Identification and Characterization of MicroRNA in the Dairy Goat (Capra Hircus) Mammary Gland by Solexa Deep-sequencing Technology

Overview

Journal Mol Biol Rep

Specialty Molecular Biology

Date 2012 Jul 6

PMID 22763736

Citations 40

Authors

Zhibin Ji

Guizhi Wang

Zhijing Xie

Chunlan Zhang

Jianmin Wang

Affiliations

Soon will be listed here.

Abstract

microRNAs (miRNAs) perform critical roles in various biological and metabolic processes by regulating gene expression at the post-transcriptional level. To investigate the functional roles of miRNAs in the lactating mammary gland of Capra hircus, a library was constructed from the lactating mammary glands of Laoshan dairy goats (C. hircus) during early lactation. The miRNA expression profiles were systematically screened, and miRNAs were identified and characterized using Solexa deep-sequencing technology and bioinformatics. As a result, a total of 18,031,615 clean reads were obtained representing 305,711 unique sRNAs. A total of 12,086,616 sRNAs representing 3,701 unique sRNAs matched the known Bos taurus miRNA precursors in miRBase 17.0, and 300 known miRNAs and 15 miRNA were discovered. In addition, 131 novel miRNAs sequences were also obtained, and 147,703 putative targets were predicted. GO and KEGG pathway analysis showed that the majority of targets were involved in cellular processes and metabolic pathways. The 290 known miRNAs, 14 miRNA and 38 novel miRNAs were validated by sequencing a second library that was constructed from the same tissues as the first library. Our study provided the first large-scale identification and characterization of miRNAs in the mammary gland tissue of the dairy goat. The results indicate that the regulation of miRNA-mediated gene expression occurs during early lactation in dairy goats. This study significantly enriches the C. hircus miRNA repertoire and provides a reference for the elucidation of complex miRNA-mediated regulatory networks for gene expression in the physiology and developmental progression of the lactating mammary gland.

Citing Articles

Hormonal regulation of miRNA during mammary gland development.

Confuorti C, Jaramillo M, Plante I Biol Open. 2024; 13(6).

PMID: 38712984 PMC: 11190577. DOI: 10.1242/bio.060308.

miR-497 Regulates through the Pathway to Participate in Fatty Acid Synthesis in Bovine Mammary Epithelial Cells.

Chu S, Yang Y, Nazar M, Chen Z, Yang Z Genes (Basel). 2023; 14(6).

PMID: 37372404 PMC: 10298674. DOI: 10.3390/genes14061224.

MicroRNAs in Ruminants and Their Potential Role in Nutrition and Physiology.

Ojo O, Kreuzer-Redmer S Vet Sci. 2023; 10(1).

PMID: 36669058 PMC: 9867202. DOI: 10.3390/vetsci10010057.

Identification and Characterization of MicroRNAs Involving in Initial Sex Differentiation of Gonads.

Li X, Lin S, Fan S, Huang X, Zhang Z, Qin Z Biology (Basel). 2022; 11(3).

PMID: 35336829 PMC: 8945268. DOI: 10.3390/biology11030456.

The Role of microRNAs in the Mammary Gland Development, Health, and Function of Cattle, Goats, and Sheep.

Dysin A, Barkova O, Pozovnikova M Noncoding RNA. 2021; 7(4).

PMID: 34940759 PMC: 8708473. DOI: 10.3390/ncrna7040078.

References

Pillai R, Bhattacharyya S, Filipowicz W . Repression of protein synthesis by miRNAs: how many mechanisms?. Trends Cell Biol. 2007; 17(3):118-26. DOI: 10.1016/j.tcb.2006.12.007. View

Song L, Tuan R . MicroRNAs and cell differentiation in mammalian development. Birth Defects Res C Embryo Today. 2006; 78(2):140-9. DOI: 10.1002/bdrc.20070. View

Ucar A, Vafaizadeh V, Jarry H, Fiedler J, Klemmt P, Thum T . miR-212 and miR-132 are required for epithelial stromal interactions necessary for mouse mammary gland development. Nat Genet. 2010; 42(12):1101-8. DOI: 10.1038/ng.709. View

Jones-Rhoades M, Bartel D . Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell. 2004; 14(6):787-99. DOI: 10.1016/j.molcel.2004.05.027. View

Tanaka T, Haneda S, Imakawa K, Sakai S, Nagaoka K . A microRNA, miR-101a, controls mammary gland development by regulating cyclooxygenase-2 expression. Differentiation. 2009; 77(2):181-7. DOI: 10.1016/j.diff.2008.10.001. View

Brennecke J, Stark A, Russell R, Cohen S . Principles of microRNA-target recognition. PLoS Biol. 2005; 3(3):e85. PMC: 1043860. DOI: 10.1371/journal.pbio.0030085. View

Stark A, Lin M, Kheradpour P, Pedersen J, Parts L, Carlson J . Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007; 450(7167):219-32. PMC: 2474711. DOI: 10.1038/nature06340. View

Kim K, Chadalapaka G, Lee S, Yamada D, Sastre-Garau X, Defossez P . Identification of oncogenic microRNA-17-92/ZBTB4/specificity protein axis in breast cancer. Oncogene. 2011; 31(8):1034-44. PMC: 3288192. DOI: 10.1038/onc.2011.296. View

Nakamoto M, Jin P, ODonnell W, Warren S . Physiological identification of human transcripts translationally regulated by a specific microRNA. Hum Mol Genet. 2005; 14(24):3813-21. DOI: 10.1093/hmg/ddi397. View

10.

Yousef M, Showe L, Showe M . A study of microRNAs in silico and in vivo: bioinformatics approaches to microRNA discovery and target identification. FEBS J. 2009; 276(8):2150-6. DOI: 10.1111/j.1742-4658.2009.06933.x. View

11.

John B, Enright A, Aravin A, Tuschl T, Sander C, Marks D . Human MicroRNA targets. PLoS Biol. 2004; 2(11):e363. PMC: 521178. DOI: 10.1371/journal.pbio.0020363. View

12.

Li G, Li Y, Li X, Ning X, Li M, Yang G . MicroRNA identity and abundance in developing swine adipose tissue as determined by Solexa sequencing. J Cell Biochem. 2011; 112(5):1318-28. DOI: 10.1002/jcb.23045. View

13.

Richert M, Schwertfeger K, Ryder J, Anderson S . An atlas of mouse mammary gland development. J Mammary Gland Biol Neoplasia. 2001; 5(2):227-41. DOI: 10.1023/a:1026499523505. View

14.

Zhao Y, Ransom J, Li A, Vedantham V, von Drehle M, Muth A . Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell. 2007; 129(2):303-17. DOI: 10.1016/j.cell.2007.03.030. View

15.

Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q . MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics. 2010; 11:148. PMC: 2838851. DOI: 10.1186/1471-2164-11-148. View

16.

Wang L, Liu H, Li D, Chen H . Identification and characterization of maize microRNAs involved in the very early stage of seed germination. BMC Genomics. 2011; 12:154. PMC: 3066126. DOI: 10.1186/1471-2164-12-154. View

17.

Georgantas 3rd R, Hildreth R, Morisot S, Alder J, Liu C, Heimfeld S . CD34+ hematopoietic stem-progenitor cell microRNA expression and function: a circuit diagram of differentiation control. Proc Natl Acad Sci U S A. 2007; 104(8):2750-5. PMC: 1796783. DOI: 10.1073/pnas.0610983104. View

18.

Stefani G, Slack F . Small non-coding RNAs in animal development. Nat Rev Mol Cell Biol. 2008; 9(3):219-30. DOI: 10.1038/nrm2347. View

19.

Huang J, Ju Z, Li Q, Hou Q, Wang C, Li J . Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int J Biol Sci. 2011; 7(7):1016-26. PMC: 3164151. DOI: 10.7150/ijbs.7.1016. View

20.

Pogue A, Cui J, Li Y, Zhao Y, Culicchia F, Lukiw W . Micro RNA-125b (miRNA-125b) function in astrogliosis and glial cell proliferation. Neurosci Lett. 2010; 476(1):18-22. DOI: 10.1016/j.neulet.2010.03.054. View