Technical advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

Joshi, Anagha, Pooley, Christopher, Freeman, Tom C., Lennartsson, Andreas, Babina, Magda, Schmidl, Christian, Geijtenbeek, Teunis, Michoel, Tom, Severin, Jessica, Itoh, Masayoshi, Lassmann, Timo, Kawaji, Hideya, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair R. R., Rehli, Michael and Hume, David A. (2015) Technical advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells. Journal of Leukocyte Biology, 97 5: 985-995. doi:10.1189/jlb.6TA1014-477RR


Author Joshi, Anagha
Pooley, Christopher
Freeman, Tom C.
Lennartsson, Andreas
Babina, Magda
Schmidl, Christian
Geijtenbeek, Teunis
Michoel, Tom
Severin, Jessica
Itoh, Masayoshi
Lassmann, Timo
Kawaji, Hideya
Hayashizaki, Yoshihide
Carninci, Piero
Forrest, Alistair R. R.
Rehli, Michael
Hume, David A.
Title Technical advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells
Journal name Journal of Leukocyte Biology   Check publisher's open access policy
ISSN 1938-3673
0741-5400
Publication date 2015-02-25
Sub-type Article (original research)
DOI 10.1189/jlb.6TA1014-477RR
Open Access Status DOI
Volume 97
Issue 5
Start page 985
End page 995
Total pages 11
Place of publication Oxford, United Kingdom
Publisher John Wiley & Sons
Language eng
Subject 2403 Immunology
1307 Cell Biology
Abstract 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 ismade 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.
Keyword CAGE
Hematopoiesis
Transcriptome
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Faculty of Medicine
 
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Created: Fri, 20 Apr 2018, 09:21:15 EST