Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus

Registro completo de metadados
MetadadosDescriçãoIdioma
Autor(es): dc.contributorBioinformat & Computat Sci BioCoS-
Autor(es): dc.contributorUniversidade Estadual Paulista (Unesp)-
Autor(es): dc.contributorInt Atom Energy Agcy Collaborating Ctr Anim Genom-
Autor(es): dc.contributorCINECA-
Autor(es): dc.contributorUniv Tuscia-
Autor(es): dc.contributorCNR-
Autor(es): dc.creatorArhondakis, S.-
Autor(es): dc.creatorMilanesi, M. [UNESP]-
Autor(es): dc.creatorCastrignano, T.-
Autor(es): dc.creatorGioiosa, S.-
Autor(es): dc.creatorValentini, A.-
Autor(es): dc.creatorChillemi, G.-
Data de aceite: dc.date.accessioned2022-02-22T00:09:52Z-
Data de disponibilização: dc.date.available2022-02-22T00:09:52Z-
Data de envio: dc.date.issued2020-12-09-
Data de envio: dc.date.issued2020-12-09-
Data de envio: dc.date.issued2020-02-18-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1111/age.12917-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/196585-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/196585-
Descrição: dc.descriptionVertebrate genomes are mosaics of megabase-size DNA segments with a fairly homogeneous base composition, called isochores. They are divided into five families characterized by different guanine-cytosine (GC) levels and linked to several functional and structural properties. The increased availability of fully sequenced genomes allows the investigation of isochores in several species, assessing their level of conservation across vertebrate genomes. In this work, we characterized the isochores in Bos taurus using the ARS-UCD1.2 genome version. The comparison of our results with the well-studied human isochores and those of other mammals revealed a large conservation in isochore families, in number, average GC levels and gene density. Exceptions to the established increase in gene density with the increase in isochores (GC%) were observed for the following gene biotypes: tRNA, small nuclear RNA, small nucleolar RNA and pseudogenes that have their maximum number in H2 and H1 isochores. Subsequently, we assessed the ontology of all gene biotypes looking for functional classes that are statistically over- or under-represented in each isochore. Receptor activity and sensory perception pathways were significantly over-represented in L1 and L2 (GC-poor) isochores. This was also validated for the horse genome. Our analysis of housekeeping genes confirmed a preferential localization in GC-rich isochores, as reported in other species. Finally, we assessed the SNP distribution of a bovine high-density SNP chip across the isochores, finding a higher density in the GC-rich families, reflecting a potential bias in the chip, widely used for genetic selection and biodiversity studies.-
Descrição: dc.descriptionItalian Ministry of Education, University and Research-
Descrição: dc.descriptionDIBAF-Department of University of Tuscia Project 'Landscape 4.0 - food, wellbeing and environment'-
Descrição: dc.descriptionBioinformat & Computat Sci BioCoS, Boniali 11-19, Khania 73134, Greece-
Descrição: dc.descriptionSao Paulo State Univ, Dept Support Prod & Anim Hlth, Sch Vet Med, 16050-680 R Clovis Pestana 793 Dona Amelia, Aracatuba, SP, Brazil-
Descrição: dc.descriptionInt Atom Energy Agcy Collaborating Ctr Anim Genom, 16050-680 R Clovis Pestana 793 Dona Amelia, Aracatuba, SP, Brazil-
Descrição: dc.descriptionCINECA, SCAI Super Comp Applicat & Innovat Dept, Rome, Italy-
Descrição: dc.descriptionUniv Tuscia, Dept Innovat Biol Agrofood & Forest Syst, DIBAF, Via S Camillo de Lellis Snc, I-01100 Viterbo, Italy-
Descrição: dc.descriptionCNR, IBIOM, Inst Biomembranes Bioenerget & Mol Biotechnol, Bari, Italy-
Descrição: dc.descriptionSao Paulo State Univ, Dept Support Prod & Anim Hlth, Sch Vet Med, 16050-680 R Clovis Pestana 793 Dona Amelia, Aracatuba, SP, Brazil-
Formato: dc.format358-368-
Idioma: dc.languageen-
Publicador: dc.publisherWiley-Blackwell-
Relação: dc.relationAnimal Genetics-
???dc.source???: dc.sourceWeb of Science-
Palavras-chave: dc.subjectbovine DNA chip-
Palavras-chave: dc.subjectcow-
Palavras-chave: dc.subjectgenome composition-
Palavras-chave: dc.subjectisochores-
Palavras-chave: dc.subjectolfactory receptor-
Título: dc.titleEvidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

Não existem arquivos associados a este item.