RNA polymerase II dynamics shape enhancer–promoter interactions

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RNA polymerase II dynamics shape enhancer–promoter interactions. / Barshad, Gilad; Lewis, James J.; Chivu, Alexandra G.; Abuhashem, Abderhman; Krietenstein, Nils; Rice, Edward J.; Ma, Yitian; Wang, Zhong; Rando, Oliver J.; Hadjantonakis, Anna Katerina; Danko, Charles G.

In: Nature Genetics, Vol. 55, 2023, p. 1370-1380.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Barshad, G, Lewis, JJ, Chivu, AG, Abuhashem, A, Krietenstein, N, Rice, EJ, Ma, Y, Wang, Z, Rando, OJ, Hadjantonakis, AK & Danko, CG 2023, 'RNA polymerase II dynamics shape enhancer–promoter interactions', Nature Genetics, vol. 55, pp. 1370-1380. https://doi.org/10.1038/s41588-023-01442-7

APA

Barshad, G., Lewis, J. J., Chivu, A. G., Abuhashem, A., Krietenstein, N., Rice, E. J., Ma, Y., Wang, Z., Rando, O. J., Hadjantonakis, A. K., & Danko, C. G. (2023). RNA polymerase II dynamics shape enhancer–promoter interactions. Nature Genetics, 55, 1370-1380. https://doi.org/10.1038/s41588-023-01442-7

Vancouver

Barshad G, Lewis JJ, Chivu AG, Abuhashem A, Krietenstein N, Rice EJ et al. RNA polymerase II dynamics shape enhancer–promoter interactions. Nature Genetics. 2023;55:1370-1380. https://doi.org/10.1038/s41588-023-01442-7

Author

Barshad, Gilad ; Lewis, James J. ; Chivu, Alexandra G. ; Abuhashem, Abderhman ; Krietenstein, Nils ; Rice, Edward J. ; Ma, Yitian ; Wang, Zhong ; Rando, Oliver J. ; Hadjantonakis, Anna Katerina ; Danko, Charles G. / RNA polymerase II dynamics shape enhancer–promoter interactions. In: Nature Genetics. 2023 ; Vol. 55. pp. 1370-1380.

Bibtex

@article{cd3dee7e1df64e1bab4496cd7fe4a41e,
title = "RNA polymerase II dynamics shape enhancer–promoter interactions",
abstract = "How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer–promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer–promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer–promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer–promoter communication.",
author = "Gilad Barshad and Lewis, {James J.} and Chivu, {Alexandra G.} and Abderhman Abuhashem and Nils Krietenstein and Rice, {Edward J.} and Yitian Ma and Zhong Wang and Rando, {Oliver J.} and Hadjantonakis, {Anna Katerina} and Danko, {Charles G.}",
note = "Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.",
year = "2023",
doi = "10.1038/s41588-023-01442-7",
language = "English",
volume = "55",
pages = "1370--1380",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - RNA polymerase II dynamics shape enhancer–promoter interactions

AU - Barshad, Gilad

AU - Lewis, James J.

AU - Chivu, Alexandra G.

AU - Abuhashem, Abderhman

AU - Krietenstein, Nils

AU - Rice, Edward J.

AU - Ma, Yitian

AU - Wang, Zhong

AU - Rando, Oliver J.

AU - Hadjantonakis, Anna Katerina

AU - Danko, Charles G.

N1 - Publisher Copyright: © 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2023

Y1 - 2023

N2 - How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer–promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer–promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer–promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer–promoter communication.

AB - How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer–promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer–promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer–promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer–promoter communication.

U2 - 10.1038/s41588-023-01442-7

DO - 10.1038/s41588-023-01442-7

M3 - Journal article

C2 - 37430091

AN - SCOPUS:85164344000

VL - 55

SP - 1370

EP - 1380

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

ER -

ID: 360404604