Abstract
BackgroundIn the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP) allows the isolation of in vivo binding sites of transcription factors and provides a powerful tool for examining gene regulation. Crosslinked chromatin is immunoprecipitated with antibodies against specific transcription factors, thus enriching for sequences bound in vivo by these factors in the immunoprecipitated DNA. Cloning and sequencing the immunoprecipitated sequences allows identification of transcription factor target genes. Routinely, thousands of such sequenced clones are used in BLAST searches to map their exact location in the genome and the genes located in the vicinity. These genes represent potential targets of the transcription factor of interest. Such bioinformatics analysis is very laborious if performed manually and for this reason there is a need for developing bioinformatic tools to automate and facilitate it.ResultsIn order to facilitate this analysis we generated TF Target Mapper (Transcription Factor Target Mapper). TF Target Mapper is a BLAST search tool allowing rapid extraction of annotated information on genes around each hit. It combines sequence cleaning/filtering, pattern searching and BLAST searches with extraction of information on genes located around each BLAST hit and comparisons of the output list of genes or gene ontology IDs with user-implemented lists. We successfully applied and tested TF Target Mapper to analyse sequences bound in vivo by the transcription factor GATA-1. We show that TF Target Mapper efficiently extracted information on genes around ChIPed sequences, thus identifying known (e.g. α-globin and ζ-globin) and potentially novel GATA-1 gene targets.ConclusionTF Target Mapper is a very efficient BLAST search tool that allows the rapid extraction of annotated information on the genes around each hit. It can contribute to the comprehensive bioinformatic transcriptome/regulome analysis, by providing insight into the mechanisms of action of specific transcription factors, thus helping to elucidate the pathways these factors regulate.
Highlights
In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors
General description of TF Target Mapper tool In order to facilitate the analysis of large sequence data collections of cloned DNA obtained from chromatin immunoprecipitations we generated a software tool called TF Target Mapper (Transcription Factor Target Mapper)
Our preliminary data showed that most of these sequences were enriched in the GATA1 immunoprecipitated material, increasing the possibility of them being real targets of GATA-1. These results further demonstrate the value of TF Target Mapper in identifying gene targets in chromatin immunoprecipitation approaches
Summary
In the current era of high throughput genomics a major challenge is the genome-wide identification of target genes for specific transcription factors. Chromatin immunoprecipitation (ChIP) allows the isolation of in vivo binding sites of transcription factors and provides a powerful tool for examining gene regulation. Thousands of such sequenced clones are used in BLAST searches to map their exact location in the genome and the genes located in the vicinity These genes represent potential targets of the transcription factor of interest. Chromatin immunoprecipitation (ChIP) allows the isolation of in vivo binding sites of transcription factors and is a powerful tool for examining gene regulation [1]. Cloning and sequencing the ChIPed DNA allows the identification of novel transcription factor target genes Thousands of such sequenced clones are used in BLAST searches to map their exact location in the genome. Information on specific combinations of transcription factor binding sites on user submitted sequences needs to be extracted, as it strengthens the prediction for a sequence being real or background
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