A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues

Alexander J. Cammack, Arnav Moudgil, Jiayang Chen, Michael J. Vasek, Mark Shabsovich, Katherine McCullough, Allen Yen, Tomas Lagunas, Susan E. Maloney, June He, Xuhua Chen, Misha Hooda, Michael N. Wilkinson, Timothy M. Miller, Robi D. Mitra, Joseph D. Dougherty

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF-occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only end-point snapshots of TF binding. Alternatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do not require TF-specific antibodies and offer the potential for unique applications, such as recording of TF occupancy over time and cell type specificity through conditional expression of the TF-enzyme fusion. Here, we create a viral toolkit for one such method, calling cards, and demonstrate that these reagents can be delivered to the live mouse brain and used to report TF occupancy. Further, we establish a Cre-dependent calling cards system and, in proof-of-principle experiments, show utility in defining cell type-specific TF profiles and recording and integrating TF-binding events across time. This versatile approach will enable unique studies of TF-mediated gene regulation in live animal models.

Original languageEnglish
Pages (from-to)10003-10014
Number of pages12
JournalProceedings of the National Academy of Sciences of the United States of America
Volume117
Issue number18
DOIs
StatePublished - May 5 2020

Keywords

  • Brain
  • Enhancer
  • Epigenetics
  • Recording
  • Transcription factor

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