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A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo

BACKGROUND: Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identifie...

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Autores principales: Yoshihara, Minako, Sato, Tetsuya, Saito, Daisuke, Ohara, Osamu, Kuramoto, Takashi, Suyama, Mikita
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372274/
https://www.ncbi.nlm.nih.gov/pubmed/28356074
http://dx.doi.org/10.1186/s12863-017-0497-3
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author Yoshihara, Minako
Sato, Tetsuya
Saito, Daisuke
Ohara, Osamu
Kuramoto, Takashi
Suyama, Mikita
author_facet Yoshihara, Minako
Sato, Tetsuya
Saito, Daisuke
Ohara, Osamu
Kuramoto, Takashi
Suyama, Mikita
author_sort Yoshihara, Minako
collection PubMed
description BACKGROUND: Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region. RESULTS: To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated. Our target capture method has a unique feature, i.e., it covers not only exonic regions but also conserved non-coding sequences (CNSs) among vertebrates; therefore, it has the potential to detect regulatory mutations. We identified a deletion of approximately 50 kb in length approximately 50 kb upstream of Ednrb. A comparative analysis with the epigenomic data in the corresponding region in humans and mice showed that one of the CNSs might be an enhancer. Further comparison with Hi-C data, which provide information about chromosome conformation, indicated that the putative enhancer is spatially close to the promoter of Ednrb, suggesting that it acts as an enhancer of Ednrb. CONCLUSIONS: These in silico data analyses strongly suggest that the identified deletion in the intergenic region upstream of Ednrb, which might contain a melanocyte-specific enhancer, is the mutation causative of the head spot phenotype in the KFRS4/Kyo rat strain. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-017-0497-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-53722742017-03-31 A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo Yoshihara, Minako Sato, Tetsuya Saito, Daisuke Ohara, Osamu Kuramoto, Takashi Suyama, Mikita BMC Genet Research Article BACKGROUND: Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region. RESULTS: To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated. Our target capture method has a unique feature, i.e., it covers not only exonic regions but also conserved non-coding sequences (CNSs) among vertebrates; therefore, it has the potential to detect regulatory mutations. We identified a deletion of approximately 50 kb in length approximately 50 kb upstream of Ednrb. A comparative analysis with the epigenomic data in the corresponding region in humans and mice showed that one of the CNSs might be an enhancer. Further comparison with Hi-C data, which provide information about chromosome conformation, indicated that the putative enhancer is spatially close to the promoter of Ednrb, suggesting that it acts as an enhancer of Ednrb. CONCLUSIONS: These in silico data analyses strongly suggest that the identified deletion in the intergenic region upstream of Ednrb, which might contain a melanocyte-specific enhancer, is the mutation causative of the head spot phenotype in the KFRS4/Kyo rat strain. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-017-0497-3) contains supplementary material, which is available to authorized users. BioMed Central 2017-03-29 /pmc/articles/PMC5372274/ /pubmed/28356074 http://dx.doi.org/10.1186/s12863-017-0497-3 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Yoshihara, Minako
Sato, Tetsuya
Saito, Daisuke
Ohara, Osamu
Kuramoto, Takashi
Suyama, Mikita
A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo
title A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo
title_full A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo
title_fullStr A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo
title_full_unstemmed A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo
title_short A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo
title_sort deletion in the intergenic region upstream of ednrb causes head spot in the rat strain kfrs4/kyo
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5372274/
https://www.ncbi.nlm.nih.gov/pubmed/28356074
http://dx.doi.org/10.1186/s12863-017-0497-3
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