Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network
Abstract Background Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of th...
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crspringernat:10.1186/1752-0509-5-58 2023-05-15T17:51:43+02:00 Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network Ryu, Taewoo Mavromatis, Charalampos Harris Bayer, Till Voolstra, Christian R Ravasi, Timothy 2011 http://dx.doi.org/10.1186/1752-0509-5-58 https://link.springer.com/content/pdf/10.1186/1752-0509-5-58.pdf en eng Springer Science and Business Media LLC BMC Systems Biology volume 5, issue 1 ISSN 1752-0509 Applied Mathematics Computer Science Applications Molecular Biology Modeling and Simulation Structural Biology journal-article 2011 crspringernat https://doi.org/10.1186/1752-0509-5-58 2022-01-04T15:37:01Z Abstract Background Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of the paucity of genome-wide studies on corals and the application of systems approaches that incorporate the latter. Like in any other organism, the response of corals to stress is tightly controlled by the coordinated interplay of many transcription factors. Results Here, we develop and apply a new system-wide approach in order to infer combinatorial transcription factor networks of the reef-building coral Acropora millepora . By integrating sequencing-derived transcriptome measurements, a network of physically interacting transcription factors, and phylogenetic network footprinting we were able to infer such a network. Analysis of the network across a phylogenetically broad sample of five species, including human, reveals that despite the apparent simplicity of corals, their transcription factors repertoire and interaction networks seem to be largely conserved. In addition, we were able to identify interactions among transcription factors that appear to be species-specific lending strength to the novel concept of "Taxonomically Restricted Interactions". Conclusions This study provides the first look at transcription factor networks in corals. We identified a transcription factor repertoire encoded by the coral genome and found consistencies of the domain architectures of transcription factors and conserved regulatory subnetworks across eumetazoan species, providing insight into how regulatory networks have evolved. Article in Journal/Newspaper Ocean acidification Springer Nature (via Crossref) BMC Systems Biology 5 1 |
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Springer Nature (via Crossref) |
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English |
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Applied Mathematics Computer Science Applications Molecular Biology Modeling and Simulation Structural Biology |
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Applied Mathematics Computer Science Applications Molecular Biology Modeling and Simulation Structural Biology Ryu, Taewoo Mavromatis, Charalampos Harris Bayer, Till Voolstra, Christian R Ravasi, Timothy Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network |
topic_facet |
Applied Mathematics Computer Science Applications Molecular Biology Modeling and Simulation Structural Biology |
description |
Abstract Background Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of the paucity of genome-wide studies on corals and the application of systems approaches that incorporate the latter. Like in any other organism, the response of corals to stress is tightly controlled by the coordinated interplay of many transcription factors. Results Here, we develop and apply a new system-wide approach in order to infer combinatorial transcription factor networks of the reef-building coral Acropora millepora . By integrating sequencing-derived transcriptome measurements, a network of physically interacting transcription factors, and phylogenetic network footprinting we were able to infer such a network. Analysis of the network across a phylogenetically broad sample of five species, including human, reveals that despite the apparent simplicity of corals, their transcription factors repertoire and interaction networks seem to be largely conserved. In addition, we were able to identify interactions among transcription factors that appear to be species-specific lending strength to the novel concept of "Taxonomically Restricted Interactions". Conclusions This study provides the first look at transcription factor networks in corals. We identified a transcription factor repertoire encoded by the coral genome and found consistencies of the domain architectures of transcription factors and conserved regulatory subnetworks across eumetazoan species, providing insight into how regulatory networks have evolved. |
format |
Article in Journal/Newspaper |
author |
Ryu, Taewoo Mavromatis, Charalampos Harris Bayer, Till Voolstra, Christian R Ravasi, Timothy |
author_facet |
Ryu, Taewoo Mavromatis, Charalampos Harris Bayer, Till Voolstra, Christian R Ravasi, Timothy |
author_sort |
Ryu, Taewoo |
title |
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network |
title_short |
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network |
title_full |
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network |
title_fullStr |
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network |
title_full_unstemmed |
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network |
title_sort |
unexpected complexity of the reef-building coral acropora millepora transcription factor network |
publisher |
Springer Science and Business Media LLC |
publishDate |
2011 |
url |
http://dx.doi.org/10.1186/1752-0509-5-58 https://link.springer.com/content/pdf/10.1186/1752-0509-5-58.pdf |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_source |
BMC Systems Biology volume 5, issue 1 ISSN 1752-0509 |
op_doi |
https://doi.org/10.1186/1752-0509-5-58 |
container_title |
BMC Systems Biology |
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5 |
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1 |
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1766158940613115904 |