Genome-wide de Novo Prediction of Proximal and Distal Tissue-Specific Enhancers

Journal Article · Thu Nov 03 04:00:00 EST 2005 · Genome Research, N/A, N/A, January 7, 2007, pp. 1

OSTI ID:899445

Loots, G G; Ovcharenko, I V

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 Laboratory (LLNL), Livermore, CA
• Sponsoring Organization: USDOE
• DOE Contract Number: W-7405-ENG-48
• OSTI ID: 899445
• Report Number(s): UCRL-JRNL-216861
• 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

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
99 GENERAL AND MISCELLANEOUS
FORECASTING
GENE REGULATION
GENES
TRANSCRIPTION
TRANSCRIPTION FACTORS
VERTEBRATES