Abstract
Transcription of tRNA genes by RNA polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the local chromatin proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII-regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced, and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and tuning the physiological response to changing metabolic demands.
| Original language | English |
|---|---|
| Pages (from-to) | 4205-4221.e9 |
| Journal | Molecular Cell |
| Volume | 83 |
| Issue number | 23 |
| DOIs | |
| Publication status | Published - 7 Dec 2023 |
Keywords
- chromatin
- chromatin proteome
- nutrient signaling
- RNA polymerase III
- tDNA
- transcription
- tRNA
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In: Molecular Cell, Vol. 83, No. 23, 07.12.2023, p. 4205-4221.e9.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly
AU - van Breugel, Maria Elize
AU - van Kruijsbergen, Ila
AU - Mittal, Chitvan
AU - Lieftink, Cor
AU - Brouwer, Ineke
AU - van den Brand, Teun
AU - Kluin, Roelof J.C.
AU - Hoekman, Liesbeth
AU - Menezes, Renée X.
AU - van Welsem, Tibor
AU - Del Cortona, Andrea
AU - Malik, Muddassir
AU - Beijersbergen, Roderick L.
AU - Lenstra, Tineke L.
AU - Verstrepen, Kevin J.
AU - Pugh, B. Franklin
AU - van Leeuwen, Fred
N1 - Funding Information: This research was supported by an institutional grant of the Dutch Cancer Society and of the Dutch Ministry of Health, Welfare, and Sport, by the Dutch Research Council (grant NWO-NCI-LIFT-731.015.405 to F.v.L. and grant 016.Veni.192.071 to I.B.), by the US National Institutes of Health (grant GM145217 to B.F.P.), by the Dutch NWO X-omics Initiative (to L.H.), and by support for T.L.L. by the Oncode Institute (which is partly financed by the Dutch Cancer Society) and the European Research Council (ERC Starting Grant 755695 BURSTREG). The funders had no role in study design, data collection, interpretation, or the decision to submit the work for publication. We thank David Tollervey and Tomasz Turowksi for sharing the CRAC dataset on RNAPIII transcripts and discussing the project. We thank Evelina Tuttuci for sharing the pET542 and pET543 plasmids and Johan van Heerden and Frank Bruggeman for discussing the project. We thank Ben Morris for help with re-arraying yeast libraries by robotics and Pascale Daran-Lapujade for advice regarding the neutral X-2 locus. We thank João Caetano and Mireia Novell Cardona for their input in the PH and AA studies. We thank Folkert van Werven and Fabian Moretto for analysis of Ty1 expression. We thank the Genomics Core Facility, Robotics Facility, High Throughput Screening Facility, Proteomics Facility, High Performance Computing Facility, and Flow Cytometry Facility of the NKI for assistance. We thank members of the F.v.L. lab for helpful discussions. We acknowledge the following resources: Yeast Genome Database (SGD Project), BioRender.com , Platform for Epigenomic and Genomic Research, RRID: SCR_021861 ; Cornell University Biotechnology Resource Center Epigenomics Core Facility, RRID: SCR_021287 ; Cornell University BRC Genomics Core Facility, and RRID: SCR_021727 ; Pennsylvania State University’s Institute for Computational and Data Sciences Advanced Cyberinfrastructure. Funding Information: This research was supported by an institutional grant of the Dutch Cancer Society and of the Dutch Ministry of Health, Welfare, and Sport, by the Dutch Research Council (grant NWO-NCI-LIFT-731.015.405 to F.v.L. and grant 016.Veni.192.071 to I.B.), by the US National Institutes of Health (grant GM145217 to B.F.P.), by the Dutch NWO X-omics Initiative (to L.H.), and by support for T.L.L. by the Oncode Institute (which is partly financed by the Dutch Cancer Society) and the European Research Council (ERC Starting Grant 755695 BURSTREG). The funders had no role in study design, data collection, interpretation, or the decision to submit the work for publication. We thank David Tollervey and Tomasz Turowksi for sharing the CRAC dataset on RNAPIII transcripts and discussing the project. We thank Evelina Tuttuci for sharing the pET542 and pET543 plasmids and Johan van Heerden and Frank Bruggeman for discussing the project. We thank Ben Morris for help with re-arraying yeast libraries by robotics and Pascale Daran-Lapujade for advice regarding the neutral X-2 locus. We thank João Caetano and Mireia Novell Cardona for their input in the PH and AA studies. We thank Folkert van Werven and Fabian Moretto for analysis of Ty1 expression. We thank the Genomics Core Facility, Robotics Facility, High Throughput Screening Facility, Proteomics Facility, High Performance Computing Facility, and Flow Cytometry Facility of the NKI for assistance. We thank members of the F.v.L. lab for helpful discussions. We acknowledge the following resources: Yeast Genome Database (SGD Project), BioRender.com, Platform for Epigenomic and Genomic Research, RRID:SCR_021861; Cornell University Biotechnology Resource Center Epigenomics Core Facility, RRID:SCR_021287; Cornell University BRC Genomics Core Facility, and RRID:SCR_021727; Pennsylvania State University's Institute for Computational and Data Sciences Advanced Cyberinfrastructure. Conceptualization, M.E.v.B. I.v.K. and F.v.L.; methodology, M.E.v.B. I.v.K. C.M. R.X.M. and F.v.L.; software, C.M. C.L. R.J.C.K. T.v.d.B. and A.D.C.; investigation, M.E.v.B. I.v.K. C.M. I.B. T.v.W. M.M. and L.H.; formal analysis, M.E.v.B. I.v.K. C.M. C.L. R.J.C.K. I.B. T.v.d.B. M.M. L.H. A.D.C. B.F.P. and F.v.L.; data curation, M.E.v.B. and C.M.; visualization, M.E.v.B. and C.M.; writing – original draft, M.E.v.B. and F.v.L.; writing – review & editing, M.E.v.B. F.v.L. C.M. B.F.P. I.B. T.v.d.B. R.J.C.K. I.v.K. C.L. T.L.L. R.X.M. and A.D.C.; funding acquisition, F.v.L. B.F.P. L.H. T.L.L. R.L.B. and K.J.V.; supervision, F.v.L. B.F.P. T.L.L. R.L.B. and K.J.V. B.F.P. is an owner of and has a financial interest in Peconic, which uses the ChIP-exo technology (U.S. Patent 20100323361A1) implemented in this study and could potentially benefit from the outcomes of this research. We support inclusive, diverse, and equitable conduct of research. Publisher Copyright: © 2023 Elsevier Inc.
PY - 2023/12/7
Y1 - 2023/12/7
N2 - Transcription of tRNA genes by RNA polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the local chromatin proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII-regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced, and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and tuning the physiological response to changing metabolic demands.
AB - Transcription of tRNA genes by RNA polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the local chromatin proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII-regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced, and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and tuning the physiological response to changing metabolic demands.
KW - chromatin
KW - chromatin proteome
KW - nutrient signaling
KW - RNA polymerase III
KW - tDNA
KW - transcription
KW - tRNA
UR - http://www.scopus.com/inward/record.url?scp=85178086330&partnerID=8YFLogxK
U2 - https://doi.org/10.1016/j.molcel.2023.10.037
DO - https://doi.org/10.1016/j.molcel.2023.10.037
M3 - Article
C2 - 37995691
SN - 1097-2765
VL - 83
SP - 4205-4221.e9
JO - Molecular Cell
JF - Molecular Cell
IS - 23
ER -