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	Genome-wide analysis of mammalian promoter architecture and evolution Piero Carninci^1,^2,²¹, Albin Sandelin^1,^3,²¹, Boris Lenhard^1,^3,^20,²¹, Shintaro Katayama¹, Kazuro Shimokawa¹, Jasmina Ponjavic^1,²⁰, Colin A M Semple^1,⁴, Martin S Taylor^1,⁵, Pär G Engström³, Martin C Frith^1,⁶, Alistair R R Forrest⁶, Wynand B Alkema³, Sin Lam Tan⁷, Charles Plessy², Rimantas Kodzius^1,², Timothy Ravasi^1,^6,⁸, Takeya Kasukawa^1,⁹, Shiro Fukuda¹, Mutsumi Kanamori-Katayama¹, Yayoi Kitazume¹, Hideya Kawaji^1,⁹, Chikatoshi Kai¹, Mari Nakamura¹, Hideaki Konno¹, Kenji Nakano^1,⁹, Salim Mottagui-Tabar^3,²⁰, Peter Arner¹⁰, Alessandra Chesi¹¹, Stefano Gustincich¹¹, Francesca Persichetti¹², Harukazu Suzuki¹, Sean M Grimmond⁶, Christine A Wells¹⁹, Valerio Orlando¹³, Claes Wahlestedt^3,²⁰, Edison T Liu¹⁴, Matthias Harbers¹⁵, Jun Kawai^1,², Vladimir B Bajic^1,^7,¹⁶, David A Hume^1,^6,²¹ & Yoshihide Hayashizaki^1,^2,^17,¹⁸ ¹ Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. ² Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. ³ Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius v. 35, S-171 77 Stockholm, Sweden. ⁴ UK Medical Research Council (MRC) Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK. ⁵ University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK. ⁶ Australian Research Council (ARC) Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane Qld, 4072, Australia. ⁷ Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613, Singapore. ⁸ Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, 0412 La Jolla, California 92093, USA. ⁹ Broadband Communication Service Business Unit, Network Service Solution Business Group, NTT Software Corporation, Teisan Kannai Bldg. 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan. ¹⁰ Department of Medicine, Karolinska Institute, Huddinge University Hospital, S 141 86 Huddinge, Sweden. ¹¹ The Giovanni Armenise–Harvard Foundation Laboratory, Sector of Neurobiology, International School for Advanced Studies-Scuola Internazionale Superiore Studi Avanzati (I.S.A.S.-S.I.S.S.A.), AREA Science Park, Padriciano 99, 34012 Trieste, Italy. ¹² Sector of Neurobiology, I.S.A.S.-S.I.S.S.A., AREA Science Park, Padriciano 99, 34012 Trieste, Italy. ¹³ Dulbecco Telethon Institute, Institute of Genetics and Biophysics, Consiglio Nazionale delle Ricerche (IGB CNR), Epigenetics and Genome Reprogramming Laboratory, Pietro Castellino Street 111, Napoli, 80131, Italy. ¹⁴ Genome Institute of Singapore, 60 Biopolis Street #02-01, Singapore 138672. ¹⁵ Kabushiki Kaisha Dnaform, 1-3-35, Mita, Minato-ku, Tokyo, 108-0073, Japan. ¹⁶ South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, South Africa. ¹⁷ Yokohama City University, 1-7-29 Suehiro-cho Tsurumi-ku Yokohama 230-0045 Japan. ¹⁸ Graduate School of Comprehensive Human Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi Ibaraki-ken, 305-8577, Japan. ¹⁹ The Eskitis Institute for Cell and Molecular Therapies, Griffith University, Nathan Campus, Kessels Road, Queensland 4111, Australia. ²⁰ Present addresses: Bergen Center for Computational Science, Unifob AS, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway (B.L.), Scripps Florida, Jupiter, Florida 33458, USA (C.W.), Department of Molecular Medicine, National Public Health Instititute, Department of Medical Genetics, University of Helsinki, Biomedicum, FIN-00251 Helsinki, Finland (S.M.-T.) and MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK (J.P.). ²¹ These authors contributed equally to this work. Correspondence should be addressed to David A Hume d.hume@imb.uq.edu.au or Yoshihide Hayashizaki yosihide@gsc.riken.jp Published in Nature Genetics Article supplement(s): [Supplemental Research Data]

	Transcriptional Network Dynamics in Macrophage Activation Roland Nilsson^1,2, Vladimir B. Bajic³, Harukazu Suzuki⁴, Diego di Bernardo⁵, Johan Björkegren^1,2, Shintaro Katayama⁴, James F. Reid⁷, Matthew J. Sweet⁸, Manuela Gariboldi⁷, Piero Carninci^4,5, Yosihide Hayashizaki^4,6, David A. Hume^6,8,, Jesper Tegner^1,2, and Timothy Ravasi^4,6,9,. ¹Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden, ²Computational Biology, IFM, Linkoping University, Linkoping, Sweden. ³Knowledge Extraction Lab, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613. ⁴Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan, ⁵Telethon Institute for Genetics and Medicine, Naples, Italy, ⁶Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan, ⁷Department of Experimental Oncology, Istituto Nazionale per lo Studio e la Cura dei Tumori, Milan, Italy, ⁸ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia, and ⁹Department of Bioengineering, Jacobs School of Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. ^ Corresponding authors Status: Submitted Article supplement(s): [Supplemental Research Data]

	The c-Jun N-terminal kinases are important for development and survival of macrophages S. Roy Himes, David P. Sester, Timothy Ravasi, Stephen L. Cronau, Tedjo Sasmono, and David A. Hume. CRC for Chronic Inflammatory Disease, Institute for Molecular Biosciences, University of Queensland, Brisbane, Australia 4072 Address for correspondence: Prof. D. A. Hume Institute for Molecular Biosciences Queensland Biosciences Precinct Bldg. 80, Services Rd. University of Queensland Brisbane, Queensland Australia 4072 Telephone: 61-7-3346-2074 Facsimile: 61-7-3346 Article supplement(s): [Supplemental Research Data]

	Alternate transcription of the Toll-like receptor signalling cascade. Christine A Wells1,2Alistair Chalk1,3, Alistair Forrest2, Darrin Taylor2, Nic Waddell2, Kate Schroder2, S. Roy Himes2, Geoffrey Faulkner2, Sandra Lo1, Takeya Kasukawa4, Hideya Kawaji4, Chikatoshi Kai4, Jun Kawai4,5, Shintaro Katayama4, Piero Carninci4 , Yoshihide Hayashizaki4, David A Hume2, and Sean M Grimmond2 1. Eskitis Institute for Cell and Molecular Therapies, School of Biological and Biomedical Sciences, Griffith University, Brisbane, Australia Corresponding author. 2. The Institute for Molecular Biosciences, The University of QLD, Brisbane, Australia 3. Karolinska Institutet, Sweden 4. Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. 5. Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan Status: Submitted Article supplement(s): [Supplemental Research Data]

	EXPRESSION OF A C-FMS(CSF-1R)-EGFP TRANSGENE IN GRANULOCYTES AND MACROPHAGES REFLECTS CLOSELY-RELATED TRANSCRIPTIONAL PROFILES AND IMPLIES TRANSLATIONAL CONTROL OF LINEAGE DIVERGENCE. R. Tedjo Sasmono, Stephen L. Cronau, Timothy Ravasi, Rangi Kandane, Michael J. Hickey, Andrew D. Cook, S. Roy Himes, John A. Hamilton and David A. Hume. Status: Submitted Article supplement(s): [Supplemental Research Data]