Article history: Received: 07-07-2017, Accepted: 24-08-2017, Published online: 25-09-2017
Corresponding author: A. Jerome
E-mail: firstname.lastname@example.orgCitation: Jerome A, Thirumaran SMK, Kala SN (2017) Repertoire of noncoding RNAs in corpus luteum of early pregnancy in buffalo (Bubalus bubalis), Veterinary World, 10(9): 1129-1134.
Aim: The present study was designed to identify other noncoding RNAs (ncRNAs) in the corpus luteum (CL) during early pregnancy in buffalo.
Materials and Methods: For this study, CL (n=2) from two buffalo gravid uteri, obtained from the slaughter house, was transported to laboratory after snap freezing in liquid nitrogen (-196°C). The stage of pregnancy was determined by measuring the crown-rump region of the fetus. This was followed by isolation of RNA and deep sequencing. Post-deep sequencing, the obtained reads were checked and aligned against various ncRNA databases (GtRNA, RFAM, and deep guide). Various parameters, namely, frequency of specific ncRNAs, length, mismatch, and genomic location target in several model species were deciphered.
Results: Frequency of piwi-interacting RNAs (piwi-RNAs), having target location in rodents and human genomes, were significantly higher compared to other piwi-RNAs and ncRNAs. Ribosomal RNAs (rRNAs) deduced had nucleotides (nts) ranging from 17 to 50 nts, but the occurrence of small length rRNAs was more than lengthier fragments. The target on 16S rRNA species confirms the conservation of 16S rRNA across species. With respect to transfer RNA (tRNA), the abundantly occurring tRNAs were unique with no duplication. Small nucleolar RNAs (snoRNAs), identified in this study, showed a strong tendency for coding box C/D snoRNAs in comparison to H/ACA snoRNAs. Regulatory and evolutionary implications of these identified ncRNAs are yet to be delineated in many species, including buffaloes.
Conclusion: This is the first report of identification of other ncRNAs in CL of early pregnancy in buffalo.
Keywords: buffalo, corpus luteum, noncoding RNA, pregnancy.
1. Niswender, G.D., Juengel, J.L., Silva, P.J., Rollyson, M.K. and McIintush, E.W. (2000) Mechanisms controlling the function and life span of the corpus luteum. Physiol. Rev., 80: 1-29. [PubMed]
2. Atli, M.O., Bender, R.W., Mehta, V., Bastos, M.R., Luo, W., Vezina, C.M. and Wiltbank, M.C. (2012) Patterns of gene expression in the bovine corpus luteum following repeated intrauterine infusions of low doses of prostaglandin F2 alpha. Biol. Reprod., 86: 130. [Crossref] [PubMed] [PMC]
3. Campanile, G., Neglia, G., Gasparrini, B., Galiero, G., Prandi, A., Di Palo, R., D'Occhio, M.J. and Zicarelli, L. (2005) Embryonic mortality in buffaloes synchronized and mated by AI during the seasonal decline in reproductive function. Theriogenology, 63: 2334-2340. [Crossref] [PubMed]
4. Maalouf, S.W., Liu, S.W., Albert, I. and Pate, J.L. (2014) Regulating life or death: Potential role of microRNA in rescue of the corpus luteum. Mol. Cell. Endocrinol., 398: 78-88. [Crossref] [PubMed]
8. Wahid, F., Khan, T., Hwang, K.H. and Kim, Y.Y. (2009) Piwi-interacting RNAs (piRNAs) in animals: The story so far. African J. Biotech., 8(17): 4002-4006.
10. Kowalczykiewicz, D., Pawlak, P., Lechniak, D. and Wrzesinski, J. (2012) Altered expression of porcine piwi genes and piRNA during development. PLoS One, 7(8): e43816. [PubMed]
11. Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J., 17: 1. [PubMed]
12. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10: R25. [PubMed]
13. Kozomara, A. and Griffiths-Jones, S. (2011) MiRBase: Integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39: D152-D157. [PubMed]
14. Kozomara, A. and Griffiths-Jones, S. (2014) MiRBase: Annotating high con?dence microRNAs using deep sequencing data. Nucleic Acids Res., 42: D68-D73. [PubMed]
15. Chan, P.P. and Lowe, T.M. (2009) GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res.,37: D93-D97. [PubMed]
16. Lakshmi, S.S. and Agrawal, S. (2008) piRNABank: A web resource on classified and clustered piwi-interacting RNAs. Nucleic Acids Res., 36: D173-D177. [PubMed]
17. Nawrocki, E.P., Burge, S.W., Bateman, A., Daub, J., Eberhardt, R.Y., Eddy, S.R., Floden, E.W., Gardner, P.P., Jones, T.A., Tate, J. and Finn, R.D. (2014) Rfam 12.0: Updates to the RNA families database. Nucleic Acids Res., 10: 1093.
18. Yang, J.H., Shao, P., Zhou, H., Chen, Y.Q. and Qu, L.H. (2010) Deepbase: A database for deeply annotating and mining deep sequencing data. Nucleic Acids Res., 38 suppl 1: D123-D130. [PubMed]
20. Schultz, N., Hamra, F.K. and Garbers, D.L. (2003) A multitude of genes expressed solely in meiotic or post-meiotic spermatogenic cells offers a myriad of contraceptive targets. Proc. Natl. Acad. Sci. U S A., 100: 12201-12206. [Crossref] [PubMed] [PMC]
23. Brennecke, J., Aravin, A.A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R. and Hannon, G.J. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell, 128: 1089-1103. [Crossref] [PubMed]
24. Gunawardane, L.S., Saito, K., Nishida, K.M., Miyoshi, K., Kawamura, Y., Nagami, T., Siomi, H. and Siomi, M.C. (2007) A slicer-mediated mechanism for repeat-associated siRNA 51 end formation in Drosophila. Science, 315: 1587-1590. [Crossref] [PubMed]
26. Feng, L., Sheppard, K., Namgoong, S., Ambrogelly, A., Polycarpo, C., Randau, L., Tumbula-Hansen, D. and Soll, D. (2004) Aminoacyl tRNA synthesis by pre-translational amino acid modification. RNA Biol., 1: 16-20. [Crossref] [PubMed]
29. Huttenhofer, A., Brosius, J. and Bachellerie, J.P. (2002) RNomics, identification and function of small, non-messenger RNAs. Curr. Opin. Chem. Biol., 6: 835-843. [Crossref][Crossref] [PubMed]