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


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.

SUBMITTER: Cammack AJ 

PROVIDER: S-EPMC7211997 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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

Cammack Alexander J AJ   Moudgil Arnav A   Chen Jiayang J   Vasek Michael J MJ   Shabsovich Mark M   McCullough Katherine K   Yen Allen A   Lagunas Tomas T   Maloney Susan E SE   He June J   Chen Xuhua X   Hooda Misha M   Wilkinson Michael N MN   Miller Timothy M TM   Mitra Robi D RD   Dougherty Joseph D JD  

Proceedings of the National Academy of Sciences of the United States of America 20200416 18


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  ...[more]

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