore, UK and the United States to publish three milestone papers in the journal Nature Genetics, along side the companion articles in BioMed Central, that challenge current notions of how genes are controlled in mammals.

In one Genome Biology article, researchers have created a novel database and set of interfaces to interpret biological networks and compare large high-throughput expression datasets. For more details please access the database (

Another study helps address major challenges in genomics including unravelling the orchestration of correct gene expression. FANTOM researchers have developed a suite of computer programs to identify chromatin conformation signatures, which could provide a completely novel class of human disease biomarkers. Further details of the software are available online at

The international FANTOM4 research collaboration yielded a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles along a differentiation time course of the human THP-1 cell line and data regarding chromatin status. These data are detailed in a new article from Genome Biology, and are also available as an integrated web resource (

Further research published in BMC Bioinformatics highlights two new data-driven normalization methods for quantitative reverse transcriptase polymerase chain reaction (qPCR) experiments with larger data sets. Another study published in Genome Biology includes the first genome-wide analysis of EGR-1 binding sites implicated in cell differentiation in human monoblastoma THP-1 cells.

Dr. Harukazu Suzuki, the scientific coordinator said, "We are proud that we have created groundbreaking research in understanding more about how genes regulate cells at the molecular level and we want to acknowledge all consortium members for their great contribution to the research effort."

These are the first papers to be published from the consortium using BioMed Central's new cross-journal thematic series ability. And there are more to follow - a full list is available from the FANTOM4 series homepage (


Contact: Charlotte Webber
BioMed Central

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