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Joshi A, Pooley C, Freeman TC, Lennartsson A, Babina M, Schmidl C, Geijtenbeek T, Michoel T, Severin J, Itoh M, Lassmann T, Kawaji H, Hayashizaki Y, Carninci P, Forrest ARR, Rehli M, Hume DA. Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells. J Leukoc Biol 2015; 97:985-995. [PMID: 25717144 PMCID: PMC4398258 DOI: 10.1189/jlb.6ta1014-477rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/23/2015] [Accepted: 01/28/2015] [Indexed: 11/24/2022] Open
Abstract
Analysis of the myeloid transcriptome by integrating 91 samples from the myeloid lineage and AML cell lines to predict novel regulatory interactions, enhancers, miRNAs, and lincRNAs. The generation of myeloid cells from their progenitors is regulated at the level of transcription by combinatorial control of key transcription factors influencing cell-fate choice. To unravel the global dynamics of this process at the transcript level, we generated transcription profiles for 91 human cell types of myeloid origin by use of CAGE profiling. The CAGE sequencing of these samples has allowed us to investigate diverse aspects of transcription control during myelopoiesis, such as identification of novel transcription factors, miRNAs, and noncoding RNAs specific to the myeloid lineage. We further reconstructed a transcription regulatory network by clustering coexpressed transcripts and associating them with enriched cis-regulatory motifs. With the use of the bidirectional expression as a proxy for enhancers, we predicted over 2000 novel enhancers, including an enhancer 38 kb downstream of IRF8 and an intronic enhancer in the KIT gene locus. Finally, we highlighted relevance of these data to dissect transcription dynamics during progressive maturation of granulocyte precursors. A multifaceted analysis of the myeloid transcriptome is made available (www.myeloidome.roslin.ed.ac.uk). This high-quality dataset provides a powerful resource to study transcriptional regulation during myelopoiesis and to infer the likely functions of unannotated genes in human innate immunity.
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Affiliation(s)
- Anagha Joshi
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Christopher Pooley
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Tom C Freeman
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Andreas Lennartsson
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Magda Babina
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Christian Schmidl
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Teunis Geijtenbeek
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | | | - Tom Michoel
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Jessica Severin
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Masayoshi Itoh
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Timo Lassmann
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Hideya Kawaji
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Yoshihide Hayashizaki
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Piero Carninci
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Alistair R R Forrest
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - Michael Rehli
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
| | - David A Hume
- *The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan
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