Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals
Genetic variation in cis-regulatory elements is thought to be a major driving force in morphological and physiological changes. However, identifying transcription factor binding events that code for complex traits remains a challenge, motivating novel means of detecting putatively important binding...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182171/ http://www.ncbi.nlm.nih.gov/pubmed/30137416 https://doi.org/10.1093/nar/gky741 |
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ftpubmed:oai:pubmedcentral.nih.gov:6182171 2023-05-15T18:43:22+02:00 Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals Berger, Mark J Wenger, Aaron M Guturu, Harendra Bejerano, Gill 2018-10-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182171/ http://www.ncbi.nlm.nih.gov/pubmed/30137416 https://doi.org/10.1093/nar/gky741 en eng Oxford University Press http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182171/ http://www.ncbi.nlm.nih.gov/pubmed/30137416 http://dx.doi.org/10.1093/nar/gky741 © 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. CC-BY Computational Biology Text 2018 ftpubmed https://doi.org/10.1093/nar/gky741 2018-10-21T00:23:51Z Genetic variation in cis-regulatory elements is thought to be a major driving force in morphological and physiological changes. However, identifying transcription factor binding events that code for complex traits remains a challenge, motivating novel means of detecting putatively important binding events. Using a curated set of 1154 high-quality transcription factor motifs, we demonstrate that independently eroded binding sites are enriched for independently lost traits in three distinct pairs of placental mammals. We show that these independently eroded events pinpoint the loss of hindlimbs in dolphin and manatee, degradation of vision in naked mole-rat and star-nosed mole, and the loss of external testes in white rhinoceros and Weddell seal. We additionally show that our method may also be utilized with more than two species. Our study exhibits a novel methodology to detect cis-regulatory mutations which help explain a portion of the molecular mechanism underlying complex trait formation and loss. Text Weddell Seal PubMed Central (PMC) Weddell Nucleic Acids Research 46 18 9299 9308 |
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Computational Biology |
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Computational Biology Berger, Mark J Wenger, Aaron M Guturu, Harendra Bejerano, Gill Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals |
topic_facet |
Computational Biology |
description |
Genetic variation in cis-regulatory elements is thought to be a major driving force in morphological and physiological changes. However, identifying transcription factor binding events that code for complex traits remains a challenge, motivating novel means of detecting putatively important binding events. Using a curated set of 1154 high-quality transcription factor motifs, we demonstrate that independently eroded binding sites are enriched for independently lost traits in three distinct pairs of placental mammals. We show that these independently eroded events pinpoint the loss of hindlimbs in dolphin and manatee, degradation of vision in naked mole-rat and star-nosed mole, and the loss of external testes in white rhinoceros and Weddell seal. We additionally show that our method may also be utilized with more than two species. Our study exhibits a novel methodology to detect cis-regulatory mutations which help explain a portion of the molecular mechanism underlying complex trait formation and loss. |
format |
Text |
author |
Berger, Mark J Wenger, Aaron M Guturu, Harendra Bejerano, Gill |
author_facet |
Berger, Mark J Wenger, Aaron M Guturu, Harendra Bejerano, Gill |
author_sort |
Berger, Mark J |
title |
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals |
title_short |
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals |
title_full |
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals |
title_fullStr |
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals |
title_full_unstemmed |
Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals |
title_sort |
independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals |
publisher |
Oxford University Press |
publishDate |
2018 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182171/ http://www.ncbi.nlm.nih.gov/pubmed/30137416 https://doi.org/10.1093/nar/gky741 |
geographic |
Weddell |
geographic_facet |
Weddell |
genre |
Weddell Seal |
genre_facet |
Weddell Seal |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182171/ http://www.ncbi.nlm.nih.gov/pubmed/30137416 http://dx.doi.org/10.1093/nar/gky741 |
op_rights |
© 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. |
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CC-BY |
op_doi |
https://doi.org/10.1093/nar/gky741 |
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Nucleic Acids Research |
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46 |
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18 |
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9299 |
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9308 |
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1766233748459749376 |