Identification of SNP variations and different microRNA binding sites at 3-UTR region of bovine HSP90AA1 gene among different Indian breeds of cattle

RAJIB DEB; GYANENDRA S SENGAR; BASAVRAJ SAJJANAR; UMESH SINGH; INDRA SINGH; RANI ALEX; T V RAJA; SUSHIL KUMAR; R R ALYETHODI; V BHANUPRAKASH

doi:10.56093/ijans.v87i5.70243

Authors

RAJIB DEB ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
GYANENDRA S SENGAR ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
BASAVRAJ SAJJANAR ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
UMESH SINGH ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
INDRA SINGH ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
RANI ALEX ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
T V RAJA ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
SUSHIL KUMAR ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
R R ALYETHODI ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India
V BHANUPRAKASH ICAR-Central Institute for Research on Cattle, Meerut, Uttar Pradesh India

https://doi.org/10.56093/ijans.v87i5.70243

Keywords:

Cattle, HSP90AA1, Mutation, miRNAs, 3’untranslated region (UTR)

Abstract

Present study was aimed to identify mutations/SNPs and predict microRNAs within the 3-untranslated region of bovine Hsp90 AA1 gene. A total of 28 mutations were identified in the 3-untranslated region of bovine Hsp90 gene among 4 indigenous zebu breeds and 1 crossbred population. Results revealed that, natural mutational changes are more in crossbred cattle compared to indigenous zebu animals and the difference was statistically significant. Prediction of microRNA binding site revealed that there are atleast 7 different micro RNAs, which may interact at 3-untranslated region of bovine Hsp90AA1 gene among different breeds of cattle investigated. Out of the 7 microRNAs, miR8882 and miR3796 were the most commonly distributed among the 4 breeds while the miR9491
and miR-2277-5p were restricted to Gir and Ongole breeds respectively. While miR8882 binding site were unanimous, miR3796 showed variation among the breeds. This indicate that there exists differences in the microRNA binding sites of the 3-untranslated region among cattle breeds.

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References

Blackshear P J. 2002. Tristetraprolin and other CCCH tandem zinc-finger proteins in the regulation of mRNA turnover. Biochemical Society Transactions 30: 945–52. DOI: https://doi.org/10.1042/bst0300945

Chen C-YA, Xu N and Shyu A B. 2002. Highly selective actions of HuR in antagonizing AU-rich element-mediated mRNA destabilization. Molecular and Cellular Biology 22: 7268 –78. DOI: https://doi.org/10.1128/MCB.22.20.7268-7278.2002

Csermely P, Schnaider T, So C, Prohászka Z and Nardai G. 1998. The 90–kDa molecular chaperone family: structure, function and clinical applications. A comprehensive review. Pharmacology and Therapeutics 79(2): 129–68. DOI: https://doi.org/10.1016/S0163-7258(98)00013-8

Deb R, Sajjanar B, Singh U, Kumar S, Singh R, Sengar G and Sharma A. 2014. Effect of heat stress on the expression profile of Hsp90 among Sahiwal (Bos indicus) and Frieswal (Bos indicus × Bos taurus) breed of cattle: A comparative study. Gene 536(2): 435–40. DOI: https://doi.org/10.1016/j.gene.2013.11.086

Doench J G, Petersen C P and Sharp P A. 2003. siRNAs can function as miRNAs. Genes and Development 17: 438–42. DOI: https://doi.org/10.1101/gad.1064703

Franco-Zorrilla J M, Valli A, Todesco M, Mateos I, Puga M I, Rubio-Somoza I, Leyva A, Weigel D, Garcia J A and Paz- Ares J. 2007. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics 39: 1033– 37. DOI: https://doi.org/10.1038/ng2079

Leung A K, Calabrese J M and Sharp P A. 2006. Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules. Proceedngs of National Academy of Sciences of the United States of America 103: 18125–30. DOI: https://doi.org/10.1073/pnas.0608845103

Raineri I, Wegmueller D, Gross B, Certa U and Moroni C. 2004. Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference. Nucleic Acids Research 32:1279 –88. DOI: https://doi.org/10.1093/nar/gkh282

Sambrook J and Russel D W. 2001. Molecular Cloning: A Laboratory Manual. 3rd edn, Vol. 1, Cold Spring Harbour Laboratory Press, New York, USA.