Identification of microRNAs in corpus luteum of pregnancy in buffalo (Bubalus bubalis) by deep sequencing

Document Type : Short paper

Authors

1 Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana-125001, India

2 Southern Regional Research Station, ICAR-Central Sheep and Wool Research Institute, Tamilnadu-624103, India

3 Animal Genetics and Breeding Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana-125001, India

Abstract

This study was aimed to identify miRNAs of corpus luteum (CL) in buffaloes during pregnancy. For this study, CL (n=2) were collected from gravid uteri of buffalo and RNA was isolated. Following this, the purity and integrity of RNA was checked and used for deep sequencing using Illumina Hiseq 2500 platform. The reads’ quality was checked prior to in silico analyses viz. identification of conserved, novel and target of miRNAs. In this study, out of identified miRNAs (3018), 3013 were known and 5 were novel miRNAs on alignment with reference genomes. In addition, prediction of putative target genes for identified abundant miRNAs revealed several genes viz. HOX, KLF4, NCOR2, CDKN2Z, MAPK7, COX2, PPARA, PTEN, ASS3A, ELK1, CASP3, BCL211, MCL1, CCND2, Cyclin A2 and CDC25A during early pregnancy in buffalo. These predicted target genes have been associated with various cellular house-keeping processes including apoptosis. In conclusion, this study reports the identification of conserved and novel microRNAs (miRNAs) in CL during pregnancy in buffalo by deep sequencing.

Keywords

References

Betel, D; Wilson, M; Gabow, A; Marks, DS and Sander, C (2008). The microRNA.org resource: targets and expression. Nucleic Acids Res., 36: D149-D153.
Blanchette, M; Kent, WJ; Riemer, C; Elnitski, L; Smit, AF; Roskin, KM; Baertsch, R; Rosenbloom, K; Clawson, H; Green, ED; Haussler, D and Miller, W (2004). Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14: 708-715.
Campanile, G; Di Palo, R; Neglia, G; Vecchio, D; Gasparrini, B; Prandi, A; Galiero, G and D’Occhio, MJ (2007). Corpus luteum function and embryonic mortality in buffaloes treated with a GnRH agonist; hCG and progesterone. Theriogenology. 67: 1393-1398.
Dillies, MA; Rau, A; Aubert, J; Hennequet-Antier, C; Jeanmougin, M; Servant, N; Keime, C; Marot, G; Castel, D; Estelle, J; Guernec, G; Jagla, B; Jouneau, L; Laloë, D; Le Gall, C; Schaëffer, B; Le Crom, S; Guedj, M and Jaffrézic, F (2013). A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform., 14: 671-683.
Friedländer, MR; Mackowiak, SD; Li, N; Chen, W and Rajewsky, N (2012). miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res., 40: 37-52.
Hossain, MM; Sohel, MMH; Schellander, K and Tesfaye, D (2012). Characterization and importance of microRNAs in mammalian gonadal functions. Cell Tissue Res., 349: 679-690.
Hsu, SD; Tseng, YT; Shrestha, S; Lin, YL; Khaleel, A; Chou, CH; Chu, CF; Huang, HY; Lin, CM; Ho, SY; Jian, TY; Lin, FM; Chang, TH; Weng, SL; Liao, KW; Liao, IE; Liu, CC and Huang, HD (2013). miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res., 42:D78-D85. http://www.ansci.wisc.edu/jjp1/ansci_repro/ lab/female_anatomy/crown_rump_calculators.htm. Website visited on 20th June 2015.
Kozomara, A and Griffiths-Jones, S (2014). MiRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res., 42: D68-D73.
Langmead, B; Trapnell, C; Pop, M and Salzberg, SL (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10: R25.
Maalouf, SW; Liu, WS; Albert, I and Pate, JL (2014). Regulating life or death: potential role of microRNA in rescue of the corpus luteum. Mol. Cell Endocrinol., 398: 78-88.
Martin, M (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads EMB Net. Journal 17.1 http://dx.doi.org/10.14806/ej.17.1.200.
Niswender, GD; Juengel, JL; Silva, PJ; Rollyson, MK and McIntush, EW (2000). Mechanisms controlling the function and life span of the corpus luteum. Physiol. Rev., 80: 1-29.
Orom, UA; Nielsen, FC and Lund, AH (2008). MicroRNA-10a binds the 5’UTR of ribosomal protein mRNAs and enhances their translation. Mol. Cell., 30: 460-471.
Portt, L; Norman, G; Clapp, C; Greenwood, M and Greenwood, MT (2011). Anti-apoptosis and cell survival: a review. Biochim. Biophys. Acta., 1813: 238-259.

Files

Share

How to cite

Statistics