Genome-wide de Novo Prediction of Proximal and Distal Tissue-Specific Enhancers
Determining how transcriptional regulatory networks are encoded in the human genome is essential for understanding how cellular processes are directed. Here, we present a novel approach for systematically predicting tissue specific regulatory elements (REs) that blends genome-wide expression profiling, vertebrate genome comparisons, and pattern analysis of transcription factor binding sites. This analysis yields 4,670 candidate REs in the human genome with distinct tissue specificities, the majority of which reside far away from transcription start sites. We identify key transcription factors (TFs) for 34 distinct tissues and demonstrate that tissue-specific gene expression relies on multiple regulatory pathways employing similar, but different cohorts of interacting TFs. The methods and results we describe provide a global view of tissue specific gene regulation in humans, and propose a strategy for deciphering the transcriptional regulatory code in eukaryotes.
- Research Organization:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- W-7405-ENG-48
- OSTI ID:
- 899445
- Report Number(s):
- UCRL-JRNL-216861; TRN: US200708%%297
- Journal Information:
- Genome Research, N/A, N/A, January 7, 2007, pp. 1, Journal Name: Genome Research, N/A, N/A, January 7, 2007, pp. 1
- Country of Publication:
- United States
- Language:
- English
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