Abstract
MicroRNAs (miRNAs) are small non-coding RNAs ~ 19–25 nucleotides long that are involved in the regulation of gene expression. They negatively regulate the gene expression via inhibition or complete degradation of mRNAs by binding the complementary target sequences in 3′ untranslated region. The present investigation was aimed at profiling of miRNAs expressed in the Bubaline mammary tissue at dry stage of lactation cycle. Small RNAs were isolated from freshly collected mammary tissues and T4 RNA ligase was used to ligate the enriched miRNAs with 3′ and 5′ linker sequences in two separate reactions. cDNA copies were synthesized from linkered small RNAs followed by the PCR amplification. The PCR products were resolved on 15% non-denaturing polyacrylamide gel electrophoresis by gelstar staining. The PCR products were cloned using pGEM®-T easy vector system and the desired clones (with linkered small RNA sequences) were confirmed using restriction digestion of plasmids with EcoRI. Out of 15 Bubaline small RNA sequences, eight sequences (Seq. ID I–VIII) matched the size range of miRNA molecules i.e., 18–26 nucleotides. The Bubaline small RNA sequences II and III showed partial alignment with various mammalian and non-mammalian miRNAs. The small RNA sequences obtained in the present study did not show any perfect match with already reported mRNA, rRNA or tRNA sequences in different databases. Hence, only the Bubaline small RNA sequences that showed partial homology with miRNAs were considered as putative Bubaline miRNAs. The present study established the basic repertoire of miRNAs expressed at dry stage of lactation in Bubaline mammary gland.
Similar content being viewed by others
References
Ahmad SF, Panigrahi M, Bhushan B (2017) Micro RNAs in farm animal reproduction: A mini review. SKUAST J Res 19(1):1–11
Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ (2009) The deep evolution of metazoan microRNAs. Evol Dev 11(1):50–68
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genetics 37(7):766–770
Xin L, Jie Z, Chunhui Z, Tiesong L, Jihong W, Qingwei L (2015) The identification and verification of species-specific microRNAs and their precursors in Lampetra japonica. Yi chuan Hereditas 37(3):283–291
Yao S (2016) MicroRNA biogenesis and their functions in regulating stem cell potency and differentiation. Biol Proced Online 18(1):8
Hébert SS, De Strooper B (2009) Alterations of the microRNA network cause neurodegenerative disease. Trends Neurosci 32(4):199–206
Bonauer A, Boon A, Dimmeler R S (2010) Vascular micrornas. Curr Drug Targets 11(8):943–949
Gao FB, Gascon E (2012) Cause or effect: misregulation of microRNA pathways in neurodegeneration. Front Neurosci 6:48
Iorio MV, Croce CM (2012) MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review. EMBO Mol Med 4(3):143–159
Thum T (2012) MicroRNA therapeutics in cardiovascular medicine. EMBO Mol Med 4(1):3–14
Sawada S, Akimoto T, Takahashi M, Sakurai R, Shinkai S, Ushida T, Fujiwara Y, Suzuki K (2014) Effect of aging and sex on circulating microRNAs in humans. Adv Aging Res 3(02):152–159
Jena MK (2017) MicroRNAs in the development and neoplasia of the mammary gland. F1000Research 2017:6
Watson CJ, Khaled WT (2008) Mammary development in the embryo and adult: a journey of morphogenesis and commitment. Development 135(6):995–1003
Strucken EM, Laurenson YC, Brockmann GA (2015) Go with the flow—biology and genetics of the lactation cycle. Front Genetics 6:118
Modepalli V, Kumar A, Hinds LA, Sharp JA, Nicholas KR, Lefevre C (2014) Differential temporal expression of milk miRNA during the lactation cycle of the marsupial tammar wallaby (Macropus eugenii). BMC Genom 15(1):1012
Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M (2011) The genome of Theobroma cacao. Nat Genetics 43(2):101
Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WW, Yan Au W, Srivastava G, Czader MB, Rizzieri DA, Lagoo AS (2010) Hematologic Malignancies Research Consortium: Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood 116(23):e118–e127
Wang Z, Xue X, Sun J, Luo R, Xu X, Jiang Y, Zhang Q, Pan W (2010) An “in-depth” description of the small non-coding RNA population of Schistosoma japonicum schistosomulum. PLoS Negl Trop Dis 4(2):e596
Mohammed J, Flynt AS, Siepel A, Lai EC (2013) The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA 19(9):1295–1308
Kuchenbauer F, Morin RD, Argiropoulos B, Petriv I, Griffith M, Heuser M, Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y (2008) In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 18(11):1787–1797
Linsen SE, de Wit E, de Bruijn E, Cuppen E (2010) Small RNA expression and strain specificity in the rat. BMC Genom 11(1):249
Fu X, Adamski M, Thompson EM (2008) Altered miRNA repertoire in the simplified chordate, Oikopleura dioica. Mol Biol Evol 25(6):1067–1080
Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19(11):1288–1293
Lyson TR, Sperling EA, Heimberg AM, Gauthier JA, King BL, Peterson KJ (2012) MicroRNAs support a turtle + lizard clade. Biol Lett 8(1):104–107
Li SC, Chan WC, Ho MR, Tsai KW, Hu LY, Lai CH, Hsu CN, Hwang PP, Lin WC (2010) Discovery and characterization of medaka miRNA genes by next generation sequencing platform. BMC Genom BioMed Central 11(4):S8
Lui WO, Pourmand N, Patterson BK, Fire A (2007) Patterns of known and novel small RNAs in human cervical cancer. Cancer Res 67(13):6031–6043
Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120(1):21–24
Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC, Capuco AV, Smith TP (2007) Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. Physiol Genom 29(1):35–43
Gu Z, Eleswarapu S, Jiang H (2007) Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland. FEBS Lett 581(5):981–988
Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He T (2009) In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach. Genomics 94(2):125–131
Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Sewer A, Zavolan M, Nair V (2007) Marek’s disease virus type 2 (MDV-2)-encoded microRNAs show no sequence conservation with those encoded by MDV-1. J Virol 81(13):7164–7170
Heimberg AM, Cowper-Sal R, Sémon M, Donoghue PC, Peterson KJ (2010) microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate. Proc Natl Acad Sci 107(45):19379–19383
Campo-Paysaa F, Sémon M, Cameron RA, Peterson KJ, Schubert M (2011) microRNA complements in deuterostomes: origin and evolution of microRNAs. Evol Dev 13(1):15–27
Waidner LA, Morgan RW, Anderson AS, Bernberg EL, Kamboj S, Garcia M, Riblet SM, Ouyang M, Isaacs GK, Markis M, Meyers BC (2009) MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specific. Virology 388(1):128–136
Akhtar MM, Micolucci L, Islam MS, Olivieri F, Procopio AD (2015) Bioinformatic tools for microRNA dissection. Nucleic Acids Res 44(1):24–44
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129(7):1401–1414
Acknowledgements
The authors are thankful to the Director, ICAR-Indian Veterinary Research Institute (ICAR-IVRI), for providing the necessary funding, support and facilities to carry out this work.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest for this manuscript.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Khade, K.A., Panigrahi, M., Ahmad, S.F. et al. Cloning and characterization of Bubaline mammary miRNAs: An in silico approach. Mol Biol Rep 46, 1257–1262 (2019). https://doi.org/10.1007/s11033-019-04594-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11033-019-04594-0