Abstract:
:Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. We have developed an unbiased genomic method called sequence tag analysis of genomic enrichment (STAGE) to identify the direct binding targets of transcription factors in vivo. STAGE is based on high-throughput sequencing of concatemerized tags derived from target DNA enriched by chromatin immunoprecipitation. We first used STAGE in yeast to confirm that RNA polymerase III genes are the most prominent targets of the TATA-box binding protein. We optimized the STAGE protocol and developed analysis methods to allow the identification of transcription factor targets in human cells. We used STAGE to identify several previously unknown binding targets of human transcription factor E2F4 that we independently validated by promoter-specific PCR and microarray hybridization. STAGE provides a means of identifying the chromosomal targets of DNA-associated proteins in any sequenced genome.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Kim J,Bhinge AA,Morgan XC,Iyer VRdoi
10.1038/nmeth726keywords:
subject
Has Abstractpub_date
2005-01-01 00:00:00pages
47-53issue
1eissn
1548-7091issn
1548-7105pii
nmeth726journal_volume
2pub_type
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