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Magotra A, Gupta ID, Ahmad T, Alex R. Polymorphism in DNA repair gene BRCA1 associated with clinical mastitis and production traits in indigenous dairy cattle. Res Vet Sci 2020; 133:194-201. [PMID: 33011602 DOI: 10.1016/j.rvsc.2020.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/10/2020] [Accepted: 09/16/2020] [Indexed: 11/24/2022]
Abstract
The present study was conducted on Karan Fries cows to identify SNPs in breast cancer 1 (BRCA1) gene and their association with inflammation of mammary gland and production traits. Chi square analysis showed significant association of both SNPs i.e. G43737229T (P < 0.01) and G43761121A (P < 0.05) with incidence of clinical mastitis. Logistic modeling showed that GG genotype cows of G43737229T SNP was less susceptible to mastitis in comparison to TT genotype cows as the odds ratio of TT against GG for the non-incidence of mastitis was less i.e. 0.23. Whereas, cows with genotype AA of G43761121A SNP were less prone to clinical mastitis in comparison to GG genotype cows. G-T haplotype and GGTT combined genotype exhibited maximum mastitis incidences. Least squares analysis revealed significant association of G43737229T SNP with total milk yield (P < 0.01), 305 days milk yield (P < 0.01) and lactation length (P < 0.05). The TT and GT genotyped Karan Fries cows were associated with higher milk yields during first and second lactation, as well as with first lactation length. These observations on SNPs, genotypes and combined genotypes of BRCA1 gene and their differential association with the incidence of mastitis and production traits can be utilized as an aid to selection for simultaneous improvement of both antagonistic traits.
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Affiliation(s)
- Ankit Magotra
- Department of Animal Genetics and Breeding, Lala Lajpat Rai University of Veterinary and Animal Sciences (LUVAS), Hisar, India.
| | - I D Gupta
- Dairy Cattle Breeding Division, ICAR- National Dairy Research Institute, 132001, Haryana, India
| | - Tavsief Ahmad
- Department of Animal Genetics and Breeding SKAUST-Kashmir, Jammu and Kashmir, India
| | - Rani Alex
- Dairy Cattle Breeding Division, ICAR- National Dairy Research Institute, 132001, Haryana, India
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Ikpeme E, Udensi O, Kooffreh M, Etta H, Ushie B, Echea E, Ozoje M. In silico Analysis of BRCA1 Gene and its Phylogenetic Relationship in some Selected Domestic Animal Species. ACTA ACUST UNITED AC 2016. [DOI: 10.3923/tb.2017.1.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Profiling of Bovine Breast Cancer 1, Early Onset (BRCA1) Gene Among Frieswal (HF × Sahiwal) Cows and Their Association with Mastitis. NATIONAL ACADEMY SCIENCE LETTERS-INDIA 2014. [DOI: 10.1007/s40009-014-0283-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Investigation on BRCA1 SNPs and its effects on mastitis in Chinese commercial cattle. Gene 2012; 505:190-4. [PMID: 22583824 DOI: 10.1016/j.gene.2012.05.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 04/22/2012] [Accepted: 05/06/2012] [Indexed: 11/21/2022]
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Yuan Z, Chu G, Dan Y, Li J, Zhang L, Gao X, Gao H, Li J, Xu S, Liu Z. BRCA1: a new candidate gene for bovine mastitis and its association analysis between single nucleotide polymorphisms and milk somatic cell score. Mol Biol Rep 2012; 39:6625-31. [PMID: 22327776 DOI: 10.1007/s11033-012-1467-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Accepted: 01/23/2012] [Indexed: 01/25/2023]
Abstract
Bovine mastitis is a very complex and common disease of dairy cattle and a major source of economic losses to the dairy industry worldwide. In this study, the bovine breast cancer 1, early onset gene (BRCA1) was taken as a candidate gene for mastitis resistance. The main object of this study was to investigate whether the BRCA1 gene was associated with mastitis in cattle. Through DNA sequencing, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and Created Restriction Site PCR (CRS-PCR) methods, three SNPs (G22231T, T25025A, and C28300A) were detected and twenty-four combinations of these SNPs were observed. The single SNP and their genetic effects on somatic cell score (SCS) were evaluated and a significant association with SCS was found in C28300A. The mean of genotype EE was significantly lower than those of genotypes EF and FF. The results of combined genotypes analysis of three SNPs showed that BBDDFF genotype with the highest SCS were easily for the mastitis susceptibility, whereas AACCEE genotype with the lowest SCS were favorable for the mastitis resistance. The information provided in the present study will be very useful for improving mastitis resistance in dairy cattle by marker-assisted selection.
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Affiliation(s)
- Zhengrong Yuan
- Center for Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
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Sugiura T, Matsuyama S, Akiyosi H, Takenaka S, Yamate J, Kuwamura M, Aoki M, Shimada T, Ohashi F, Kubo K. Expression Patterns of the BRCA1 Splicing Variants in Canine Normal Tissues and Mammary Gland Tumors. J Vet Med Sci 2007; 69:587-92. [PMID: 17611353 DOI: 10.1292/jvms.69.587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Human BRCA1 is familial breast cancer susceptibility gene. Recently, decreased BRCA1 mRNA and protein expression has been identified in sporadic breast tumors. In the reported human BRCA1 splicing variants, delta11b lacks the majority of exon11 and is suspected to have a distinct function in normal tissues. The splicing variants display a variety of expression pattern in breast cancer samples. Although mammary gland tumor is important disease in dog, there are few reports for BRCA1 in the canine tumors. In this study, we examined the relative amounts of BRCA1 splicing variants mRNA in canine normal and mammary tumor samples by RT-PCR to investigate whether there is the altered expression of variant mRNAs in the canine tumor as reported in human. The exon11b-defecting RT-PCR products were observed in all the normal tissues examined and the nucleotide sequence was quite similar to that of human BRCA1 delta11b. In some tumor samples, we did not detect the products targeted for exon10-13 and exon14-15, while these products were observed in all the normal samples examined. Especially, the relative amounts of the exon11-defecting products were remarkably decreased in most of the tumors (11/16).
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Affiliation(s)
- Takaaki Sugiura
- Laboratory of Veterinary Radiology, Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
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Abstract
For the last 15 yr, a great deal of knowledge has been accumulated on health beneficial factors, protein and nonprotein, of bovine milk fat globule membrane (MFGM). Among the health-beneficial components of the MFGM are cholesterolemia-lowering factor, inhibitors of cancer cell growth, vitamin binders, inhibitor of Helicobacter pylori, inhibitor of beta-glucuronidase of the intestinal Escherichia coli, xanthine oxidase as a bactericidal agent, butyrophilin as a possible suppressor of multiple sclerosis, and phospholipids as agents against colon cancer, gastrointestinal pathogens, Alzheimer's disease, depression, and stress. All of the above compel us to consider bovine MFGM as a potential nutraceutical.
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Horwitz AA, Sankaran S, Parvin JD. Direct stimulation of transcription initiation by BRCA1 requires both its amino and carboxyl termini. J Biol Chem 2006; 281:8317-20. [PMID: 16473884 DOI: 10.1074/jbc.c500475200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Published experiments suggest that BRCA1 interaction with RNAPII and regulation of a number of target genes may be central to its role as a tumor suppressor. Previous in vivo and in vitro work has implicated the carboxyl terminus of BRCA1 in transcriptional stimulation, but the mechanism of action remains unknown, and whether the full-length protein stimulates transcription is controversial. BRCA1 interacts with a number of enhancer-binding transcriptional activators, suggesting that these factors recruit BRCA1 to promoters, where it stimulates RNA synthesis. To investigate whether BRCA1 has intrinsic transcriptional activity, we established a fully purified transcription assay. We demonstrate here that BRCA1 stimulates transcription initiation across a range of promoters. Both the amino and carboxyl termini of BRCA1 are required for this activity, but the BRCA1-binding partner, BARD1, is not. Our data support a model whereby BRCA1 stabilizes productive preinitiation complexes and thus stimulates transcription.
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Affiliation(s)
- Andrew A Horwitz
- Program in Biology and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
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Pettigrew C, Wayte N, Lovelock PK, Tavtigian SV, Chenevix-Trench G, Spurdle AB, Brown MA. Evolutionary conservation analysis increases the colocalization of predicted exonic splicing enhancers in the BRCA1 gene with missense sequence changes and in-frame deletions, but not polymorphisms. Breast Cancer Res 2005; 7:R929-39. [PMID: 16280041 PMCID: PMC1410749 DOI: 10.1186/bcr1324] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 08/24/2005] [Accepted: 09/02/2005] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Aberrant pre-mRNA splicing can be more detrimental to the function of a gene than changes in the length or nature of the encoded amino acid sequence. Although predicting the effects of changes in consensus 5' and 3' splice sites near intron:exon boundaries is relatively straightforward, predicting the possible effects of changes in exonic splicing enhancers (ESEs) remains a challenge. METHODS As an initial step toward determining which ESEs predicted by the web-based tool ESEfinder in the breast cancer susceptibility gene BRCA1 are likely to be functional, we have determined their evolutionary conservation and compared their location with known BRCA1 sequence variants. RESULTS Using the default settings of ESEfinder, we initially detected 669 potential ESEs in the coding region of the BRCA1 gene. Increasing the threshold score reduced the total number to 464, while taking into consideration the proximity to splice donor and acceptor sites reduced the number to 211. Approximately 11% of these ESEs (23/211) either are identical at the nucleotide level in human, primates, mouse, cow, dog and opossum Brca1 (conserved) or are detectable by ESEfinder in the same position in the Brca1 sequence (shared). The frequency of conserved and shared predicted ESEs between human and mouse is higher in BRCA1 exons (2.8 per 100 nucleotides) than in introns (0.6 per 100 nucleotides). Of conserved or shared putative ESEs, 61% (14/23) were predicted to be affected by sequence variants reported in the Breast Cancer Information Core database. Applying the filters described above increased the colocalization of predicted ESEs with missense changes, in-frame deletions and unclassified variants predicted to be deleterious to protein function, whereas they decreased the colocalization with known polymorphisms or unclassified variants predicted to be neutral. CONCLUSION In this report we show that evolutionary conservation analysis may be used to improve the specificity of an ESE prediction tool. This is the first report on the prediction of the frequency and distribution of ESEs in the BRCA1 gene, and it is the first reported attempt to predict which ESEs are most likely to be functional and therefore which sequence variants in ESEs are most likely to be pathogenic.
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Affiliation(s)
- Christopher Pettigrew
- School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Nicola Wayte
- School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia, Queensland, Australia
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Paul K Lovelock
- School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia, Queensland, Australia
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | | | | | - Amanda B Spurdle
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Melissa A Brown
- School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia, Queensland, Australia
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Judkins T, Hendrickson BC, Deffenbaugh AM, Scholl T. Single nucleotide polymorphisms in clinical genetic testing: the characterization of the clinical significance of genetic variants and their application in clinical research for BRCA1. Mutat Res 2005; 573:168-79. [PMID: 15829246 DOI: 10.1016/j.mrfmmm.2004.07.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Accepted: 07/23/2004] [Indexed: 05/02/2023]
Abstract
Clinical genetic testing is increasingly employed in the medical management of cancer patients. These tests support a variety of clinical decisions by providing results that indicate risk for future disease, confirmation of diagnoses, and more recently, therapeutic selection and prognosis. Most genetic variation detected during clinical testing involves single nucleotide polymorphisms (SNPs). Continued advances in the technologies of genetic analyses make these tests increasingly sensitive, cost-effective and timely, which contribute to their increased utilization. Conversely, it has proven difficult to characterize the clinical significance of genetic variants that do not obviously truncate the open reading frames of genes. These genetic variants of uncertain clinical significance diminish the value of genetic test results. This article highlights a variety of approaches that have emerged from research in diverse disciplines to solve the problem, including the application of information about common SNPs in multiple methods to better characterize clinically uncertain variants. Hereditary breast/ovarian cancer, and in particular BRCA1, provides a framework for this discussion. BRCA1 is particularly interesting in this respect since clinical genetic testing by direct DNA sequencing for over 50,000 patients in North America has revealed approximately 1500 genetic variants to date. This large data set combined with the clinical significance of BRCA1 have resulted in research groups selecting BRCA1 as a preferred gene to evaluate novel methods in this field. Finally, the lessons learned through work with BRCA1 are highly applicable to many other genes associated with cancer risk.
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Affiliation(s)
- Thaddeus Judkins
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT 84018, USA
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Abstract
The human BRCA1 tumor suppressor interacts with transcriptional machinery, including RNA polymerase II (RNA pol II). We demonstrated that interaction with RNA pol II is a conserved feature of BRCA1 proteins from several species. We found that full-length BRCA1 proteins universally fail to activate transcription in classic GAL4-UAS one-hybrid assays and that the activity associated with the human BRCA1 C terminus was poorly conserved in closely related homologs of the gene. Fractionation studies demonstrated that BRCA1 proteins from all species tested interacted specifically with hyperphosphorylated pol II (IIO), in preference to hypophosphorylated RNA pol II (IIA) expected at promoters. BRCA1-RNA pol II complexes showed evidence of a multiply phosphorylated heptad repeat domain in the catalytic subunit (p220) of RNA pol II, and the complex was highly functional in transcriptional run-off assays. Interestingly, endogenous BRCA1 associated with a large fraction of the processive RNA pol II activity present in undamaged cells, and the interaction was disrupted by DNA-damaging agents. Preferential interaction with processive RNA pol II in undamaged cells places BRCA1 in position to link late events in transcription with repair processes in eukaryotic cells.
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Affiliation(s)
- Susan A Krum
- Molecular Biology Institute, The David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
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