Study gene regulatory networks involved in Lactogenesis in dairy cow mammary tissue using RNA-Seq data

Document Type : Research Paper

Authors

Abstract

In this study to gain insights into transcriptional regulation Lactogenesis in mammary tissue, at the first high expression genes in lactogenesis in three different condition were identified by RNA-Seq data analysis. This three conditions including comparison of the dairy cow mammary tissue in 35 days before and 3 days after birth, dairy cow mammary tissue in 7 days before and 3 days after birth and dairy cow mammary tissue in 7 and 35 days before birth. To investigate the biological processes of significant high expression genes in three different condition mentioned above, the DAVID software was used. The only significant terms (P<0.05) related to biological processes were considered. Then promoter regions of these genes were extracted to identify candidate transcription factors involved in this mechanisms. Assuming that changes in the transcription level of co-expressed genes may result from the coordinated action of a limited number of transcription factors, we looked for over-represented putative transcription factor binding sites in the promoters of these genes. Promoter analysis by using Genomatix software lead to identify of 24 novel transcription factors candidates activating in lactogenesis. In this study in order to visualization of regulatory networks containing transcription factors and that regulate the genes, STRING software were used. According to the results, 24 new candidates transcription factor introduced in this study has good potential for more investigation in the laboratory.

Keywords

References

Bakhtiarizadeh, M.R., Moradi-Shahrbabak, M. and Ebrahimie, E. (2014). Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue. Genes & Genomics. 36(1): 105-117.
Bernardo, G.M. (2012). Discerning the role of FOXA1 in mammary gland development and breast cancer, Case Western Reserve University. 1-240.
Bernardo, G.M., Lozada, K. L., Miedler, J.D., Harburg, G., Hewitt, S.C., Mosley, J.D., Godwin, A.K., Korach, K.S., Visvader, J.E. and Kaestner, K.H. (2010). FOXA1 is an essential determinant of ERα expression and mammary ductal morphogenesis. Development. 137(12): 2045-2054.
Bionaz, M. and Loor,  J.J. (2008). ACSL1, AGPAT6, FABP3, LPIN1, and SLC27A6 are the most abundant isoforms in bovine mammary tissue and their expression is affected by stage of lactation. The Journal of nutrition. 138(6): 1019-1024.
Bionaz, M. and Loor, J.J. (2008). Gene networks driving bovine milk fat synthesis during the lactation cycle. BMC genomics. 9(1): 1.
Bionaz, M. and Loor, J.J. (2011). Gene networks driving bovine mammary protein synthesis during the lactation cycle. Bioinformatics and biology insights. 5: 83.
 Buermans, H. and Den Dunnen, J. )2014(. Next generation sequencing technology: advances and applications. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease. 1842 (10): 1932-1941. Caroli, A., Chessa, S. and Erhardt, G. (2009). Invited review: Milk protein polymorphisms in cattle: Effect on animal breeding and human nutrition. Journal of dairy science. 92(11): 5335-5352.
Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein,  M. and Werner, T. (2005). MatInspector and beyond: promoter analysis based on transcription factor binding sites.Bioinformatics. 21(13): 2933-2942.
D'Alessandro, A., Zolla, L. and Scaloni, A. (2011). The bovine milk proteome: cherishing, nourishing and fostering molecular complexity. An interactomics and functional overview. Molecular BioSystems. 7(3): 579-597.
Dentice, M., Luongo, C., Elefante, A., Romino, R., Ambrosio, R., Vitale, M., Rossi, G., Fenzi, G. and Salvatore, D. (2004). Transcription factor Nkx-2.5 induces sodium/iodide symporter gene expression and participates in retinoic acid-and lactation-induced transcription in mammary cells. Molecular and cellular biology. 24(18): 7863-7877.
Elsasser, T.H., Capuco, A.V., Caperna, T.J., Martínez, A., Cuttitta, F. and Kahl, S. (2007). Adrenomedullin (AM) and adrenomedullin binding protein (AM-BP) in the bovine mammary gland and milk: Effects of stage of lactation and experimental intramammary E. coli infection. Domestic animal endocrinology. 32(2): 138-154.
Fatima, A. (2014). Analysis of hepatic microRNA expression in postpartum dairy cows in negative energy balance.
Finucane, K.A., McFadden, T.B., Bond, J.P., Kennelly,  J.J. and Zhao,  F.Q. (2008). Onset of lactation in the bovine mammary gland: gene expression profiling indicates a strong inhibition of gene expression in cell proliferation. Functional & integrative genomics. 8(3): 251-264.
Fonteh, F.A., Grandison, A.S. and Lewis, M.J. (2002). Variations of lactoperoxidase activity and thiocyanate content in cows' and goats' milk throughout lactation. Journal of Dairy Research. 69(03): 401-409.
Gao, Y., Lin, X., Shi, K., Yan, Z. and Wang, Z. (2013). Bovine mammary gene expression profiling during the onset of lactation.PloS one. 8(8): e70393.
Huang, D.W., Sherman, B.T.and Lempicki, R.A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols. 4(1): 44-57.
Huang, S., Wang, J., Yue, W., Chen, J.,  Gaughan, S., Lu, W., Lu, G. and Wang, C. (2015). Transcriptomic variation of hepatopancreas reveals the energy metabolism and biological processes associated with molting in Chinese mitten crab, Eriocheir sinensis. Scientific reports. 5.
Huott, M.L., Josephson, R.V., Hens, J.R., Rogers, G.W. and Patton, S. (1995). Polymorphic forms of the epithelial mucin, PAS-I (MUC1), in milk of Holstein cows (Bos taurus).Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology. 111(4): 559-565
. Jalili, R. 2013. Next Generation Sequencing Methods and Its Impacts on Genomics and Clinical Applications. Jensen, L.J., Kuhn, M., Stark, M., Chaffron, S., Creevey, C., Muller, J., Doerks, T., Julien, P., Roth, A. and Simonovic, M.  (2009). STRING 8—a global view on proteins and their functional interactions in 630 organisms. Nucleic acids research, 37(suppl 1): D412-D416. Keating, A., Davoren, P., Smith, T., Ross, R. and Cairns, M. (2007). Bovine κ-casein gene promoter haplotypes with potential implications for milk protein expression. Journal of dairy science. 90(9): 4092-4099.
Kishore, A., Mukesh, M., Sobti, R.C., Mishra, B.P. and Sodhi, M. (2013). Variations in the regulatory region of alpha s1-casein milk protein gene among tropically adapted Indian native (Bos Indicus) cattle. ISRN biotechnology . 1-10.
 Le, T.D., Liu, L., Zhang, J., Liu, B. and Li, J. (2015). From miRNA regulation to miRNA–TF co-regulation: computational approaches and challenges. Briefings in bioinformatics,16(3): 475-496.
Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lu, L., and Law, M. )2012(. Comparison of next-generation sequencing systems. BioMed Research International, 2012. 1-11.
 Lupoli, B., Johansson, B., Uvnas-Moberg, K. and Svennersten-Sjaunja, K. (2001). Effect of suckling on the release of oxytocin, prolactin, cortisol, gastrin, cholecystokinin, somatostatin and insulin in dairy cows and their calves. Journal of Dairy Research. 68(02): 175-187.
Mazière, C., Morlière, P., Massy, Z., Kamel, S., Louandre, C., Conte, M.A. and Mazière, J.C. (2005). Oxidized low-density lipoprotein elicits an intracellular calcium rise and increases the binding activity of the transcription factor NFAT. Free Radical Biology and Medicine. 38(4): 472-480.
Mellenberger, R., Bauman, D. and Nelson, D. (1973). Metabolic adaptations during lactogenesis. Fatty acid and lactose synthesis in cow mammary tissue. Biochemical Journal. 136(3): 741-748.
Najafpanah, M.J., Sadeghi, M., and Bakhtiarizadeh, M.R. )2013(. Reference genes selection for quantitative real-time PCR using RankAggreg method in different tissues of Capra hircus. PloS one; 8 (12): e83041.
Yamada, M., Murakami, K., Wallingford, J. C. and Yuki, Y. (2002). Identification of low‐abundance proteins of bovine colostral and mature milk using two‐dimensional electrophoresis followed by microsequencing and mass spectrometry. Electrophoresis. 23(7‐8): 1153-1160.
Yu, F., Shi, Y., Wang, J., Li, J., Fan, D. and Ai, W. (2013). Deficiency of Kruppel‐like factor KLF4 in mammary tumor cells inhibits tumor growth and pulmonary metastasis and is accompanied by compromised recruitment of myeloid‐derived suppressor cells. International journal of cancer. 133(12): 2872-2883.
Zhang, L., Boeren, S., Hageman, J.A., van Hooijdonk, T., Vervoort, J. and Hettinga, K. (2015). Perspective on calf and mammary gland development through changes in the bovine milk proteome over a complete lactation.Journal of dairy science. 98(8): 5362-5373.
Zhao, F., McParland, S., Kearney, F. , Du, L. and Berry, D. P. (2015). Detection of selection signatures in dairy and beef cattle using high-density genomic information. Genetics Selection Evolution. 47(1): 1.
Ntambi, J.M. and Miyazaki, M. (2003). Recent insights into stearoyl-CoA desaturase-1. Current opinion in lipidology, 14(3): 255-261.
 Ogg, S.L., Weldon, A.K., Dobbie, L., Smith, A.J. and Mather, I.H. (2004). Expression of butyrophilin (Btn1a1) in lactating mammary gland is essential for the regulated secretion of milk–lipid droplets. Proceedings of the National Academy of Sciences of the United States of America, 101(27): 10084-10089.
Ogorevc, J., Kunej, T., Razpet, A. and Dovc, P. (2009). Database of cattle candidate genes and genetic markers for milk production and mastitis. Animal genetics. 40(6): 832-851.
Oliver, C.H., Khaled, W.T., Frend, H., Nichols, J. and Watson, C. J.  (2012). The Stat6-regulated KRAB domain zinc finger protein Zfp157 regulates the balance of lineages in mammary glands and compensates for loss of Gata-3. Genes & development. 26(10):1086-1097.
Pallesen, L.T., Pedersen, L.R.L., Petersen, T.E. and Rasmussen, J.T. (2007). Characterization of carbohydrate structures of bovine MUC15 and distribution of the mucin in bovine milk. Journal of dairy science. 90(7): 3143-3152.
Prinzenberg, E.M.,  Weimann, C., Brandt, H., Bennewitz, J. , Kalm, E., Schwerin, M. and Erhardt, G. (2003). Polymorphism of the bovine CSN1S1 promoter: linkage mapping, intragenic haplotypes, and effects on milk production traits. Journal of dairy science. 86(8): 2696-2705.
Rachagani, S. and Gupta, I.D. (2008). Bovine kappa-casein gene polymorphism and its association with milk production traits. Genetics and Molecular Biology. 31(4): 893-897.
Rasero, R., Sacchi, P., Rosati, S., Cauvin, E. and Maione, S. (2002). Molecular analysis of the length polymorphic MUC1 gene in cattle. Journal of Animal Breeding and Genetics. 119(5): 342-349.
Rinchev-Alarnold, A., Belair, L. and Djiane, J. (2002). Developmental expression of pIgR gene in sheep mammary gland and hormonal regulation. Journal of dairy research. 69(01): 13-26.
Sakurai, A., Sakai, Y. and Yatabe, Y. (2011). Thyroid transcription factor‐1 expression in rare cases of mammary ductal carcinoma. Histopathology. 59(1): 145-148.
Schennink, A., Stoop, W., Visker, M.W.,  Heck, J., Bovenhuis, H., Van Der Poel, J., Van Valenberg, H. and Van Arendonk, J. (2007). DGAT1 underlies large genetic variation in milk‐fat composition of dairy cows. Animal genetics. 38(5): 467-473.
Sigl, T., H. Meyer and S. Wiedemann (2012). "Gene expression of six major milk proteins in primary bovine mammary epithelial cells isolated from milk during the first twenty weeks of lactation." Czech J Anim Sci 57: 469-480.
Sordillo, L.M. and K.L. Streicher (2002). "Mammary gland immunity and mastitis susceptibility." Journal of mammary gland biology and neoplasia 7(2): 135-146.
Sorensen, M., Nørgaard, J.V., Theil, P.K., Vestergaard, M. and Sejrsen, K. (2006). Cell turnover and activity in mammary tissue during lactation and the dry period in dairy cows. Journal of dairy science. 89(12): 4632-4639.
Spelman, R., Ford, C., McElhinney, P., G. and Snell, R. (2002). Characterization of the DGAT1 gene in the New Zealand dairy population. Journal of Dairy Science. 85(12): 3514-3517.
Spitsberg, V.L., Matitashvili, E. and Gorewit, R. C. (1995). Association and Coexpression of Fatty‐Acid‐Binding Protein and Glycoprotein CD36 in the Bovine Mammary Gland. European Journal of Biochemistry. 230(3): 872-878.
Suchyta, S.P., Sipkovsky, S., Halgren, R.G., Kruska, R., Elftman, M., Weber-Nielsen, M., Vandehaar, M.J., Xiao, L.,
Twigger, A. J., Hodgetts, S., Filgueira, L., Hartmann, P. E.and Hassiotou, F. (2013). From Breast Milk to Brains The Potential of Stem Cells in Human Milk. Journal of Human Lactation. 29(2): 136-139.
Wang, M., Moisá, S., Khan, M., Wang, J.,  Bu, D. and Loor, J. (2012). MicroRNA expression patterns in the bovine mammary gland are affected by stage of lactation. Journal of dairy science. 95(11): 6529-6535.
Animal Sciences Journal
Volume 30, Issue 115
September 2017
Pages 193-205

Files

Share

How to cite

Statistics