Drosophila 3' UTRs are more complex than protein-coding sequences.

The 3' UTRs of eukaryotic genes participate in a variety of post-transcriptional (and some transcriptional) regulatory interactions. Some of these interactions are well characterised, but an undetermined number remain to be discovered. While some regulatory sequences in 3' UTRs may be cons...

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Autores principales:	Manjula Algama, Christopher Oldmeadow, Edward Tasker, Kerrie Mengersen, Jonathan M Keith
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1918fd60797c4b869747077fa805b7d5
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spelling	oai:doaj.org-article:1918fd60797c4b869747077fa805b7d52021-11-18T08:19:35ZDrosophila 3' UTRs are more complex than protein-coding sequences.1932-620310.1371/journal.pone.0097336https://doaj.org/article/1918fd60797c4b869747077fa805b7d52014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24824035/?tool=EBIhttps://doaj.org/toc/1932-6203The 3' UTRs of eukaryotic genes participate in a variety of post-transcriptional (and some transcriptional) regulatory interactions. Some of these interactions are well characterised, but an undetermined number remain to be discovered. While some regulatory sequences in 3' UTRs may be conserved over long evolutionary time scales, others may have only ephemeral functional significance as regulatory profiles respond to changing selective pressures. Here we propose a sensitive segmentation methodology for investigating patterns of composition and conservation in 3' UTRs based on comparison of closely related species. We describe encodings of pairwise and three-way alignments integrating information about conservation, GC content and transition/transversion ratios and apply the method to three closely related Drosophila species: D. melanogaster, D. simulans and D. yakuba. Incorporating multiple data types greatly increased the number of segment classes identified compared to similar methods based on conservation or GC content alone. We propose that the number of segments and number of types of segment identified by the method can be used as proxies for functional complexity. Our main finding is that the number of segments and segment classes identified in 3' UTRs is greater than in the same length of protein-coding sequence, suggesting greater functional complexity in 3' UTRs. There is thus a need for sustained and extensive efforts by bioinformaticians to delineate functional elements in this important genomic fraction. C code, data and results are available upon request.Manjula AlgamaChristopher OldmeadowEdward TaskerKerrie MengersenJonathan M KeithPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 5, p e97336 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Manjula Algama Christopher Oldmeadow Edward Tasker Kerrie Mengersen Jonathan M Keith Drosophila 3' UTRs are more complex than protein-coding sequences.
description	The 3' UTRs of eukaryotic genes participate in a variety of post-transcriptional (and some transcriptional) regulatory interactions. Some of these interactions are well characterised, but an undetermined number remain to be discovered. While some regulatory sequences in 3' UTRs may be conserved over long evolutionary time scales, others may have only ephemeral functional significance as regulatory profiles respond to changing selective pressures. Here we propose a sensitive segmentation methodology for investigating patterns of composition and conservation in 3' UTRs based on comparison of closely related species. We describe encodings of pairwise and three-way alignments integrating information about conservation, GC content and transition/transversion ratios and apply the method to three closely related Drosophila species: D. melanogaster, D. simulans and D. yakuba. Incorporating multiple data types greatly increased the number of segment classes identified compared to similar methods based on conservation or GC content alone. We propose that the number of segments and number of types of segment identified by the method can be used as proxies for functional complexity. Our main finding is that the number of segments and segment classes identified in 3' UTRs is greater than in the same length of protein-coding sequence, suggesting greater functional complexity in 3' UTRs. There is thus a need for sustained and extensive efforts by bioinformaticians to delineate functional elements in this important genomic fraction. C code, data and results are available upon request.
format	article
author	Manjula Algama Christopher Oldmeadow Edward Tasker Kerrie Mengersen Jonathan M Keith
author_facet	Manjula Algama Christopher Oldmeadow Edward Tasker Kerrie Mengersen Jonathan M Keith
author_sort	Manjula Algama
title	Drosophila 3' UTRs are more complex than protein-coding sequences.
title_short	Drosophila 3' UTRs are more complex than protein-coding sequences.
title_full	Drosophila 3' UTRs are more complex than protein-coding sequences.
title_fullStr	Drosophila 3' UTRs are more complex than protein-coding sequences.
title_full_unstemmed	Drosophila 3' UTRs are more complex than protein-coding sequences.
title_sort	drosophila 3' utrs are more complex than protein-coding sequences.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/1918fd60797c4b869747077fa805b7d5
work_keys_str_mv	AT manjulaalgama drosophila3utrsaremorecomplexthanproteincodingsequences AT christopheroldmeadow drosophila3utrsaremorecomplexthanproteincodingsequences AT edwardtasker drosophila3utrsaremorecomplexthanproteincodingsequences AT kerriemengersen drosophila3utrsaremorecomplexthanproteincodingsequences AT jonathanmkeith drosophila3utrsaremorecomplexthanproteincodingsequences
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Drosophila 3' UTRs are more complex than protein-coding sequences.

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