Identification of the core promoter of ZNFO, an oocyte-specific maternal effect gene in cattle

Zhang, Mingxiang; Chaney, Heather L.; Current, J.; Yao, Jianbo

doi:10.1016/j.gene.2021.145717

Cited by 5 publications

(3 citation statements)

References 25 publications

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“…Maternal effects, which result from variation in the environment provided by dams to their progeny, are recognized as being important for a variety of traits expressed at, and after birth in beef cattle (Campêlo et al, 2004;Zhang et al, 2021). In addition, the study by Linde (2018) showed that the impact of a low energy diet on the expression of DNA methyltransferase 3B (DNMT3B) increased expression in the Bonsmara compared to the Nguni.…”

Section: Discussionmentioning

confidence: 99%

Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation

et al. 2022

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Climate change is a major influencing factor in beef production. The greenhouse gases produced from livestock production systems contribute to the overall greenhouse gas emissions. The aim of this study was to identify selection signatures within and between Nguni and Bonsmara cattle in relation to production and adaptation. For this purpose, genomic 150 K single nucleotide polymorphism data from Nguni (n = 231) and Bonsmara (n = 252) cattle in South Africa were used. Extended haplotype homozygosity (EHH) based analysis was executed within each population using integrated haplotype score (iHS). The R package rehh was used for detecting selection signatures across the two populations with cross population EHH (XP-EHH). Total of 121 regions of selection signatures were detected (p < 0.0001) in the Bonsmara and Nguni populations. Several genes relating to DNA methylation, heat stress, feed efficiency and nitrogen metabolism were detected within and between each population. These regions also included QTLs associated with residual feed intake, residual gain, carcass weight, stature and body weight in the Bonsmara, while QTLs associated with conception rate, shear force, tenderness score, juiciness, temperament, heat tolerance, feed efficiency and age at puberty were identified in Nguni. Based on the results of the study it is recommended that the Nguni and Bonsmara be utilized in crossbreeding programs as they have beneficial traits that may allow them to perform better in the presence of climate change. Results of this study coincide with Nguni and Bonsmara breed characteristics and performance, and furthermore support informative crossbreeding programs to enhance livestock productivity in South Africa.

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Section: Discussionmentioning

confidence: 99%

Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation

et al. 2022

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“…[ 33 ]. In mammals, SNPs polymorphism in the promoter region were found to be central to the transcriptional regulatory mechanism in vitro, regulating the activity of the promoter region [ 34 ]. The presence of the c.905G>A SNP in the promoter region of the adenosine monophosphate deaminase 1 ( AMPD1 ) gene in chickens was found to alter the ability to bind transcription factors, and the rate-limiting step of the purine nucleotide cycle was enhanced, mainly maintaining freshness of fresh chicken meat [ 35 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of the Association of Two SNPs in the Promoter Regions of the PPP2R5C and SLC39A5 Genes with Litter Size in Yunshang Black Goats

Wang

Li²,

Liu³

et al. 2022

Animals

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Screening for candidate genes and genetic variants associated with litter size is important for goat breeding. The aim of this study was to analyze the relationship between single nucleotide polymorphisms (SNPs) in PPP2R5C and SLC39A5 and litter size in Yunshang black goats. KASP genotyping was used to detect the SNP genetic markers in the PPP2R5C and SLC39A5 in a population of 569 Yunshang black goats. The results show that there were two SNPs in the PPP2R5C and SLC39A5 promoter regions. Association analysis revealed that the polymorphisms PPP2R5C g.65977743C>T and SLC39A5 g.50676693T>C were significantly associated with the litter size of the third parity of Yunshang black goats (p < 0.05). To further explore the regulatory mechanism of the two genes, the expression of different genotypes of PPP2R5C and SLC39A5 was validated by RT-qPCR and Western blotting. The expression of PPP2R5C was significantly higher in individuals with the TT genotype than in those with the TC and CC genotypes (p < 0.05). The expression of SLC39A5 was also significantly higher in individuals with the TT genotype than in TC and CC genotypes (p < 0.05). Dual luciferase reporter analysis showed that the luciferase activity of PPP2R5C-C variant was significantly higher than that of PPP2R5C-T variant (p < 0.05). The luciferase activity of SLC39A5-T variant was significantly higher than that of SLC39A5-C variant (p < 0.05). Software was used to predict the binding of transcription factors to the polymorphic sites, and the results show that SOX18, ZNF418, and ZNF667 and NKX2-4 and TBX6 might bind to PPP2R5C g.65977743C>T and SLC39A5 g.50676693T>C, respectively. These results provide new insights into the identification of candidate genes for marker-assisted selection (MAS) in goats.

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“…Moreover, TSS/TATA was 2/7 for cows compared to 2/4 for buffalos in the core promoters. Zhang et al [ 28 ] mentioned that TSS to TATA are playing an important role in RNA polymerase II transcription for the core promoter region. The core promoter region may contain various elements such as TATA.…”

Section: Discussionmentioning

confidence: 99%

The variation in promoter sequences of the Akt3 gene between cow and buffalo revealed different responses against mastitis

Farmanullah

Gouda

Zhang

et al. 2021

Journal of Genetic Engineering and Biotechnology

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Background Serine/threonine kinase 3 (AKT3) is a protein-coding gene that is associated with several cattle immune diseases including different tumors and cancers. The objective of this study was to investigate the differences in structures and functions of AKT3 of cow and buffalo cattle. Methods The sequence differences of gene-coding sequence (CDS) and core promoter region of AKT3 in cow and buffalo were analyzed by using bioinformatics tools and PCR sequencing. Also, the functional analysis of promoter regulating gene expression by RT-PCR was performed using 500 Holstein cows and buffalos. And, evaluation of AKT3 inflammatory response to the lipopolysaccharide (LPS)-induced mastitis was performed between both species. Results The results revealed the variation in 6 exons out of 13 exons of the two species of CDS. Also, 4 different regions in 3-kb promoters of the AKT3 gene were significantly different between cow and buffalo species, in which cow’s AKT3 promoter sequence region was started from − 371 to − 1247, while in buffalo, the sequence was started from − 371 to − 969 of the promoter crucial region. Thus, the promoter was overexpressed in cows compared to buffaloes. As a result, significant differences (P < 0.05) between the two species in the AKT3 gene expression level related to the LPS stimulation in their mammary epithelial cell line. Conclusions This study emphasized the great importance of the structural differences of AKT3 between the animal species on their different responses against immune diseases like mastitis.

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Identification of the core promoter of ZNFO, an oocyte-specific maternal effect gene in cattle

Cited by 5 publications

References 25 publications

Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation

Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation

Analysis of the Association of Two SNPs in the Promoter Regions of the PPP2R5C and SLC39A5 Genes with Litter Size in Yunshang Black Goats

The variation in promoter sequences of the Akt3 gene between cow and buffalo revealed different responses against mastitis

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