Evolution of promoter-proximal pausing enabled a new layer of transcription control

Alexandra G. Chivu; Brent A. Basso; Abderhman Abuhashem; Michelle M. Leger; Gilad Barshad; Edward J. Rice; Albert C. Vill; Wilfred Wong; Shao Pei Chou; Gopal Chovatiya; Rebecca Brady; Jeramiah J. Smith; Athula H. Wikramanayake; César Arenas-Mena; Ilana L. Brito; Iñaki Ruiz-Trillo; Anna Katerina Hadjantonakis; John T. Lis; James J. Lewis; Charles G. Danko

doi:10.1038/s41594-025-01718-y

Evolution of promoter-proximal pausing enabled a new layer of transcription control

Alexandra G. Chivu
, Brent A. Basso
, Abderhman Abuhashem
, Michelle M. Leger
, Gilad Barshad
, Edward J. Rice
, Albert C. Vill
, Wilfred Wong
, Shao Pei Chou
, Gopal Chovatiya
, Rebecca Brady
, Jeramiah J. Smith
, Athula H. Wikramanayake
, César Arenas-Mena
, Ilana L. Brito
, Iñaki Ruiz-Trillo
, Anna Katerina Hadjantonakis
, John T. Lis
, James J. Lewis
, Charles G. Danko

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

Promoter-proximal pausing of RNA polymerase (Pol) II is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here, we analyzed transcription in species across the tree of life. Unicellular eukaryotes display an accumulation of Pol II near transcription start sites, which we propose transitioned to the longer-lived, focused pause observed in metazoans. This transition coincided with the evolution of new subunits in the negative elongation factor (NELF) and 7SK complexes. Depletion of NELF in mammals shifted the promoter-proximal buildup of Pol II from the pause site into the early gene body and compromised transcriptional activation for a set of heat-shock genes. Our work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.

Original language	English
Pages (from-to)	282-292
Number of pages	11
Journal	Nature Structural and Molecular Biology
Volume	33
Issue number	2
DOIs	https://doi.org/10.1038/s41594-025-01718-y
State	Published - Feb 2026

Bibliographical note

Publisher Copyright:
© The Author(s), under exclusive licence to Springer Nature America, Inc. 2025.

Funding

We thank members of the C.G.D. and J.T.L. labs for valuable discussions and suggestions throughout the life of this project and M. A. Subirats for preparing samples from C . owczarzaki , C . fragrantissima and S . arctica . We acknowledge the Fundación Pública Galega Centro Tecnolóxico de Supercomputación de Galicia for access to the FinisTerraeIII supercomputer and V. Shabardina for facilitating access. Work in this publication was primarily supported by a grant from the National Aeronautics and Space Administration exobiology program (17-EXO-17-2-0112). Additional funding was also available from the National Human Genome Research Institute (R01-HG010346 and R01-HG009309) to C.G.D., the National Institute of General Medical Sciences (R01 GM147731) to I.L.B. and C.G.D., and the National Institutes of Health (NIH; RM1-GM139738) to J.T.L. A.A. was supported by the NIH (T32GM007739 and F30HD103398). M.M.L. was supported by an Ayuda Juan de la Cierva Incorporación postdoctoral fellowship (IJC2018-036657-I) from the Spanish Ministry of Science and Innovation. Work in A.K.H.’s lab was supported by the NIH (R01HD094868, R01DK127821, R01HD086478 and P30CA008748). Work in I.R.-T.’s lab was supported by a European Research Council Consolidator Grant (ERC-2012-Co-616960). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Some of the figures in this manuscript were created using BioRender.com . We thank members of the C.G.D. and J.T.L. labs for valuable discussions and suggestions throughout the life of this project and M. A. Subirats for preparing samples from C. owczarzaki, C. fragrantissima and S. arctica. We acknowledge the Fundación Pública Galega Centro Tecnolóxico de Supercomputación de Galicia for access to the FinisTerraeIII supercomputer and V. Shabardina for facilitating access. Work in this publication was primarily supported by a grant from the National Aeronautics and Space Administration exobiology program (17-EXO-17-2-0112). Additional funding was also available from the National Human Genome Research Institute (R01-HG010346 and R01-HG009309) to C.G.D., the National Institute of General Medical Sciences (R01 GM147731) to I.L.B. and C.G.D., and the National Institutes of Health (NIH; RM1-GM139738) to J.T.L. A.A. was supported by the NIH (T32GM007739 and F30HD103398). M.M.L. was supported by an Ayuda Juan de la Cierva Incorporación postdoctoral fellowship (IJC2018-036657-I) from the Spanish Ministry of Science and Innovation. Work in A.K.H.’s lab was supported by the NIH (R01HD094868, R01DK127821, R01HD086478 and P30CA008748). Work in I.R.-T.’s lab was supported by a European Research Council Consolidator Grant (ERC-2012-Co-616960). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Some of the figures in this manuscript were created using BioRender.com .

Funders	Funder number
Fundación Pública Galega Centro Tecnolóxico de Supercomputación de Galicia
National Institute of General Medical Sciences DP2GM119177 Sophie Dumont National Institute of General Medical Sciences	R01 GM147731
National Aeronautics and Space Administration	17-EXO-17-2-0112
Ayuda Juan de la Cierva Incorporación	IJC2018-036657-I
National Human Genome Research Institute	R01-HG010346, R01-HG009309
Ministerio de Ciencia, Innovación y Universidades	R01DK127821, R01HD086478, P30CA008748, R01HD094868
National Institutes of Health (NIH)	RM1-GM139738, F30HD103398, T32GM007739
H2020 European Research Council	ERC-2012-Co-616960

ASJC Scopus subject areas

Structural Biology
Molecular Biology

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10.1038/s41594-025-01718-y

Cite this

Chivu, A. G., Basso, B. A., Abuhashem, A., Leger, M. M., Barshad, G., Rice, E. J., Vill, A. C., Wong, W., Chou, S. P., Chovatiya, G., Brady, R., Smith, J. J., Wikramanayake, A. H., Arenas-Mena, C., Brito, I. L., Ruiz-Trillo, I., Hadjantonakis, A. K., Lis, J. T., Lewis, J. J., & Danko, C. G. (2026). Evolution of promoter-proximal pausing enabled a new layer of transcription control. Nature Structural and Molecular Biology, 33(2), 282-292. https://doi.org/10.1038/s41594-025-01718-y

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abstract = "Promoter-proximal pausing of RNA polymerase (Pol) II is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here, we analyzed transcription in species across the tree of life. Unicellular eukaryotes display an accumulation of Pol II near transcription start sites, which we propose transitioned to the longer-lived, focused pause observed in metazoans. This transition coincided with the evolution of new subunits in the negative elongation factor (NELF) and 7SK complexes. Depletion of NELF in mammals shifted the promoter-proximal buildup of Pol II from the pause site into the early gene body and compromised transcriptional activation for a set of heat-shock genes. Our work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.",

author = "Chivu, \{Alexandra G.\} and Basso, \{Brent A.\} and Abderhman Abuhashem and Leger, \{Michelle M.\} and Gilad Barshad and Rice, \{Edward J.\} and Vill, \{Albert C.\} and Wilfred Wong and Chou, \{Shao Pei\} and Gopal Chovatiya and Rebecca Brady and Smith, \{Jeramiah J.\} and Wikramanayake, \{Athula H.\} and C{\'e}sar Arenas-Mena and Brito, \{Ilana L.\} and I{\~n}aki Ruiz-Trillo and Hadjantonakis, \{Anna Katerina\} and Lis, \{John T.\} and Lewis, \{James J.\} and Danko, \{Charles G.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature America, Inc. 2025.",

year = "2026",

month = feb,

doi = "10.1038/s41594-025-01718-y",

language = "English",

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Chivu, AG, Basso, BA, Abuhashem, A, Leger, MM, Barshad, G, Rice, EJ, Vill, AC, Wong, W, Chou, SP, Chovatiya, G, Brady, R, Smith, JJ, Wikramanayake, AH, Arenas-Mena, C, Brito, IL, Ruiz-Trillo, I, Hadjantonakis, AK, Lis, JT, Lewis, JJ & Danko, CG 2026, 'Evolution of promoter-proximal pausing enabled a new layer of transcription control', Nature Structural and Molecular Biology, vol. 33, no. 2, pp. 282-292. https://doi.org/10.1038/s41594-025-01718-y

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AU - Ruiz-Trillo, Iñaki

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Evolution of promoter-proximal pausing enabled a new layer of transcription control

Abstract

Bibliographical note

Funding

ASJC Scopus subject areas

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