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Biblioteca(s): |
Embrapa Gado de Leite. |
Data corrente: |
06/02/2017 |
Data da última atualização: |
30/01/2023 |
Tipo da produção científica: |
Artigo em Periódico Indexado |
Autoria: |
CHEN, Z.; HAGEN, D. E.; WANG, J.; ELSIK, C. G.; JI, T.; SIQUEIRA, L. G. B.; HANSEN, P. J.; RIVERA, R. M. |
Afiliação: |
Zhiyuan Chen, University of Missouri, Columbia, MO, USA; Darren E. Hagen, University of Missouri, Columbia, MO, USA; Juanbin Wang, University of Missouri, Columbia, MO, USA; Christine G. Elsik, University of Missouri, Columbia, MO, USA; Tieming Ji, University of Missouri, Columbia, MO, USA; LUIZ GUSTAVO BRUNO SIQUEIRA, CNPGL; Peter J. Hansen, University of Florida, Gainesville, FL, USA; Rocio M. Rivera, University of Missouri, Columbia, MO. |
Título: |
Global assessment of imprinted gene expression in the bovine conceptus by next generation sequencing. |
Ano de publicação: |
2016 |
Fonte/Imprenta: |
Epigenetics, v. 11, n. 7, p. 501-516, 2016. |
Idioma: |
Português |
Conteúdo: |
Abstract Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ∼105 Bos taurus indicus × Bos taurus taurus F1 conceptuses using RNA sequencing. To accomplish this, we developed a bioinformatics pipeline to identify parent-specific single nucleotide polymorphism alleles after filtering adenosine to inosine (A-to-I) RNA editing sites. We identified 53 genes subject to monoallelic expression. Twenty three are genes known to be imprinted in the cow and an additional 7 have previously been characterized as imprinted in human and/or mouse that have not been reported as imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinted clusters, whereas the other 13 genes are distributed throughout the bovine genome and are not close to any known imprinted clusters. To exclude potential cis-eQTL effects on allele expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus × Bos taurus taurus conceptuses and identified 8 novel bovine imprinted genes. Further, we identified 671 candidate A-to-I RNA editing sites and describe random X-inactivation in day 15 bovine extraembryonic membranes. Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effects. MenosAbstract Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ∼105 Bos taurus indicus × Bos taurus taurus F1 conceptuses using RNA sequencing. To accomplish this, we developed a bioinformatics pipeline to identify parent-specific single nucleotide polymorphism alleles after filtering adenosine to inosine (A-to-I) RNA editing sites. We identified 53 genes subject to monoallelic expression. Twenty three are genes known to be imprinted in the cow and an additional 7 have previously been characterized as imprinted in human and/or mouse that have not been reported as imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinted clusters, whereas the other 13 genes are distributed throughout the bovine genome and are not close to any known imprinted clusters. To exclude potential cis-eQTL effects on allele expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus × Bos taurus taurus conceptuses and identified 8 novel bovine imprinted genes. Further, we identified 671 candidate A-to-I RNA edit... Mostrar Tudo |
Palavras-Chave: |
A-to-I RNA editing; Allele-specific gene expression; Next generation sequencing; X chromosome inactivation. |
Thesaurus Nal: |
genomic imprinting. |
Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/154835/1/Cnpgl-2016-Epigenetics-Global.pdf
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Marc: |
LEADER 02519naa a2200265 a 4500 001 2062831 005 2023-01-30 008 2016 bl uuuu u00u1 u #d 100 1 $aCHEN, Z. 245 $aGlobal assessment of imprinted gene expression in the bovine conceptus by next generation sequencing.$h[electronic resource] 260 $c2016 520 $aAbstract Genomic imprinting is an epigenetic mechanism that leads to parental-allele-specific gene expression. Approximately 150 imprinted genes have been identified in humans and mice but less than 30 have been described as imprinted in cattle. For the purpose of de novo identification of imprinted genes in bovine, we determined global monoallelic gene expression in brain, skeletal muscle, liver, kidney and placenta of day ∼105 Bos taurus indicus × Bos taurus taurus F1 conceptuses using RNA sequencing. To accomplish this, we developed a bioinformatics pipeline to identify parent-specific single nucleotide polymorphism alleles after filtering adenosine to inosine (A-to-I) RNA editing sites. We identified 53 genes subject to monoallelic expression. Twenty three are genes known to be imprinted in the cow and an additional 7 have previously been characterized as imprinted in human and/or mouse that have not been reported as imprinted in cattle. Of the remaining 23 genes, we found that 10 are uncharacterized or unannotated transcripts located in known imprinted clusters, whereas the other 13 genes are distributed throughout the bovine genome and are not close to any known imprinted clusters. To exclude potential cis-eQTL effects on allele expression, we corroborated the parental specificity of monoallelic expression in day 86 Bos taurus taurus × Bos taurus taurus conceptuses and identified 8 novel bovine imprinted genes. Further, we identified 671 candidate A-to-I RNA editing sites and describe random X-inactivation in day 15 bovine extraembryonic membranes. Our results expand the imprinted gene list in bovine and demonstrate that monoallelic gene expression can be the result of cis-eQTL effects. 650 $agenomic imprinting 653 $aA-to-I RNA editing 653 $aAllele-specific gene expression 653 $aNext generation sequencing 653 $aX chromosome inactivation 700 1 $aHAGEN, D. E. 700 1 $aWANG, J. 700 1 $aELSIK, C. G. 700 1 $aJI, T. 700 1 $aSIQUEIRA, L. G. B. 700 1 $aHANSEN, P. J. 700 1 $aRIVERA, R. M. 773 $tEpigenetics$gv. 11, n. 7, p. 501-516, 2016.
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Embrapa Gado de Leite (CNPGL) |
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Registro Completo
Biblioteca(s): |
Embrapa Café. |
Data corrente: |
17/05/2024 |
Data da última atualização: |
20/05/2024 |
Tipo da produção científica: |
Capítulo em Livro Técnico-Científico |
Autoria: |
PICOLI, E. A. de T.; RESENDE, M. D. V. de; ODA, S. |
Afiliação: |
EDGARD AUGUSTO DE TOLEDO PICOLI, UNIVERSIDADE FEDERAL DE VIÇOSA; MARCOS DEON VILELA DE RESENDE, CNPCA; SHINITIRO ODA, CONSULTOR EXTERNO. |
Título: |
Come hell or high water: breeding the profile of eucalyptus tolerance to abiotic stress focusing water deficit. |
Ano de publicação: |
2021 |
Fonte/Imprenta: |
In: Gupta, D. K., Palma, J. M. (ed.). Plant Growth and Stress Physiology. Cham, Switzerland: Springer, 2021. |
Páginas: |
p. 91-127 |
ISSN: |
(Plant in Challenging Environments, 3). |
DOI: |
https://doi.org/10.1007/978-3-030-78420-1_5 |
Idioma: |
Inglês |
Notas: |
Chapter 5. |
Conteúdo: |
ABSTRACT - Here we approach eucalypt profile to meet a breeding program aiming at water stress tolerance. Eucalyptus embrace over 700 species although the core of genotypes used in commercial plantations has as little as nine species and their hybrids. Plantations are expected to fulfill the demand for harvesting timber and other commercial uses, sometimes, notwithstanding with plant survival resilience as not all tolerance strategies will fit industry interests. The diversity of eucalyptus strategies in response to drought join its variability in size, from shrubs to high trees, and adaptations to climates, from xeric to lowlands. There are several reports on eucalypts submitted to abiotic stress that contribute to the understanding of the sustained growth, although only a few recommend genotypes to be cultivated under these conditions. Different sets of structural, nutritional, physiological and other features, subsidize plant adaptability and growth, in a kind of functional homeostasis. Growth and adaptability traits are considered as markers for water stress tolerance or, at least, as a baseline for comparison. Some of these traits are found in responses to abiotic stresses other than water deficit and may be inherent or evolved for particular species. These processes may be the result from acclimatization or speciation/environmental selection what support selection for tolerance be performed under water deficit conditions. Our early experience indicates that joint analysis of selected, high accuracy and suitable heritability biomarkers support the identification of commercial eucalypt genotypes to be cultured under water scarcity conditions. MenosABSTRACT - Here we approach eucalypt profile to meet a breeding program aiming at water stress tolerance. Eucalyptus embrace over 700 species although the core of genotypes used in commercial plantations has as little as nine species and their hybrids. Plantations are expected to fulfill the demand for harvesting timber and other commercial uses, sometimes, notwithstanding with plant survival resilience as not all tolerance strategies will fit industry interests. The diversity of eucalyptus strategies in response to drought join its variability in size, from shrubs to high trees, and adaptations to climates, from xeric to lowlands. There are several reports on eucalypts submitted to abiotic stress that contribute to the understanding of the sustained growth, although only a few recommend genotypes to be cultivated under these conditions. Different sets of structural, nutritional, physiological and other features, subsidize plant adaptability and growth, in a kind of functional homeostasis. Growth and adaptability traits are considered as markers for water stress tolerance or, at least, as a baseline for comparison. Some of these traits are found in responses to abiotic stresses other than water deficit and may be inherent or evolved for particular species. These processes may be the result from acclimatization or speciation/environmental selection what support selection for tolerance be performed under water deficit conditions. Our early experience indicates that joint analy... Mostrar Tudo |
Thesagro: |
Água; Eucalipto; Genótipo. |
Thesaurus NAL: |
Abiotic stress; Eucalyptus; Stress tolerance; Water stress. |
Categoria do assunto: |
-- |
Marc: |
LEADER 02575naa a2200277 a 4500 001 2164313 005 2024-05-20 008 2021 bl uuuu u00u1 u #d 022 $a(Plant in Challenging Environments, 3). 024 7 $ahttps://doi.org/10.1007/978-3-030-78420-1_5$2DOI 100 1 $aPICOLI, E. A. de T. 245 $aCome hell or high water$bbreeding the profile of eucalyptus tolerance to abiotic stress focusing water deficit.$h[electronic resource] 260 $c2021 300 $ap. 91-127 500 $aChapter 5. 520 $aABSTRACT - Here we approach eucalypt profile to meet a breeding program aiming at water stress tolerance. Eucalyptus embrace over 700 species although the core of genotypes used in commercial plantations has as little as nine species and their hybrids. Plantations are expected to fulfill the demand for harvesting timber and other commercial uses, sometimes, notwithstanding with plant survival resilience as not all tolerance strategies will fit industry interests. The diversity of eucalyptus strategies in response to drought join its variability in size, from shrubs to high trees, and adaptations to climates, from xeric to lowlands. There are several reports on eucalypts submitted to abiotic stress that contribute to the understanding of the sustained growth, although only a few recommend genotypes to be cultivated under these conditions. Different sets of structural, nutritional, physiological and other features, subsidize plant adaptability and growth, in a kind of functional homeostasis. Growth and adaptability traits are considered as markers for water stress tolerance or, at least, as a baseline for comparison. Some of these traits are found in responses to abiotic stresses other than water deficit and may be inherent or evolved for particular species. These processes may be the result from acclimatization or speciation/environmental selection what support selection for tolerance be performed under water deficit conditions. Our early experience indicates that joint analysis of selected, high accuracy and suitable heritability biomarkers support the identification of commercial eucalypt genotypes to be cultured under water scarcity conditions. 650 $aAbiotic stress 650 $aEucalyptus 650 $aStress tolerance 650 $aWater stress 650 $aÁgua 650 $aEucalipto 650 $aGenótipo 700 1 $aRESENDE, M. D. V. de 700 1 $aODA, S. 773 $tIn: Gupta, D. K., Palma, J. M. (ed.). Plant Growth and Stress Physiology. Cham, Switzerland: Springer, 2021.
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