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Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities
Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its en...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009668/ https://www.ncbi.nlm.nih.gov/pubmed/29659982 http://dx.doi.org/10.1093/nar/gky244 |
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author | Rennie, Sarah Dalby, Maria Lloret-Llinares, Marta Bakoulis, Stylianos Dalager Vaagensø, Christian Heick Jensen, Torben Andersson, Robin |
author_facet | Rennie, Sarah Dalby, Maria Lloret-Llinares, Marta Bakoulis, Stylianos Dalager Vaagensø, Christian Heick Jensen, Torben Andersson, Robin |
author_sort | Rennie, Sarah |
collection | PubMed |
description | Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The seemingly separable layer of regulation by gene promoters with housekeeping enhancer potential is also indicated by chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements. |
format | Online Article Text |
id | pubmed-6009668 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-60096682018-06-25 Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities Rennie, Sarah Dalby, Maria Lloret-Llinares, Marta Bakoulis, Stylianos Dalager Vaagensø, Christian Heick Jensen, Torben Andersson, Robin Nucleic Acids Res Gene regulation, Chromatin and Epigenetics Mammalian gene promoters and enhancers share many properties. They are composed of a unified promoter architecture of divergent transcripton initiation and gene promoters may exhibit enhancer function. However, it is currently unclear how expression strength of a regulatory element relates to its enhancer strength and if the unifying architecture is conserved across Metazoa. Here we investigate the transcription initiation landscape and its associated RNA decay in Drosophila melanogaster. We find that the majority of active gene-distal enhancers and a considerable fraction of gene promoters are divergently transcribed. We observe quantitative relationships between enhancer potential, expression level and core promoter strength, providing an explanation for indirectly related histone modifications that are reflecting expression levels. Lowly abundant unstable RNAs initiated from weak core promoters are key characteristics of gene-distal developmental enhancers, while the housekeeping enhancer strengths of gene promoters reflect their expression strengths. The seemingly separable layer of regulation by gene promoters with housekeeping enhancer potential is also indicated by chromatin interaction data. Our results suggest a unified promoter architecture of many D. melanogaster regulatory elements, that is universal across Metazoa, whose regulatory functions seem to be related to their core promoter elements. Oxford University Press 2018-06-20 2018-04-06 /pmc/articles/PMC6009668/ /pubmed/29659982 http://dx.doi.org/10.1093/nar/gky244 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Gene regulation, Chromatin and Epigenetics Rennie, Sarah Dalby, Maria Lloret-Llinares, Marta Bakoulis, Stylianos Dalager Vaagensø, Christian Heick Jensen, Torben Andersson, Robin Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities |
title | Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities |
title_full | Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities |
title_fullStr | Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities |
title_full_unstemmed | Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities |
title_short | Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities |
title_sort | transcription start site analysis reveals widespread divergent transcription in d. melanogaster and core promoter-encoded enhancer activities |
topic | Gene regulation, Chromatin and Epigenetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6009668/ https://www.ncbi.nlm.nih.gov/pubmed/29659982 http://dx.doi.org/10.1093/nar/gky244 |
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