"Calling cards" for DNA-binding proteins in mammalian cells.
The ability to chronicle transcription-factor binding events throughout the development of an organism would facilitate mapping of transcriptional networks that control cell-fate decisions. We describe a method for permanently recording protein-DNA interactions in mammalian cells. We endow transcription factors with the ability to deposit a transposon into the genome near to where they bind. The transposon becomes a "calling card" that the transcription factor leaves behind to record its visit to the genome. The locations of the calling cards can be determined by massively parallel DNA sequencing. We show that the transcription factor SP1 fused to the piggyBac transposase directs insertion of the piggyBac transposon near SP1 binding sites. The locations of transposon insertions are highly reproducible and agree with sites of SP1-binding determined by ChIP-seq. Genes bound by SP1 are more likely to be expressed in the HCT116 cell line we used, and SP1-bound CpG islands show a strong preference to be unmethylated. This method has the potential to trace transcription-factor binding throughout cellular and organismal development in a way that has heretofore not been possible.
Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, Missouri 63108, USA.
Haoyi
H
Wang
David
D
Mayhew
Xuhua
X
Chen
Mark
M
Johnston
Robi David
RD
Mitra
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D018899:CpG Islands; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D023061:Gene Order; D006801:Humans; D016254:Mutagenesis, Insertional; D059372:Nucleotide Motifs; D016329:Sp1 Transcription Factor / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D019895:Transposases / Q000235:genetics / Q000378:metabolism*
D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; D016329:Sp1 Transcription Factor; D014157:Transcription Factors; D019895:Transposases