The TARGET system: rapid identification of direct targets of transcription factors by gene regulation in plant cells

Authors: Brooks, Matthew; REED, KELSEY - Virginia Polytechnic Institution & State University; KROUK, GABRIEL - National Center For Scientific Research; CORUZZI, GLORIA - New York University; BARGMANN, BASTIAAN, O.R. - Virginia Polytechnic Institution & State University

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 10/21/2021
Publication Date: 10/21/2022
Citation: Brooks, M.D., Reed, K., Krouk, G., Coruzzi, G.M., Bargmann, B. 2022. The TARGET system: rapid identification of direct targets of transcription factors by gene regulation in plant cells. In: Song, Q., Tao, Z., editors. Transcription Factor Regulatory Networks. Methods in Molecular Biology. Volume 2594. New York, NY: Humana. p. 1-12. https://doi.org/10.1007/978-1-0716-2815-7_1
DOI: https://doi.org/10.1007/978-1-0716-2815-7_1

Interpretive Summary:

Technical Abstract: The TARGET system allows for the rapid identification of direct regulated gene targets of transcription factors (TFs). It employs the transient transformation of plant protoplasts with inducible nuclear entry of the TF and subsequent transcriptomic and/or ChIP-seq analysis. The ability to separate direct TF–target gene regulatory interactions from indirect downstream responses and the significantly shorter amount of time required to perform the assay, compared to the generation of transgenics, make this plant cell-based approach a valuable tool for a higher throughput approach to identify the genome-wide targets of multiple TFs, to build validated transcriptional networks in plants. Here, we describe the use of the TARGET system in Arabidopsis seedling root protoplasts to map the gene regulatory network downstream of transcription factors-of-interest.