Genomic Imprinting and Imprinted Gene Clusters in the Bovine Genome

Imumorin, Ikhide G.; Peters, Sunday O.; Donato, Marcos De

doi:10.1002/9781119949930.ch6

Cited by 7 publications

(8 citation statements)

References 97 publications

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“…Very few imprinted genes have been identified in some livestock species (cattle, sheep, pig and rabbit) to be associated with the economically important traits such as milk yield, fat and meat deposition, fetal development, growth and carcass traits. Although the bovine genome is the best characterized livestock genome with high sequence coverage and with the highest percentage of annotated genes, however, less than two dozen imprinted genes have been experimentally validated (Imumorin et al, 2012). Imprinted genes are characterized by some genetic and epigenetic features.…”

Section: Introductionmentioning

confidence: 99%

“…These features are being used to analyze known and putative imprinted genes (Khatib et al, 2007;Luedi et al, 2007). Recently, a large cluster of imprinted genes has been mapped to the bovine chromosome 29 (Imumorin et al, 2012). Bovine chromosome (Bta) 29 is the equivalent of human chromosome (Hg) 11 and mouse chromosome (Mm) 7 which contains the highest number of imprinted genes.…”

Section: Introductionmentioning

confidence: 99%

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DNA Sequence Characteristics and Phylogenetics of Putative Imprinted Genes on Bovine Chromosome 29

Bamidele¹,

Omitogun²,

Imumorin³

2015

JAS

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Cattle are important livestock species with huge genetic resource for food security, agriculture and livelihoods. Over 60% of its genes are homologous to all mammalian species which creates a molecular basis for conducting comparative genomic analysis. Genomic imprinting has been implicated in a variety of biological functions and so identification of new or verification of known imprinted genes in livestock species is of high agricultural and biomedical importance. Fourteen (14) putative imprinted genes on bovine chromosome 29 (Bta 29) as well as the human (Hg 11) and mouse (Mm 7) orthologs were computationally characterized with respect to the CpG islands (CGI), transcription factor binding elements and sequence motif. Phylogenetic analysis was conducted across the three species for each of the genes identified to have promoter CGI. Promoter CGI were identified in ASCL2, TSSC4, CDKN1C, KCNQ1, PHLDA2 and NAP1L4. The promoter CGI were enriched with CpG containing transcription factor binding sites. Generally, it was observed that cattle was more closely related to human than mouse and that natural selection was the force driving the evolutionary change between the three species. Protein kinase motifs involved in phosphorylation were identified in the amino-acid sequences of ASCL2, TSSC4, PHLDA2 and NAP1L4. Our results suggest the post-translation regulation of imprinting and that the predicted promoter CGI can be assayed to determine molecular function, gene expression and DNA methylation status of the bovine putative imprinted genes.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DNA Sequence Characteristics and Phylogenetics of Putative Imprinted Genes on Bovine Chromosome 29

Bamidele¹,

Omitogun²,

Imumorin³

2015

JAS

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“…However, it may also mean that the putative imprinted TSSC4 gene had been switched off in the skin tissues of the respective developmental stages investigated by this study as well as other previous studies. According to Imumorin et al [16] this may be due to the fact that epigenetic mechanisms regulating genomic imprinting could be influenced by the prevailing developmental stage of the animal.…”

Section: Discussionmentioning

confidence: 99%

Tissue Expression Profiles of 5 Putative Imprinted Genes in Bovine Chromosome 29

Bamidele¹,

Omitogun²,

Imumorin³

2016

OJAS

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Genomic imprinting is an epigenetic process that regulates gene expression in the mammalian genome. Although there are specific imprinting differences between the mammalian species, cattle present unique opportunity for characterizing imprinted genes because of its sub-species classification. Five putative imprinted genes (TSSC4, CDKN1C, KCNQ1, PHLDA2 and NAP1L4) on bovine chromosome 29 (Bta 29) which had been characterized to have promoter CGI were quantitatively assayed for their relative expression across eight tissues (muscle, brain, liver, kidney, spinal cord, heart, lymph and skin) sampled in Angus cattle. The differential abundance of these genes in muscle and skin tissues of Angus, White Fulani and N'Dama cattle breeds was comparatively analyzed. These three breeds are representative of the Bos taurus and Bos indicus cattle sub-species while the two tissues are selected based on their strategic economic importance in cattle production. All the genes, except TSSC4, were relatively expressed across all the tissues. It was observed that Angus had the highest differential abundance in muscle tissues for TSSC4, PHLDA2 and NAP1L4 while N'Dama and White Fulani were the most abundant for KCNQ1 and NAP1L4 in skin tissues. The study identified marked differences in the expression profiles of the genes in both muscle and skin tissues of the three breeds that were characteristics of their genetics, environment and nutrition.

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“…This has been described in insects,1–4 higher plants,5–7 and mammals, but the latter is where it has mostly been studied 8–12. This pattern of expression ranges from a small but significant bias toward one parental allele to a complete shutdown of one of the parental alleles 13. To date, out of the about 25 000 genes described in the human genome, only 212 have been reported to show imprinted expression, 123 in mouse and 20 in cattle (Geneimprint, http://www.geneimprint.com).…”

Section: Introductionmentioning

confidence: 94%

Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting

Donato

Hussain

Rodulfo

et al. 2017

Evol Bioinform Online

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KCNQ1OT1 is located in the region with the highest number of genes showing genomic imprinting, but the mechanisms controlling the genes under its influence have not been fully elucidated. Therefore, we conducted a comparative analysis of the KCNQ1/KCNQ1OT1-CDKN1C region to study its conservation across the best assembled eutherian mammalian genomes sequenced to date and analyzed potential elements that may be implicated in the control of genomic imprinting in this region. The genomic features in these regions from human, mouse, cattle, and dog show a higher number of genes and CpG islands (detected using cpgplot from EMBOSS), but lower number of repetitive elements (including short interspersed nuclear elements and long interspersed nuclear elements), compared with their whole chromosomes (detected by RepeatMasker). The KCNQ1OT1-CDKN1C region contains the highest number of conserved noncoding sequences (CNS) among mammals, where we found 16 regions containing about 38 different highly conserved repetitive elements (using mVista), such as LINE1 elements: L1M4, L1MB7, HAL1, L1M4a, L1Med, and an LTR element: MLT1H. From these elements, we found 74 CNS showing high sequence identity (>70%) between human, cattle, and mouse, from which we identified 13 motifs (using Multiple Em for Motif Elicitation/Motif Alignment and Search Tool) with a significant probability of occurrence, 3 of which were the most frequent and were used to find transcription factor–binding sites. We detected several transcription factors (using JASPAR suite) from the families SOX, FOX, and GATA. A phylogenetic analysis of these CNS from human, marmoset, mouse, rat, cattle, dog, horse, and elephant shows branches with high levels of support and very similar phylogenetic relationships among these groups, confirming previous reports. Our results suggest that functional DNA elements identified by comparative genomics in a region densely populated with imprinted mammalian genes may be related to the regulation of imprinted gene expression.

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Genomic Imprinting and Imprinted Gene Clusters in the Bovine Genome

Cited by 7 publications

References 97 publications

DNA Sequence Characteristics and Phylogenetics of Putative Imprinted Genes on Bovine Chromosome 29

DNA Sequence Characteristics and Phylogenetics of Putative Imprinted Genes on Bovine Chromosome 29

Tissue Expression Profiles of 5 Putative Imprinted Genes in Bovine Chromosome 29

Conservation of Repeats at the Mammalian KCNQ1OT1-CDKN1C Region Suggests a Role in Genomic Imprinting

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