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Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)
Published on: January 20, 2016
"Calling cards" for DNA-binding proteins in mammalian cells
Haoyi Wang1, David Mayhew, Xuhua Chen
1Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University, School of Medicine, St. Louis, Missouri 63108, USA.
Genetics
|January 5, 2012
Summary
Researchers developed a novel method to permanently record protein-DNA interactions in mammalian cells. This technique uses transcription factors to deposit transposons, creating genomic "calling cards" for tracking binding events during development.
Area of Science:
- Molecular Biology
- Genomics
- Developmental Biology
Background:
- Mapping transcriptional networks is crucial for understanding cell-fate decisions during development.
- Existing methods for tracking transcription factor binding have limitations in recording dynamic events throughout development.
Purpose of the Study:
- To develop a method for permanently recording transcription-factor binding events in mammalian cells.
- To enable the tracing of transcription factor interactions throughout cellular and organismal development.
Main Methods:
- Engineered transcription factors to deposit transposons near their DNA binding sites.
- Utilized the piggyBac transposase system fused to the SP1 transcription factor.
- Identified transposon insertion sites using massively parallel DNA sequencing.
Main Results:
- The SP1-piggyBac transposase fusion successfully directed transposon insertion near SP1 binding sites.
- Transposon insertion sites were highly reproducible and correlated with ChIP-seq data for SP1 binding.
- Genes bound by SP1 were found to be more likely expressed, and SP1-bound CpG islands were predominantly unmethylated.
Conclusions:
- This novel method provides a permanent record of transcription factor binding events.
- The technique offers a powerful new tool for mapping transcriptional networks and understanding developmental processes.
- Potential applications include tracing transcription factor dynamics throughout development in unprecedented detail.
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