Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction.
The transcriptional response driven by Hypoxia-inducible factor (HIF) is central to the adaptation to oxygen restriction. Hence, the complete identification of HIF targets is essential for understanding the cellular responses to hypoxia. Herein we describe a computational strategy based on the combination of phylogenetic footprinting and transcription profiling meta-analysis for the identification of HIF-target genes. Comparison of the resulting candidates with published HIF1a genome-wide chromatin immunoprecipitation indicates a high sensitivity (78%) and specificity (97.8%). To validate our strategy, we performed HIF1a chromatin immunoprecipitation on a set of putative targets. Our results confirm the robustness of the computational strategy in predicting HIF-binding sites and reveal several novel HIF targets, including RE1-silencing transcription factor co-repressor (RCOR2). In addition, mapping of described polymorphisms to the predicted HIF-binding sites identified several single-nucleotide polymorphisms (SNPs) that could alter HIF binding. As a proof of principle, we demonstrate that SNP rs17004038, mapping to a functional hypoxia response element in the macrophage migration inhibitory factor (MIF) locus, prevents induction of this gene by hypoxia. Altogether, our results show that the proposed strategy is a powerful tool for the identification of HIF direct targets that expands our knowledge of the cellular adaptation to hypoxia and provides cues on the inter-individual variation in this response.
Ortiz-Barahona
Amaya
A
Department of Biochemistry, Universidad Autónoma de Madrid-Instituto de Investigaciones Biomédicas CSIC, Madrid, Spain.
Villar
Diego
D
Pescador
Nuria
N
Amigo
Jorge
J
del Peso
Luis
L
D001665:Binding Sites; D015687:Cell Hypoxia; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D056970:Co-Repressor Proteins / Q000737:chemistry* / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D051795:Hypoxia-Inducible Factor 1, alpha Subunit / Q000378:metabolism*; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide
D056970:Co-Repressor Proteins; D051795:Hypoxia-Inducible Factor 1, alpha Subunit; C000589202:Rcor2 protein, human