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Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes
Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, as opposed to conventional binding sites of transcription factors, few methods have been proposed to formally and automatically characterize them. We pres...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081344/ https://www.ncbi.nlm.nih.gov/pubmed/33861755 http://dx.doi.org/10.1371/journal.pcbi.1008909 |
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author | Menichelli, Christophe Guitard, Vincent Martins, Rafael M. Lèbre, Sophie Lopez-Rubio, Jose-Juan Lecellier, Charles-Henri Bréhélin, Laurent |
author_facet | Menichelli, Christophe Guitard, Vincent Martins, Rafael M. Lèbre, Sophie Lopez-Rubio, Jose-Juan Lecellier, Charles-Henri Bréhélin, Laurent |
author_sort | Menichelli, Christophe |
collection | PubMed |
description | Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, as opposed to conventional binding sites of transcription factors, few methods have been proposed to formally and automatically characterize them. We present here a computational approach named DExTER (Domain Exploration To Explain gene Regulation) dedicated to the identification of candidate LREs (cLREs) and apply it to the analysis of the genomes of P. falciparum and other eukaryotes. Our analyses show that all tested genomes contain several cLREs that are somewhat conserved along evolution, and that gene expression can be predicted with surprising accuracy on the basis of these long regions only. Regulation by cLREs exhibits very different behaviours depending on species and conditions. In P. falciparum and other Apicomplexan organisms as well as in Dictyostelium discoideum, the process appears highly dynamic, with different cLREs involved at different phases of the life cycle. For multicellular organisms, the same cLREs are involved in all tissues, but a dynamic behavior is observed along embryonic development stages. In P. falciparum, whose genome is known to be strongly depleted of transcription factors, cLREs are predictive of expression with an accuracy above 70%, and our analyses show that they are associated with both transcriptional and post-transcriptional regulation signals. Moreover, we assessed the biological relevance of one LRE discovered by DExTER in P. falciparum using an in vivo reporter assay. The source code (python) of DExTER is available at https://gite.lirmm.fr/menichelli/DExTER. |
format | Online Article Text |
id | pubmed-8081344 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-80813442021-05-06 Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes Menichelli, Christophe Guitard, Vincent Martins, Rafael M. Lèbre, Sophie Lopez-Rubio, Jose-Juan Lecellier, Charles-Henri Bréhélin, Laurent PLoS Comput Biol Research Article Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, as opposed to conventional binding sites of transcription factors, few methods have been proposed to formally and automatically characterize them. We present here a computational approach named DExTER (Domain Exploration To Explain gene Regulation) dedicated to the identification of candidate LREs (cLREs) and apply it to the analysis of the genomes of P. falciparum and other eukaryotes. Our analyses show that all tested genomes contain several cLREs that are somewhat conserved along evolution, and that gene expression can be predicted with surprising accuracy on the basis of these long regions only. Regulation by cLREs exhibits very different behaviours depending on species and conditions. In P. falciparum and other Apicomplexan organisms as well as in Dictyostelium discoideum, the process appears highly dynamic, with different cLREs involved at different phases of the life cycle. For multicellular organisms, the same cLREs are involved in all tissues, but a dynamic behavior is observed along embryonic development stages. In P. falciparum, whose genome is known to be strongly depleted of transcription factors, cLREs are predictive of expression with an accuracy above 70%, and our analyses show that they are associated with both transcriptional and post-transcriptional regulation signals. Moreover, we assessed the biological relevance of one LRE discovered by DExTER in P. falciparum using an in vivo reporter assay. The source code (python) of DExTER is available at https://gite.lirmm.fr/menichelli/DExTER. Public Library of Science 2021-04-16 /pmc/articles/PMC8081344/ /pubmed/33861755 http://dx.doi.org/10.1371/journal.pcbi.1008909 Text en © 2021 Menichelli et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Menichelli, Christophe Guitard, Vincent Martins, Rafael M. Lèbre, Sophie Lopez-Rubio, Jose-Juan Lecellier, Charles-Henri Bréhélin, Laurent Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes |
title | Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes |
title_full | Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes |
title_fullStr | Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes |
title_full_unstemmed | Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes |
title_short | Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes |
title_sort | identification of long regulatory elements in the genome of plasmodium falciparum and other eukaryotes |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081344/ https://www.ncbi.nlm.nih.gov/pubmed/33861755 http://dx.doi.org/10.1371/journal.pcbi.1008909 |
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