Acute perturbation strategies in interrogating RNA polymerase II elongation factor function in gene expression

Bin Zheng, Yuki Aoi, Avani P. Shah, Marta Iwanaszko, Siddhartha Das, Emily J. Rendleman, Didi Zha, Nabiha Khan, Edwin R. Smith, Ali Shilatifard*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Scopus citations


The regulation of gene expression catalyzed by RNA polymerase II (Pol II) requires a host of accessory factors to ensure cell growth, differentiation, and survival under environmental stress. Here, using the auxin-inducible degradation (AID) system to study transcriptional activities of the bromodomain and extraterminal domain (BET) and super elongation complex (SEC) families, we found that the CDK9-containing BRD4 complex is required for the release of Pol II from promoter-proximal pausing for most genes, while the CDK9-containing SEC is required for activated transcription in the heat shock response. By using both the proteolysis targeting chimera (PROTAC) dBET6 and the AID system, we found that dBET6 treatment results in two major effects: increased pausing due to BRD4 loss, and reduced enhancer activity attributable to BRD2 loss. In the heat shock response, while auxin-mediated depletion of the AFF4 subunit of the SEC has a more severe defect than AFF1 depletion, simultaneous depletion of AFF1 and AFF4 leads to a stronger attenuation of the heat shock response, similar to treatment with the SEC inhibitor KL-1, suggesting a possible redundancy among SEC family members. This study highlights the usefulness of orthogonal acute depletion/inhibition strategies to identify distinct and redundant biological functions among Pol II elongation factor paralogs.

Original languageEnglish (US)
Pages (from-to)273-285
Number of pages13
JournalGenes and Development
Issue number3
StatePublished - Feb 1 2021


  • Auxin-inducible degradation
  • BRD2
  • BRD4
  • Enhancer activity
  • Heat shock PROTAC
  • Super elongation complex
  • Transcription elongation

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology


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