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Genes Dev. 2019 Oct 1;33(19-20):1441-1455. doi: 10.1101/gad.328237.119. Epub 2019 Aug 29.

An improved auxin-inducible degron system preserves native protein levels and enables rapid and specific protein depletion.

Author information

1
Biochemistry and Molecular Genetics Department, University of Virginia, Charlottesville, Virginia 22908, USA.
2
Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA.
3
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
4
Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269, USA.
5
Cancer Center, University of Virginia, Charlottesville, Virginia 22908, USA.

Abstract

Rapid perturbation of protein function permits the ability to define primary molecular responses while avoiding downstream cumulative effects of protein dysregulation. The auxin-inducible degron (AID) system was developed as a tool to achieve rapid and inducible protein degradation in nonplant systems. However, tagging proteins at their endogenous loci results in chronic auxin-independent degradation by the proteasome. To correct this deficiency, we expressed the auxin response transcription factor (ARF) in an improved inducible degron system. ARF is absent from previously engineered AID systems but is a critical component of native auxin signaling. In plants, ARF directly interacts with AID in the absence of auxin, and we found that expression of the ARF PB1 (Phox and Bem1) domain suppresses constitutive degradation of AID-tagged proteins. Moreover, the rate of auxin-induced AID degradation is substantially faster in the ARF-AID system. To test the ARF-AID system in a quantitative and sensitive manner, we measured genome-wide changes in nascent transcription after rapidly depleting the ZNF143 transcription factor. Transcriptional profiling indicates that ZNF143 activates transcription in cis and regulates promoter-proximal paused RNA polymerase density. Rapidly inducible degradation systems that preserve the target protein's native expression levels and patterns will revolutionize the study of biological systems by enabling specific and temporally defined protein dysregulation.

KEYWORDS:

RNA polymerase pausing; ZNF143; auxin response factor; auxin-inducible degron; transcription factors

PMID:
31467088
PMCID:
PMC6771385
DOI:
10.1101/gad.328237.119
[Indexed for MEDLINE]
Free PMC Article

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