Promoter shape varies across populations and affects promoter evolution and expression noise

Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution...

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Autores principales: Schor, I.E., Degner, J.F., Harnett, D., Cannavò, E., Casale, F.P., Shim, H., Garfield, D.A., Birney, E., Stephens, M., Stegle, O., Furlong, E.E.M.
Formato: JOUR
Materias:
Article
cytometry
Drosophila
genetic variation
noise
nonhuman
priority journal
promoter region
single cell analysis
animal
evolution
genetic transcription
genetics
physiology
transcription initiation site
Animals
Biological Evolution
Genetic Variation
Noise
Promoter Regions, Genetic
Transcription Initiation Site
Transcription, Genetic
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_10614036_v49_n4_p550_Schor
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id todo:paper_10614036_v49_n4_p550_Schor
record_format dspace
spelling todo:paper_10614036_v49_n4_p550_Schor2023-10-03T16:01:08Z Promoter shape varies across populations and affects promoter evolution and expression noise Schor, I.E. Degner, J.F. Harnett, D. Cannavò, E. Casale, F.P. Shim, H. Garfield, D.A. Birney, E. Stephens, M. Stegle, O. Furlong, E.E.M. Article cytometry Drosophila genetic variation noise nonhuman priority journal promoter region single cell analysis animal evolution genetic transcription genetics noise physiology promoter region transcription initiation site Animals Biological Evolution Drosophila Genetic Variation Noise Promoter Regions, Genetic Transcription Initiation Site Transcription, Genetic Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. Here we used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). Our results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_10614036_v49_n4_p550_Schor
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic Article
cytometry
Drosophila
genetic variation
noise
nonhuman
priority journal
promoter region
single cell analysis
animal
evolution
genetic transcription
genetics
noise
physiology
promoter region
transcription initiation site
Animals
Biological Evolution
Drosophila
Genetic Variation
Noise
Promoter Regions, Genetic
Transcription Initiation Site
Transcription, Genetic
spellingShingle Article
cytometry
Drosophila
genetic variation
noise
nonhuman
priority journal
promoter region
single cell analysis
animal
evolution
genetic transcription
genetics
noise
physiology
promoter region
transcription initiation site
Animals
Biological Evolution
Drosophila
Genetic Variation
Noise
Promoter Regions, Genetic
Transcription Initiation Site
Transcription, Genetic
Schor, I.E.
Degner, J.F.
Harnett, D.
Cannavò, E.
Casale, F.P.
Shim, H.
Garfield, D.A.
Birney, E.
Stephens, M.
Stegle, O.
Furlong, E.E.M.
Promoter shape varies across populations and affects promoter evolution and expression noise
topic_facet Article
cytometry
Drosophila
genetic variation
noise
nonhuman
priority journal
promoter region
single cell analysis
animal
evolution
genetic transcription
genetics
noise
physiology
promoter region
transcription initiation site
Animals
Biological Evolution
Drosophila
Genetic Variation
Noise
Promoter Regions, Genetic
Transcription Initiation Site
Transcription, Genetic
description Animal promoters initiate transcription either at precise positions (narrow promoters) or dispersed regions (broad promoters), a distinction referred to as promoter shape. Although highly conserved, the functional properties of promoters with different shapes and the genetic basis of their evolution remain unclear. Here we used natural genetic variation across a panel of 81 Drosophila lines to measure changes in transcriptional start site (TSS) usage, identifying thousands of genetic variants affecting transcript levels (strength) or the distribution of TSSs within a promoter (shape). Our results identify promoter shape as a molecular trait that can evolve independently of promoter strength. Broad promoters typically harbor shape-associated variants, with signatures of adaptive selection. Single-cell measurements demonstrate that variants modulating promoter shape often increase expression noise, whereas heteroallelic interactions with other promoter variants alleviate these effects. These results uncover new functional properties of natural promoters and suggest the minimization of expression noise as an important factor in promoter evolution.
format JOUR
author Schor, I.E.
Degner, J.F.
Harnett, D.
Cannavò, E.
Casale, F.P.
Shim, H.
Garfield, D.A.
Birney, E.
Stephens, M.
Stegle, O.
Furlong, E.E.M.
author_facet Schor, I.E.
Degner, J.F.
Harnett, D.
Cannavò, E.
Casale, F.P.
Shim, H.
Garfield, D.A.
Birney, E.
Stephens, M.
Stegle, O.
Furlong, E.E.M.
author_sort Schor, I.E.
title Promoter shape varies across populations and affects promoter evolution and expression noise
title_short Promoter shape varies across populations and affects promoter evolution and expression noise
title_full Promoter shape varies across populations and affects promoter evolution and expression noise
title_fullStr Promoter shape varies across populations and affects promoter evolution and expression noise
title_full_unstemmed Promoter shape varies across populations and affects promoter evolution and expression noise
title_sort promoter shape varies across populations and affects promoter evolution and expression noise
url http://hdl.handle.net/20.500.12110/paper_10614036_v49_n4_p550_Schor
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