Bovine Epigenetics and Epigenomics

Tian, X. Cindy

doi:10.1002/9781118301739.ch11

Cited by 2 publications

(2 citation statements)

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“…Genomic imprinting is an evolutionary puzzle because monoallelic expression can expose deleterious recessive mutations, which are normally protected by diploidy [5]. However, imprinting may have a selective advantage because it has been maintained throughout mammalian evolution [6]. The identification of the full catalog of imprinted genes in different mammalian species will greatly facilitate the understanding of the evolutionary roles of genomic imprinting [7].…”

Section: Introductionmentioning

confidence: 99%

Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses

et al. 2018

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Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date, 263 imprinted genes have been identified among all investigated mammalian species. However, only 21 have been described in sheep, of which 11 are annotated in the current ovine genome. Here, we aim to i) use DNA/RNA high throughput sequencing to identify new monoallelically expressed and imprinted genes in day 135 ovine fetuses and ii) determine whether maternal diet (100%, 60%, or 140% of National Research Council Total Digestible Nutrients) influences expression of imprinted genes. We also reported strategies to solve technical challenges in the data analysis pipeline. We identified 80 monoallelically expressed, 13 new putative imprinted genes, and five known imprinted genes in sheep using the 263 genes stated above as a guide. Sanger sequencing confirmed allelic expression of seven genes, CASD1, COPG2, DIRAS3, INPP5F, PLAGL1, PPP1R9A, and SLC22A18. Among the 13 putative imprinted genes, five were localized in the known sheep imprinting domains of MEST on chromosome 4, DLK1/GTL2 on chromosome 18 and KCNQ1 on chromosome 21, and three were in a novel sheep imprinted cluster on chromosome 4, known in other species as PEG10/SGCE. The expression of DIRAS3, IGF2, PHLDA2, and SLC22A18 was altered by maternal diet, albeit without allelic expression reversal. Together, our results expanded the list of sheep imprinted genes to 34 and demonstrated that while the expression levels of four imprinted genes were changed by maternal diet, the allelic expression patterns were un-changed for all imprinted genes studied.

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Section: Introductionmentioning

confidence: 99%

Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses

et al. 2018

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“…For many genes in mammalian species, both the maternal and paternal alleles are equally expressed. However, the expression of some genes is determined by imprinting, an epigenetic event in which only one of the alleles inherited from one of the parents get silenced and inactivated[1]. Consequently, in a limited group of genes which are imprinted, one of the parental alleles is expressed preferentially [2].…”

Section: Introductionmentioning

confidence: 99%

Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches

et al. 2019

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Genomic imprinting results in monoallelic expression of genes in mammals and flowering plants. Understanding the function of imprinted genes improves our knowledge of the regulatory processes in the genome. In this study, we have employed classification and clustering algorithms with attribute weighting to specify the unique attributes of both imprinted (monoallelic) and biallelic expressed genes. We have obtained characteristics of 22 known monoallelically expressed (imprinted) and 8 biallelic expressed genes that have been experimentally validated alongside 208 randomly selected genes in bovine ( Bos taurus ). Attribute weighting methods and various supervised and unsupervised algorithms in machine learning were applied. Unique characteristics were discovered and used to distinguish mono and biallelic expressed genes from each other in bovine. To obtain the accuracy of classification, 10-fold cross-validation with concerning each combination of attribute weighting (feature selection) and machine learning algorithms, was used. Our approach was able to accurately predict mono and biallelic genes using the genomics and proteomics attributes.

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Bovine Epigenetics and Epigenomics

Cited by 2 publications

References 100 publications

Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses

Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses

Characterization of bovine (Bos taurus) imprinted genes from genomic to amino acid attributes by data mining approaches

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