"Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run". (December 2016)

• Record Type: Journal Article
• Authors: Doidy, Joan; Li, Ying; Neymotin, Benjamin; Edwards, Molly; Varala, Kranthi; Gresham, David; Coruzzi, Gloria
• Is Part Of: BMC genomics. Volume 17:Number 1(2016)
• Page Start: 1
• Page End: 10
• Publication Date: 2016-12
• Subjects: Transcription factor (TF) -- Target gene -- 4-thiouracil (4tU) -- Dynamic regulation -- Gene regulatory networks -- "hit-and-run" transcription -- Transcriptional regulation; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-2410-2
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Dynamic transcriptional regulation is critical for an organism's response to environmental signals and yet remains elusive to capture. Such transcriptional regulation is mediated by master transcription factors (TF) that control large gene regulatory networks. Recently, we described a dynamic mode of TF regulation named "hit-and-run". This model proposes that master TF can interact transiently with a set of targets, but the transcription of these transient targets continues after the TF dissociation from the target promoter. However, experimental evidence validating active transcription of the transient TF-targets is still lacking. Results Here, we show that active transcription continues after transient TF-target interactions by trackingde novo synthesis of RNAs made in response to TF nuclear import. To do this, we introduced an affinity-labeled 4-thiouracil (4tU) nucleobase to specifically isolate newly synthesized transcripts following conditional TF nuclear import. Thus, we extended theTARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) to include 4tU-labeling and named this new technologyTARGET -tU . Our proof-of-principle example is the master TF Basic Leucine Zipper 1 (bZIP1), a central integrator of metabolic signaling in plants. UsingTARGET -tU, we captured newly synthesized mRNAs made in response to bZIP1 nuclear import at a time when bZIP1 is no longer detectably bound to its target. Thus, the analysis ofde novo transcripomics demonstrates that bZIP1 may act as a catalyst TF to initiate a transcriptional complex ("hit"), after which active transcription by RNA polymerase continues without the TF being bound to the gene promoter ("run"). Conclusion Our findings provide experimental proof for active transcription of transient TF-targets supporting a "hit-and-run" mode of action. This dynamic regulatory model allows a master TF to catalytically propagate rapid and broad transcriptional responses to changes in environment. Thus, the functional read-out ofde novo transcripts produced by transient TF-target interactions allowed us to capture new models for genome-wide transcriptional control.