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BRD2 interconnects with BRD3 to facilitate Pol II transcription initiation and elongation to prime promoters for cell differentiation

Cellular and Molecular Life Sciences volume 79, Article number: 338 (2022) Cite this article

Abstract

The bromodomain and extraterminal motif (BET) proteins are critical drug targets for diseases. The precise functions and relationship of BRD2 with other BET proteins remain elusive mechanistically. Here, we used acute protein degradation and quantitative genomic and proteomic approaches to investigate the primary functions of BRD2 in transcription. We report that BRD2 is required for TAF3-mediated Pol II initiation at promoters with low levels of H3K4me3 and for R-loop suppression during Pol II elongation. Single and double depletion revealed that BRD2 and BRD3 function additively, independently, or perhaps antagonistically in Pol II transcription at different promoters. Furthermore, we found that BRD2 regulates the expression of different genes during embryonic body differentiation processes by promoter priming in embryonic stem cells. Therefore, our results suggest complex interconnections between BRD2 and BRD3 at promoters to fine-tune Pol II initiation and elongation for control of cell state.

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Data availability

All sequencing datasets generated in this study, including ChIA-PET, ChIP-Seq, RNA-Seq, and 4C-Seq data, have been deposited in GEO with accession GSE160557. Mass spectrometry data can be found in the PRIDE database: PXD030774.

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Acknowledgements

We thank the members of the Ji laboratory for engaging in helpful discussions. We thank Dr. Richard Young for assistance during the beginning of the studies. We thank Dr. Mario Garcia-Dominguez for the BRD2 wild-type and mutant constructs. We thank the National Center for Protein Sciences at Peking University in Beijing, China, for assistance with high-resolution fluorescence imaging and LYD for help with flow cytometry sorting, DL for help with mass spectrometry detection, and CYS and HXL for help with cell imaging. We also thank Eric Spooner at the Whitehead Proteomics Core for mass spectrometry and Tom Volkert at the Whitehead Genome Technology Core for sequencing.

Funding

This work was supported by funds from the Ministry of Science and Technology of China and the National Natural Science Foundation of China (Grants 2017YFA0506600, 31871309 and 32170569, respectively), the Qidong-SLS Innovation Fund, and grants from the Peking-Tsinghua Center for Life Sciences and the Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education at Peking University School of Life Sciences to X. J. In addition, J.H. is supported in part by the China Postdoctoral Science Foundation (2017M610700). L.C. is supported by Ministry of Science and Technology of China and the National Natural Science Foundation of China (Grants 2021YFA1100500, 32171289).

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Author notes

  1. Brian J. Abraham

    Present address: Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA

  2. Chenlu Wang and Qiqin Xu contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China

    Chenlu Wang, Qiqin Xu, Kehuan Lun, Jie Huang & Xiong Ji

  2. Hubei Key Laboratory of Cell Homeostasis, RNA Institute, College of Life Sciences, Wuhan University, Wuhan, 430072, China

    Xianhong Zhang & Liang Chen

  3. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA

    Daniel S. Day & Brian J. Abraham

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  1. Chenlu Wang
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Contributions

XJ conceived and supervised the project. CLW generated the degron mES cells and performed BRD2 degradation-related Western blots, 4C-Seq, ChIP-Seq/qPCR, RNA-Seq, differentiation-related analyses, and mass spectrometry analyses. QQX performed most of the analyses, including ChIP-Seq, RNA-Seq-related analyses and 4C-Seq, R-Loop, and conservation analyses. JH initially performed BRD2 ChIP-Seq and expression analyses during the embryonic body differentiation process. XHZ and LC generated the R-loop sequencing data. BA and DD helped with the bioinformatic analyses at the initial stage of the project. XJ performed BRD2 ChIA-PET experiments. All authors contributed to the data analyses and data interpretation. XJ wrote the manuscript with input from JH, CLW, QQX and help from the other authors.

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Correspondence to Jie Huang or Xiong Ji.

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Wang, C., Xu, Q., Zhang, X. et al. BRD2 interconnects with BRD3 to facilitate Pol II transcription initiation and elongation to prime promoters for cell differentiation. Cell. Mol. Life Sci. 79, 338 (2022). https://doi.org/10.1007/s00018-022-04349-4

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  • DOI: https://doi.org/10.1007/s00018-022-04349-4

Keywords

  • BET proteins
  • RNA Pol II
  • Cross-regulation
  • Embryonic body