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The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells

Part of the Methods in Molecular Biology book series (MIMB,volume 2594)


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.

Key words

  • Transcription factor
  • Gene regulatory network
  • Protoplast
  • Fluorescence activated cell sorting
  • RNA-seq

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This work was supported by NIH Grant R01-GM121753 to G.M.C., NIH NIGMS Fellowship F32GM116347 to M.D.B., and USDA-NIFA Hatch VA-160133 and Multistate VA-136377 projects to B.O.R.B.

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Correspondence to Bastiaan O. R. Bargmann .

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Brooks, M.D., Reed, K.M., Krouk, G., Coruzzi, G.M., Bargmann, B.O.R. (2023). The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells. In: Song, Q., Tao, Z. (eds) Transcription Factor Regulatory Networks. Methods in Molecular Biology, vol 2594. Humana, New York, NY.

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2814-0

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