Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.

Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a...

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Autores principales:	José Luis Royo, Carmen Hidalgo, Yolanda Roncero, María Angeles Seda, Altuna Akalin, Boris Lenhard, Fernando Casares, José Luis Gómez-Skarmeta
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cd2f980e59994b39a5d24e3a03e53520
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spelling	oai:doaj.org-article:cd2f980e59994b39a5d24e3a03e535202021-11-04T06:08:40ZDissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.1932-620310.1371/journal.pone.0024824https://doaj.org/article/cd2f980e59994b39a5d24e3a03e535202011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21935474/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions.José Luis RoyoCarmen HidalgoYolanda RonceroMaría Angeles SedaAltuna AkalinBoris LenhardFernando CasaresJosé Luis Gómez-SkarmetaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e24824 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q José Luis Royo Carmen Hidalgo Yolanda Roncero María Angeles Seda Altuna Akalin Boris Lenhard Fernando Casares José Luis Gómez-Skarmeta Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
description	Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions.
format	article
author	José Luis Royo Carmen Hidalgo Yolanda Roncero María Angeles Seda Altuna Akalin Boris Lenhard Fernando Casares José Luis Gómez-Skarmeta
author_facet	José Luis Royo Carmen Hidalgo Yolanda Roncero María Angeles Seda Altuna Akalin Boris Lenhard Fernando Casares José Luis Gómez-Skarmeta
author_sort	José Luis Royo
title	Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
title_short	Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
title_full	Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
title_fullStr	Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
title_full_unstemmed	Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
title_sort	dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/cd2f980e59994b39a5d24e3a03e53520
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Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions.

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