Identification of the Major miRNAs, Target Genes and Signaling Pathways Associated with Milk Production Using miRNA-Seq

Abstract

Background and objectives: miRNA molecules are short sequences (With an average length of 22 nucleotides) that regulate many biological processes by suppressing gene expression. Milk production is a physiological process that influence by a large number of genes, miRNAs and signaling pathways. In this study, identification of miRNAs, their target genes and signaling pathways were done by investigation of interspecies conserved miRNAs in mouse, cattle and goat.
Materials and methods: In this study, to investigate molecular mechanism of miRNA’s effect on milk production, firstly data were downloaded with accession number GSM1295115 for mouse species, GSM1295118 for cattle species and GSM969927 for goat species from GEO database. Identification of miRNAs was done by mirDeep2. In this study, mirwalk database was used to detect target genes of miRNA which expressed in all three species. The mirwalk database is also able to estimates target genes based on the ten other databases’ algorithms. Visualization of miRNA and their target genes’ interaction was performed by cytoscape. DAVID database was used to study target genes-related gene and signaling pathways.
Results: According to these results miR-93-5p, miR-27b-3p, miR-27a-3p and miR-200c-3p genes are the most important miRNA and Pten, Rlim, Pdik1l and Setd5 genes are the most important target genes on the process of milk production and pathways of milk components biosynthesis. One of the most important results of this study was detected Setd5 as the novel milk production process-related gene. Gene pathway analysis showed Focal adhesion pathway, MAPK signaling pathway, mTOR signaling pathway, PI3K-Akt signaling pathway and Neurotrophin signaling pathway were the most important of gene pathways which active by target genes and have a vital role in milk production biosynthesis and development of mammary glands. Theses gene pathways could effect on milk production physiologically and biologically by influencing on the development of alveolar cells, increasing branches, developing of mammary tissue, amino acid metabolism, influencing on endocrine system, prolactin signaling pathway and influencing on the milk compounds synthesis such as fat, protein and lactose.
Conclusion: According to critical role of the important miRNA in the studied network and target genes of these molecules and also investigated gene pathways, it could be used in breeding programs as the most important regulators in milk production process. This information could be used to introduce and apply candidate genes for the gene assisted selection method or genomic selection. Given that milk production is along with development and differentiation of breast tissue, miRNA molecules and target genes which investigate in this study could be the good candidates in all developmental and differential processes.

Keywords

Main Subjects


1.Anderson, S.M., Rudolph, M.C., McManaman, J.L., and Neville, M.C. 2007. Key stages in
mammary gland development. Secretory activation in the mammary gland: it's not just about
milk protein synthesis. Breast. Cancer. Res. 9: 1-7.
2.Bach, I., Rodriguez-Esteban, C., Carrière, C., Bhushan, A., Krones, A., Rose, D.W., Glass,
C.K., Andersen, B., Belmonte, J.C.I., and Rosenfeld, M.G. 1999. RLIM inhibits functional
activity of LIM homeodomain transcription factors via recruitment of the histone deacetylase
complex. Nat. Genet. 22: 394-399.
3.Baghizadeh, A., Bahaaddini, M., Mohamadabadi, M., and Askari, N. 2009. Allelic variations
in exon 2 of Caprine MHC Class II DRB3 Gene in Raeini Cashmere goat. Am-Eurasian J.
Agric. Environ. Sci. 6: 445-454.
4.Bao, Z., Lin, J., Ye, L., Zhang, Q., Chen, J., Yang, Q., and Yu, Q. 2016. Modulation of
Mammary Gland Development and Milk Production by Growth Hormone Expression in GH
Transgenic Goats. Front. Physiol. 7: 74-79.
5.Bar-Sagi, D., Fernandez, A ,.and Feramisco, J.R. 1987. Regulation of membrane turnover
byras proteins. Bioscience. Rep. 7: 427-434.
6.Bolger, A.M., Lohse, M., and Usadel, B. 2014. Trimmomatic: a flexible trimmer for Illumina
sequence data. Bioinformatics. 30: 2114-2120.
7.Booth, A.K. and Gutierrez-Hartmann, A. 2015. Signaling pathways regulating pituitary
lactotrope homeostasis and tumorigenesis, in Recent Advances in Prolactin Research.
Springer. p. 37-59.
8.Buitenhuis, B., Poulsen, N.A., Larsen, L.B., and Sehested, J. 2015 .Estimation of genetic
parameters and detection of quantitative trait loci for minerals in Danish Holstein and Danish
Jersey milk. BMC. Genet. 16: 19-25.
9.Fndrews, S., 2010. FastQC: a quality control tool for high throughput sequence data. 175-176.
10.Friedman, R.C., Farh ,K.K.H., Burge, C.B., and Bartel, D.P. 2009. Most mammalian
mRNAs are conserved targets of microRNAs. Genome. Res. 19: 92-105.
11.Gregory, P.A., Bert, A.G., Paterson, E.L., Barry, S.C., Tsykin, A., Farshid, G., Vadas, M.A.,
Khew-Goodall, Y., and Goodall, G.J. 2008. The miR-200 family and miR-205 regulate
epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat. Cell. Biol. 10: 593-
601.
12. Gu, Y., Li, M., Wang, T., Liang, Y., Zhong, Z., Wang, X., Zhou, Q., Chen, L., Lang, Q., and
He, Z. 2012. Lactation-related microRNA expression profiles of porcine breast milk
exosomes. PLoS. One. 7: e43691.
13.Hassiotou, F., Twigger, A.-J., Pundavela, J., Roselli, S., Hartmann, P., Geddes, D., and
Hondermarck, H. 2014. Neurotrophin synthesis by mammary cells during lactation (623.19).
FASEB. J. 28: 619-623.
14.Izumi, H., Kosaka, N., Shimizu, T., Sekine, K., Ochiya, T., and Takase, M. 2014. Timedependent
expression profiles of microRNAs and mRNAs in rat milk whey. PLoS. One. 9:
e88843.
15.Jankiewicz, M., Groner, B., and Desrivières, S. 2006. Mammalian target of rapamycin
regulates the growth of mammary epithelial cells through the inhibitor of deoxyribonucleic
acid binding Id1 and their functional differentiation through Id2. Mol. Endocrinol. 20: 2369-
2381.
16. Jiang, N., Wang, Y., Yu, Z., Hu, L., Liu, C., Gao, X., and Zheng, S. 2015. WISP3 (CCN6)
regulates milk protein synthesis and cell growth through mTOR signaling in dairy cow
mammary epithelial cells. DNA Cell. Biol. 34: 524-533.
17. Jiao, B., Ma, H., Shokhirev, M.N., Drung, A., Yang, Q., Shin, J., Lu, S., Byron, M.,
Kalantry, S., and Mercurio, A.M. 2012. Paternal RLIM/Rnf12 is a survival factor for milkproducing
alveolar cells. Cell. 149: 630-641.
18.Katz, E .and Streuli, C.H. 2007. The extracellular matrix as an adhesion checkpoint for
mammary epithelial function. Int. J. Biochem. Cell. Biol. 39: 715-726.
19.Kharrati, K.H., Mohammad, A.M., Ansari, M.S., Esmaili, Z.K.A., Tarang ,A., and
Nikbakhti, M. 2011. Genetic Variation of DGAT1 Gene and its Association with Milk
Production in Iranian Holstein Cattle Breed Population. IJASR. 3: 185-192.
20.Kharrati Koopaei, H., Mohammadabadi, M.R., Ansari Mahyari, S., Esmailizadeh, A.K.,
Tarang, A. and Nikbakhti, M 2012. Effect of DGAT1 variants on milk composition traits in
Iranian Holstein cattle population. Iran. J. Anim. Sci. Res. 3: 185-192. (In Persian).
21.Li, D., Xie, X., Wang, J., Bian, Y., Li, Q., Gao, X., and Wang, C. 2015. MiR-486 regulates
lactation and targets the PTEN gene in cow mammary glands. PloS one. 10: e0118284.
22.Li, Z., Liu, H., Jin, X., Lo, L., and Liu, J. 2012. Expression profiles of microRNAs from
lactating and non-lactating bovine mammary glands and identification of miRNA related to
lactation. BMC Genomics. 3: 12-22.
23.Lin, X.Z., Luo, J., Zhang, L.P., Wang, W., Shi, H.B., and Zhu, J.J. 2013. MiR-27a
suppresses triglyceride accumulation and affects gene mRNA expression associated with fat
metabolism in dairy goat mammary gland epithelial cells. Gene. 521: 15-23.
24.Melnik, B.C., John, S.M., Carrera-Bastos, P., and Cordain, L. 2012. The impact of cow's
milk-mediated mTORC1-signaling in the initiation and progression of prostate cancer. Nutr.
Metab. 9: 21-32.
25.Moghadaszadeh, M., Mohammadabadi, M.R., and Esmailizadeh, A.K. 2015. Association of
Exon 2 of BMP15 Gene with the Litter Size in the Raini Cashmere Goat. G3M. 13: 4062-
4067.
26.Naeem, A., Zhong, K., Moisá, S., Drackley, J., Moyes, K., and Loor, J. 2012. Bioinformatics
analysis of microRNA and putative target genes in bovine mammary tissue infected with
Streptococcus uberis. J. Dairy. Sci. 95: 6397-6408.
27.O'Connell, R.M., Rao, D.S., Chaudhuri, A.A., and Baltimore, D. 2010. Physiological and
pathological roles for microRNAs in the immune system. Nat. Rev. Immunol. 10: 111-122.
28.Oliver, C.H. and Watson, C.J. 2013. Making milk: A new link between STAT5 and Akt1.
JAK-STAT. 2: 2154-2168.
29.Ortega-Molina, A. and Serrano, M. 2013. PTEN in cancer, metabolism, and aging. Trends
Endocrinol. Metab. 24: 184-189.
30.Osipovich, A.B., Gangula, R., Vianna, P.G., and Magnuson, M.A. 2016. Setd5 is essential
for mammalian development and co-transcriptional regulation of histone acetylation.
Development. 14: 146-155.
31.Poissonnier, L., Villain ,G., Soncin, F., and Mattot, V. 2014. miR126-5p repression of
ALCAM and SetD5 in endothelial cells regulates leucocyte adhesion and transmigration.
Cardiovasc. Res. cvu040.
32.Raven, L.A., Cocks, B.G., Goddard, M.E., Pryce, J.E., and Hayes, B.J. .2014. Genetic
variants in mammary development, prolactin signalling and involution pathways explain
considerable variation in bovine milk production and milk composition. Genet. Select. Evol.
46: 110-117.
33.Shamsalddini, S., Mohammadabadi, M.R., and Esmailizadeh, A.K. 2016. Polymorphism of
the prolactin gene and its effect on fiber traits in goat. Russ. J. Genet. 52: 405-408.
34.Takahashi, R.U., Miyazaki, H., and Ochiya, T. 2015. The roles of microRNAs in breast
cancer. Cancers. 7: 598-616.
35.Tanaka, T., Haneda, S., Imakawa, K., Sakai, S., and Nagaoka, K. 2009. A microRNA, miR-
101a, controls mammary gland development by regulating cyclooxygenase-2 expression.
Differentiation. 77: 181-187.
36.Ucar, A., Vafaizadeh, V., Jarry, H., Fiedler, J., Klemmt, P.A., Thum, T., Groner, B., and
Chowdhury, K. 2010. miR-212 and miR-132 are required for epithelial stromal interactions
necessary for mouse mammary gland development. Nat. Genet. 42: 1101-1108.
37.Urbich, C., Kuehbacher, A., and Dimmeler, S. 2008. Role of microRNAs in vascular
diseases, inflammation and angiogenesis. Cardiovas. Res. 4: 581-588.
38.Wang, C., Long, K., Jin, L., Huang, S., Li, D., Ma, X., Wei, M., Gu, Y., Ma, J., and Zhang,
H. 2015. Identification of conserved microRNAs in peripheral blood from giant panda:
expression of mammary gland-related microRNAs during late pregnancy and early lactation.
Genet. Mol. Res. 14: 14216-14228.
39.Warnefors, M., Liechti, A., Halbert, J., Valloton, D., and Kaessmann, H. 2014. Conserved
microRNA editing in mammalian evolution, development and disease. Genome Biol. 15: 1.
40.Yang, H., Kong, W., He, L., Zhao, J.J., O'Donnell, J.D., Wang, J., Wenham, R.M., Coppola,
D., Kruk, P.A., and Nicosia, S.V. 2008. MicroRNA expression profiling in human ovarian
cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer
Res. 68: 425-433.
41.Zhang, C., Zhao, Y., Wang, Y., Wu, H., Fang, X., and Chen, H. 2014. Deep RNA sequencing
reveals that microRNAs play a key role in lactation in rats. J. Nutr. 144: 1142-1149.
42.Zhao, Y., Wang, P., Meng, J., Ji, Y., Xu, D., Chen, T., Fan, R., Yu, X., Yao, J., and Dong, C.
2015. MicroRNA-27a-3p Inhibits Melanogenesis in Mouse Skin Melanocytes by Targeting
Wnt3a. Int. J. Mol. Sci. 16: 10921-10933.