title: "Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run".
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 tracking de 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 the TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) to include 4tU-labeling and named this new technology TARGET-tU. Our proof-of-principle example is the master TF Basic Leucine Zipper 1 (bZIP1), a central integrator of metabolic signaling in plants. Using TARGET-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 of de 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").
  
  
  CONCLUSIONS
  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 of de novo transcripts produced by transient TF-target interactions allowed us to capture new models for genome-wide transcriptional control.
authors: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. joan.doidy@gmail.com.
authors: Joan
authors: J
authors: Doidy
authors: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. yl54@nyu.edu.
authors: Ying
authors: Y
authors: Li
authors: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. bneymotin@gmail.com.
authors: Benjamin
authors: B
authors: Neymotin
authors: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. me77@nyu.edu.
authors: Molly B
authors: MB
authors: Edwards
authors: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. kv15@nyu.edu.
authors: Kranthi
authors: K
authors: Varala
authors: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. dgresham@nyu.edu.
authors: David
authors: D
authors: Gresham
authors: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA. gloria.coruzzi@nyu.edu.
authors: Gloria M
authors: GM
authors: Coruzzi
mesh_terms: D050976:Basic-Leucine Zipper Transcription Factors / Q000378:metabolism*; D001665:Binding Sites; D005786:Gene Expression Regulation; D008954:Models, Biological; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D013889:Thiouracil / Q000031:analogs & derivatives; D061785:Transcription Initiation, Genetic; D014158:Transcription, Genetic
chemical_list: D050976:Basic-Leucine Zipper Transcription Factors; C114719:4-thiouracil; D013889:Thiouracil