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Research Article

Complex Loci in Human and Mouse Genomes

  • Pär G Engström,

    Affiliations: Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway, Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden

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  • Harukazu Suzuki,

    Affiliation: Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan

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  • Noriko Ninomiya,

    Affiliation: Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan

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  • Altuna Akalin,

    Affiliation: Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway

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  • Luca Sessa,

    Affiliation: Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Naples, Italy

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  • Giovanni Lavorgna,

    Affiliation: Department of Biological and Technological Research, San Raffaele Scientific Institute, Milan, Italy

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  • Alessandro Brozzi,

    Affiliations: Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy, Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy

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  • Lucilla Luzi,

    Affiliations: Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy, Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy

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  • Sin Lam Tan,

    Affiliations: Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa

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  • Liang Yang,

    Affiliation: Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore

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  • Galih Kunarso,

    Affiliation: Department of Biological Sciences, National University of Singapore, Singapore

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  • Edwin Lian-Chong Ng,

    Affiliation: Chemical and Life Sciences, Nanyang Polytechnic, Singapore

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  • Serge Batalov,

    Affiliation: Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America

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  • Claes Wahlestedt,

    Affiliations: Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden, Scripps Florida, Jupiter, Florida, United States of America

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  • Chikatoshi Kai,

    Affiliation: Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan

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  • Jun Kawai,

    Affiliations: Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan, Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan

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  • Piero Carninci,

    Affiliations: Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan, Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan

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  • Yoshihide Hayashizaki,

    Affiliations: Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan, Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan

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  • Christine Wells,

    Affiliation: School of Biomolecular and Biomedical Science, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland, Australia

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  • Vladimir B Bajic,

    Affiliations: Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa

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  • Valerio Orlando,

    Affiliation: Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Naples, Italy

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  • James F Reid,

    Affiliations: Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy, Department of Experimental Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milan, Italy

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  • Boris Lenhard mail,

    To whom correspondence should be addressed. E-mail: Boris.Lenhard@bccs.uib.no (BL); lipovich@gis.a-star.edu.sg (LL)

    Affiliations: Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway, Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden

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  • Leonard Lipovich mail

    To whom correspondence should be addressed. E-mail: Boris.Lenhard@bccs.uib.no (BL); lipovich@gis.a-star.edu.sg (LL)

    Affiliation: Genome Institute of Singapore, Singapore

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  • Published: April 28, 2006
  • DOI: 10.1371/journal.pgen.0020047
  • Published in PLOS Genetics

About the Authors

Pär G Engström, Altuna Akalin, Boris Lenhard
Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway
Pär G Engström, Claes Wahlestedt, Boris Lenhard
Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
Harukazu Suzuki, Noriko Ninomiya, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan
Luca Sessa, Valerio Orlando
Dulbecco Telethon Institute, Institute of Genetics and Biophysics CNR, Naples, Italy
Giovanni Lavorgna
Department of Biological and Technological Research, San Raffaele Scientific Institute, Milan, Italy
Alessandro Brozzi, Lucilla Luzi, James F Reid
Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
Alessandro Brozzi, Lucilla Luzi
Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
Sin Lam Tan, Liang Yang, Vladimir B Bajic
Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore
Sin Lam Tan, Vladimir B Bajic
South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
Galih Kunarso
Department of Biological Sciences, National University of Singapore, Singapore
Edwin Lian-Chong Ng
Chemical and Life Sciences, Nanyang Polytechnic, Singapore
Serge Batalov
Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
Claes Wahlestedt
Scripps Florida, Jupiter, Florida, United States of America
Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan
Christine Wells
School of Biomolecular and Biomedical Science, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland, Australia
James F Reid
Department of Experimental Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milan, Italy
Leonard Lipovich
Genome Institute of Singapore, Singapore

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

C. Kai, J. Kawai, P. Carninci, and Y. Hayashizaki contributed sequence data and managed the collaborative project together with C. Wahlestedt. P. G. Engström, B. Lenhard, and L. Lipovich compiled the dataset of TUs, pairs, and chains, performed all analyses not specifically mentioned below, and coordinated the work together with C. Wells. P. G. Engström, H. Suzuki, B. Lenhard, and L. Lipovich designed the PCR experiments together with N. Ninomiya, who performed them. L. Lipovich contributed the analyses of positional equivalents and chain conservation with assistance from P. G. Engström, G. Kunarso, and E. L.-C. Ng. The TSS distribution and sequence composition of bidirectional promoters were analyzed by P. G. Engström, A. Akalin, and B. Lenhard. P. G. Engström, L. Luzi, S. Batalov, C. Wells, J. F. Reid, and B. Lenhard performed the microarray data analysis. L. Sessa, G. Lavorgna, and V. Orlando contributed the analysis of homeotic loci. A. Brozzi, S. L. Tan, L. Yang, and V. B. Bajic contributed additional analyses that had to be excluded because of space constraints. P. G. Engström, L. Lipovich, and B. Lenhard designed and wrote the paper, with contributions from H. Suzuki, L. Luzi, V. B. Bajic, V. Orlando, and J. F. Reid.