Modelling the evolution of transcription factor binding preferences in complex eukaryotes

Abstract Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This “redundancy” of binding defines a way of organizing TFs in “motif...

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Autores principales:	Antonio Rosanova, Alberto Colliva, Matteo Osella, Michele Caselle
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/41a22669d12d43a38f9d2da0e52d2598
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spelling	oai:doaj.org-article:41a22669d12d43a38f9d2da0e52d25982021-12-02T15:05:30ZModelling the evolution of transcription factor binding preferences in complex eukaryotes10.1038/s41598-017-07761-02045-2322https://doaj.org/article/41a22669d12d43a38f9d2da0e52d25982017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-07761-0https://doaj.org/toc/2045-2322Abstract Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This “redundancy” of binding defines a way of organizing TFs in “motif families” by grouping TFs with similar binding preferences. Since these ultimately define the TF target genes, the motif family organization entails information about the structure of transcriptional regulation as it has been shaped by evolution. Focusing on the human TF repertoire, we show that a one-parameter evolutionary model of the Birth-Death-Innovation type can explain the TF empirical repartition in motif families, and allows to highlight the relevant evolutionary forces at the origin of this organization. Moreover, the model allows to pinpoint few deviations from the neutral scenario it assumes: three over-expanded families (including HOX and FOX genes), a set of “singleton” TFs for which duplication seems to be selected against, and a higher-than-average rate of diversification of the binding preferences of TFs with a Zinc Finger DNA binding domain. Finally, a comparison of the TF motif family organization in different eukaryotic species suggests an increase of redundancy of binding with organism complexity.Antonio RosanovaAlberto CollivaMatteo OsellaMichele CaselleNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Antonio Rosanova Alberto Colliva Matteo Osella Michele Caselle Modelling the evolution of transcription factor binding preferences in complex eukaryotes
description	Abstract Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This “redundancy” of binding defines a way of organizing TFs in “motif families” by grouping TFs with similar binding preferences. Since these ultimately define the TF target genes, the motif family organization entails information about the structure of transcriptional regulation as it has been shaped by evolution. Focusing on the human TF repertoire, we show that a one-parameter evolutionary model of the Birth-Death-Innovation type can explain the TF empirical repartition in motif families, and allows to highlight the relevant evolutionary forces at the origin of this organization. Moreover, the model allows to pinpoint few deviations from the neutral scenario it assumes: three over-expanded families (including HOX and FOX genes), a set of “singleton” TFs for which duplication seems to be selected against, and a higher-than-average rate of diversification of the binding preferences of TFs with a Zinc Finger DNA binding domain. Finally, a comparison of the TF motif family organization in different eukaryotic species suggests an increase of redundancy of binding with organism complexity.
format	article
author	Antonio Rosanova Alberto Colliva Matteo Osella Michele Caselle
author_facet	Antonio Rosanova Alberto Colliva Matteo Osella Michele Caselle
author_sort	Antonio Rosanova
title	Modelling the evolution of transcription factor binding preferences in complex eukaryotes
title_short	Modelling the evolution of transcription factor binding preferences in complex eukaryotes
title_full	Modelling the evolution of transcription factor binding preferences in complex eukaryotes
title_fullStr	Modelling the evolution of transcription factor binding preferences in complex eukaryotes
title_full_unstemmed	Modelling the evolution of transcription factor binding preferences in complex eukaryotes
title_sort	modelling the evolution of transcription factor binding preferences in complex eukaryotes
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/41a22669d12d43a38f9d2da0e52d2598
work_keys_str_mv	AT antoniorosanova modellingtheevolutionoftranscriptionfactorbindingpreferencesincomplexeukaryotes AT albertocolliva modellingtheevolutionoftranscriptionfactorbindingpreferencesincomplexeukaryotes AT matteoosella modellingtheevolutionoftranscriptionfactorbindingpreferencesincomplexeukaryotes AT michelecaselle modellingtheevolutionoftranscriptionfactorbindingpreferencesincomplexeukaryotes
_version_	1718388824120229888

Modelling the evolution of transcription factor binding preferences in complex eukaryotes

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