TBP facilitates RNA Polymerase I transcription following mitosis

ABSTRACT

The TATA-box binding protein (TBP) is the sole transcription factor common in the initiation complexes of the three major eukaryotic RNA Polymerases (Pol I, II and III). Although TBP is central to transcription by the three RNA Pols in various species, the emergence of TBP paralogs throughout evolution has expanded the complexity in transcription initiation. Furthermore, recent studies have emerged that questioned the centrality of TBP in mammalian cells, particularly in Pol II transcription, but the role of TBP and its paralogs in Pol I transcription remains to be re-evaluated. In this report, we show that in murine embryonic stem cells TBP localizes onto Pol I promoters, whereas the TBP paralog TRF2 only weakly associates to the Spacer Promoter of rDNA, suggesting that it may not be able to replace TBP for Pol I transcription. Importantly, acute TBP depletion does not fully disrupt Pol I occupancy or activity on ribosomal RNA genes, but TBP binding in mitosis leads to efficient Pol I reactivation following cell division. These findings provide a more nuanced role for TBP in Pol I transcription in murine embryonic stem cells.

KEYWORDS:

• RNA polymerase I
• TATA-box binding protein
• transcription initiation
• embryonic stem cells
• mitotic Bookmarking
• genome profiling

Classification:

• Biological sciences
• Cell biology

Acknowledgements

We thank R. Vander Werff and T. Stach (BRC-seq, UBC) for Illumina sequencing and S. Flibotte (LSI Bioinformatics facility, UBC) for implementation of NET-seq analyses. This work was supported by Life Sciences Institute Cores (LSI Imaging and ubcFLOW Core), supported by the UBC GREx Biological Resilience Initiative. S.S.T is a Canada Research Chair Tier 2 in Mechanisms of Gene Regulation, and is supported by the Michael Smith Foundation for Health Research. We thank Daniel Andrews, Michelle Tong and Dr. Eric Jan for providing the Nluc plasmid and T7 RNA Polymerase and consulting us on how to perform in vitro transcription.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Author contribution

Conceptualization: JZJK, TFN, SST

Methodology: JZJK, TFN

Investigation: JZJK, TFN

Visualization: JZJK, TFN

Acquisition: JZJK, SST

Project administration:

Supervision: SST

Writing – original draft: JZJK, TFN, SST

Writing – review and editing: JZJK, TFN, SST

Data and materials availability

All sequencing data have been deposited in Gene Expression Omnibus. All other data sets are available in the manuscript or in the supplementary materials. GEO IDs are in the Key Resources Table.

Data availability statement

The data that support the findings of this study are openly available in Gene Expression Omnibus reference number GSE237001.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/15476286.2024.2375097

Additional information

Funding

This work was supported by:The Canadian Institutes for Health Research Project Grant award to S.S.T. [PJT-162289].The National Sciences and Engineering Research Council Discovery Grant award to S.S.T. [RGPIN-2020-06106].