Characterization and comparative profiling of ovarian microRNAs during ovine anestrus and the breeding season
详细信息    查看全文
  • 作者：Ran Di (45)
    Jianning He (45)
    Shuhui Song (46)
    Dongmei Tian (46)
    Qiuyue Liu (45)
    Xiaojun Liang (47)
    Qing Ma (47)
    Min Sun (46)
    Jiandong Wang (47)
    Wenming Zhao (46)
    Guiling Cao (45)
    Jinxin Wang (45)
    Zhimin Yang (45)
    Ying Ge (45)
    Mingxing Chu (45)

    45. Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture     ; Institute of Animal Science ; Chinese Academy of Agricultural Sciences ; No. 2 ; Yuanmingyuan West Rd ; Beijing ; China
    46. Core Genomic Facility     ; Beijing Institute of Genomics ; Chinese Academy of Sciences ; Beijing ; China
    47. Research Center of Grass and Livestock     ; Ningxia Academy of Agriculture and Forestry Sciences ; Yinchuan ; Ningxia ; China
  • 关键词：Sheep ; Seasonal estrus ; Anestrus ; Ovary ; miRNA ; piRNA
  • 刊名：BMC Genomics
  • 出版年：2014
  • 出版时间：December 2014
  • 年：2014
  • 卷：15
  • 期：1
  • 全文大小：1,968 KB
  • 参考文献：1. Tu, YR (1989) Sheep and Goat Breeds in China: Shanghai Scientific & Technology Publishers.
    2. McBride, D, Carre, W, Sontakke, SD, Hogg, CO, Law, A, Donadeu, FX, Clinton, M (2012) Identification of miRNAs associated with the follicular-luteal transition in the ruminant ovary. Reproduct 144: pp. 221-233 CrossRef
    3. Ling, YH, Ren, CH, Guo, XF, Xu, LN, Huang, YF, Luo, JC, Zhang, YH, Zhang, XR, Zhang, ZJ (2014) Identification and characterization of microRNAs in the ovaries of multiple and uniparous goats (Capra hircus) during follicular phase. BMC Genomics 15: pp. 339 CrossRef
    4. Ji, Z, Wang, G, Xie, Z, Zhang, C, Wang, J (2012) Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology. Mol Biol Rep 39: pp. 9361-9371 CrossRef
    5. Wu, J, Zhu, H, Song, W, Li, M, Liu, C, Li, N, Tang, F, Mu, H, Liao, M, Li, X, Guan, W, Li, X, Hua, J (2014) Identification of conservative microRNAs in Saanen dairy goat testis through deep sequencing. Reprod Domest Anim 49: pp. 32-40 CrossRef
    6. Liu, Z, Xiao, H, Li, H, Zhao, Y, Lai, S, Yu, X, Cai, T, Du, C, Zhang, W, Li, J (2012) Identification of conserved and novel microRNAs in cashmere goat skin by deep sequencing. PLoS One 7: pp. e50001 CrossRef
    7. Yuan, C, Wang, X, Geng, R, He, X, Qu, L, Chen, Y (2013) Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing. BMC Genomics 14: pp. 511 CrossRef
    8. Zhang, XD, Zhang, YH, Ling, YH, Liu, Y, Cao, HG, Yin, ZJ, Ding, JP, Zhang, XR (2013) Characterization and differential expression of microRNAs in the ovaries of pregnant and non-pregnant goats (Capra hircus). BMC Genomics 14: pp. 157 CrossRef
    9. Zhang, S, Zhao, F, Wei, C, Sheng, X, Ren, H, Xu, L, Lu, J, Liu, J, Zhang, L, Du, L (2013) Identification and characterization of the miRNA transcriptome of Ovis aries. PLoS One 8: pp. e58905 CrossRef
    10. Otsuka, M, Zheng, M, Hayashi, M, Lee, JD, Yoshino, O, Lin, S, Han, J (2008) Impaired microRNA processing causes corpus luteum insufficiency and infertility in mice. J Clin Invest 118: pp. 1944-1954 CrossRef
    11. Yao, GD, Yin, MM, Lian, J, Tian, H, Liu, L, Li, X, Sun, F (2010) MicroRNA-224 is involved in transforming growth factor-beta-mediated mouse granulosa cell proliferation and granulosa cell function by targeting Smad4. Mol Endocrinol 24: pp. 540-551 CrossRef
    12. Lin, F, Li, R, Pan, ZX, Zhou, B, Yu, DB, Wang, XG, Ma, XS, Han, J, Shen, M, Liu, HL (2012) miR-26b promotes granulosa cell apoptosis by targeting ATM during follicular atresia in porcine ovary. PLoS One 7: pp. e38640 CrossRef
    13. Grivna, ST, Beyret, E, Wang, Z, Lin, H (2006) A novel class of small RNAs in mouse spermatogenic cells. Genes Dev 20: pp. 1709-1714 CrossRef
    14. Grivna, ST, Pyhtila, B, Lin, H (2006) MIWI associates with translational machinery and PIWI-interacting RNAs (piRNAs) in regulating spermatogenesis. Proc Natl Acad Sci U S A 103: pp. 13415-13420 CrossRef
    15. Lau, NC, Seto, AG, Kim, J, Kuramochi-Miyagawa, S, Nakano, T, Bartel, DP, Kingston, RE (2006) Characterization of the piRNA complex from rat testes. Science 313: pp. 363-367 CrossRef
    16. Malone, CD, Brennecke, J, Dus, M, Stark, A, McCombie, WR, Sachidanandam, R, Hannon, GJ (2009) Specialized piRNA pathways act in germline and somatic tissues of the drosophila ovary. Cell 137: pp. 522-535 CrossRef
    17. Tam, OH, Aravin, AA, Stein, P, Girard, A, Murchison, EP, Cheloufi, S, Hodges, E, Anger, M, Sachidanandam, R, Schultz, RM, Hannon, GJ (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453: pp. 534-538 CrossRef
    18. Watanabe, T, Totoki, Y, Toyoda, A, Kaneda, M, Kuramochi-Miyagawa, S, Obata, Y, Chiba, H, Kohara, Y, Kono, T, Nakano, T, Surani, MA, Sakaki, Y, Sasaki, H (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453: pp. 539-543 CrossRef
    19. Yang, CX, Du, ZQ, Wright, EC, Rothschild, MF, Prather, RS, Ross, JW (2012) Small RNA profile of the cumulus-oocyte complex and early embryos in the pig. Biol Reprod 87: pp. 117 CrossRef
    20. Li, CJ, Vagin, VV, Lee, SH, Xu, J, Ma, SM, Xi, HL, Seitz, H, Horwich, MD, Syrzycka, M, Honda, BM, Kittler, ELW, Zapp, ML, Klattenhoff, C, Schulz, N, Theurkauf, WE, Weng, ZP, Zamore, PD (2009) Collapse of germline piRNAs in the absence of argonaute3 reveals somatic piRNAs in flies. Cell 137: pp. 509-521 CrossRef
    21. Gerstl, MP, Hackl, M, Graf, AB, Borth, N, Grillari, J (2013) Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data. J Biotechnol 166: pp. 51-57 CrossRef
    22. Ding, X, Guan, H, Li, H (2013) Characterization of a piRNA binding protein Miwi in mouse oocytes. Theriogenol 79: pp. 610-615 CrossRef
    23. Hossain, MM, Ghanem, N, Hoelker, M, Rings, F, Phatsara, C, Tholen, E, Schellander, K, Tesfaye, D (2009) Identification and characterization of miRNAs expressed in the bovine ovary. BMC Genomics 10: pp. 443 CrossRef
    24. Huang, JM, Ju, ZH, Li, QL, Hou, QL, Wang, CF, Li, JB, Li, RL, Wang, LL, Sun, T, Hang, SQ, Gao, YD, Hou, MH, Zhong, JF (2011) Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int J Biol Sci 7: pp. 1016-1026 CrossRef
    25. Tripurani, SK, Xiao, CD, Salem, M, Yao, JB (2010) Cloning and analysis of fetal ovary microRNAs in cattle. Anim Reprod Sci 120: pp. 16-22 CrossRef
    26. Li, MZ, Liu, YK, Wang, T, Guan, JQ, Luo, ZG, Chen, HS, Wang, X, Chen, L, Ma, JD, Mu, ZP, Jiang, AA, Zhu, L, Lang, QL, Zhou, XC, Wang, JY, Zeng, WX, Li, N, Li, K, Gao, XL, Li, XW (2011) Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing. Int J Biol Sci 7: pp. 1045-1055 CrossRef
    27. Mishima, T, Takizawa, T, Luo, SS, Ishibashi, O, Kawahigashi, Y, Mizuguchi, Y, Ishikawa, T, Mori, M, Kanda, T, Goto, T, Takizawa, T (2008) MicroRNA (miRNA) cloning analysis reveals sex differences in miRNA expression profiles between adult mouse testis and ovary. Reproduct 136: pp. 811-822 CrossRef
    28. Ahn, HW, Morin, RD, Zhao, H, Harris, RA, Coarfa, C, Chen, ZJ, Milosavljevic, A, Marra, MA, Rajkovic, A (2010) MicroRNA transcriptome in the newborn mouse ovaries determined by massive parallel sequencing. Mol Hum Reprod 16: pp. 463-471 CrossRef
    29. Carletti, MZ, Fiedler, SD, Christenson, LK (2010) MicroRNA 21 blocks apoptosis in mouse periovulatory granulosa cells. Biol Reprod 83: pp. 286-295 CrossRef
    30. Zhang, JF, Ji, XW, Zhou, DD, Li, YQ, Lin, JK, Liu, JL, Luo, HS, Cui, S (2013) miR-143 is critical for the formation of primordial follicles in mice. Front Biosci-Landmark 18: pp. 588-597 CrossRef
    31. Yan, GJ, Zhang, LX, Fang, T, Zhang, Q, Wu, SG, Jiang, Y, Sun, HX, Hu, YL (2012) MicroRNA-145 suppresses mouse granulosa cell proliferation by targeting activin receptor IB. Febs Lett 586: pp. 3263-3270 CrossRef
    32. Jovanovic, VP, Sauer, CM, Shawber, CJ, Gomez, R, Wang, X, Sauer, MV, Kitajewski, J, Zimmermann, RC (2013) Intraovarian regulation of gonadotropin-dependent folliculogenesis depends on notch receptor signaling pathways not involving delta-like ligand 4 (Dll4). Reprod Biol Endocrin 11: pp. 43 CrossRef
    33. Trombly, DJ, Woodruff, TK, Mayo, KE (2009) Suppression of Notch signaling in the neonatal mouse ovary decreases primordial follicle formation. Endocrinol 150: pp. 1014-1024 CrossRef
    34. Vorontchikhina, MA, Zimmermann, RC, Shawber, CJ, Tang, HY, Kitajewski, J (2005) Unique patterns of Notch1, Notch4 and Jagged1 expression in ovarian vessels during folliculogenesis and corpus luteum formation. Gene Expr Patterns 5: pp. 701-709 CrossRef
    35. Craig, J, Zhu, H, Dyce, PW, Petrik, J, Li, J (2004) Leptin enhances oocyte nuclear and cytoplasmic maturation via the mitogen-activated protein kinase pathway. Endocrinol 145: pp. 5355-5363 CrossRef
    36. Ferrell, JE (1999) Xenopus oocyte maturation: new lessons from a good egg. Bioessays 21: pp. 833-842 CrossRef
    37. Carlsbecker, A, Lee, JY, Roberts, CJ, Dettmer, J, Lehesranta, S, Zhou, J, Lindgren, O, Moreno-Risueno, MA, Vaten, A, Thitamadee, S, Campilho, A, Sebastian, J, Bowman, JL, Helariutta, Y, Benfey, PN (2010) Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate. Nature 465: pp. 316-321 CrossRef
    38. Tian, T, Wang, Y, Wang, H, Zhu, Z, Xiao, Z (2010) Visualizing of the cellular uptake and intracellular trafficking of exosomes by live-cell microscopy. J Cell Biochem 111: pp. 488-496 CrossRef
    39. Kogure, T, Lin, WL, Yan, IK, Braconi, C, Patel, T (2011) Intercellular nanovesicle-mediated microRNA transfer: a mechanism of environmental modulation of hepatocellular cancer cell growth. Hepatology 54: pp. 1237-1248 CrossRef
    40. Mittelbrunn, M, Gutierrez-Vazquez, C, Villarroya-Beltri, C, Gonzalez, S, Sanchez-Cabo, F, Gonzalez, MA, Bernad, A, Sanchez-Madrid, F (2011) Unidirectional transfer of microRNA-loaded exosomes from T cells to antigen-presenting cells. Nat Commun 2: pp. 282 CrossRef
    41. Aucher, A, Rudnicka, D, Davis, DM (2013) MicroRNAs transfer from human macrophages to hepato-carcinoma cells and inhibit proliferation. J Immunol 191: pp. 6250-6260 CrossRef
    42. Karsch, FJ, Dahl, GE, Evans, NP, Manning, JM, Mayfield, KP, Moenter, SM, Foster, DL (1993) Seasonal changes in gonadotropin-releasing hormone secretion in the ewe: alteration in response to the negative feedback action of estradiol. Biol Reprod 49: pp. 1377-1383 CrossRef
    43. Barrell, GK, Moenter, SM, Caraty, A, Karsch, FJ (1992) Seasonal changes of gonadotropin-releasing hormone secretion in the ewe. Biol Reprod 46: pp. 1130-1135 CrossRef
    44. Sai Lakshmi, S, Agrawal, S (2008) piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucl Acid R 36: pp. D173-D177
    45. Houwing, S, Kamminga, LM, Berezikov, E, Cronembold, D, Girard, A, van den Elst, H, Filippov, DV, Blaser, H, Raz, E, Moens, CB, Plasterk, RH, Hannon, GJ, Draper, BW, Ketting, RF (2007) A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129: pp. 69-82 CrossRef
    46. Girard, A, Sachidanandam, R, Hannon, GJ, Carmell, MA (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442: pp. 199-202
    47. Lim, SL, Tsend-Ayush, E, Kortschak, RD, Jacob, R, Ricciardelli, C, Oehler, MK, Grutzner, F (2013) Conservation and expression of PIWI-Interacting RNA pathway genes in male and female adult gonad of amniotes. Biol Reprod 89: pp. 136 CrossRef
    48. Minakhina, S, Changela, N, Steward, R (2014) Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery. Development 141: pp. 259-268 CrossRef
    49. Yan, Z, Hu, HY, Jiang, X, Maierhofer, V, Neb, E, He, L, Hu, YH, Hu, H, Li, N, Chen, W, Khaitovich, P (2011) Widespread expression of piRNA-like molecules in somatic tissues. Nucl Acid R 39: pp. 6596-6607 CrossRef
    50. Liu, G, Lei, B, Li, Y, Tong, K, Ding, Y, Luo, L, Xia, X, Jiang, S, Deng, C, Xiong, Y, Li, F (2012) Discovery of potential piRNAs from next generation sequences of the sexually mature porcine testes. PLoS One 7: pp. e34770 CrossRef
    51. Campbell, BK, Gordon, BM, Scaramuzzi, RJ (1994) The effect of ovarian arterial infusion of transforming growth factor alpha on ovarian follicle populations and ovarian hormone secretion in ewes with an autotransplanted ovary. J Endocrinol 143: pp. 13-24 CrossRef
    52. McNeilly, JR, McNeilly, AS, Walton, JS, Cunningham, FJ (1976) Development and application of a heterologous radioimmunoassay for ovine follicle-stimulating hormone. J Endocrinol 70: pp. 69-79 CrossRef
    53. McNeilly, AS, Jonassen, JA, Fraser, HM (1986) Suppression of follicular development after chronic LHRH immunoneutralization in the ewe. J Reprod Fertil 76: pp. 481-490 CrossRef
    54. Djahanbakhch, O, Swanton, IA, Corrie, JE, McNeilly, AS (1981) Prediction of ovulation by progesterone. Lancet 2: pp. 1164-1165 CrossRef
    55. McNeilly, AS (1984) Changes in FSH and the pulsatile secretion of LH during the delay in oestrus induced by treatment of ewes with bovine follicular fluid. J Reprod Fertil 72: pp. 165-172 CrossRef
    56. Cumming, IA, Brown, JM, Goding, JR, Bryant, GD, Greenwood, FC (1972) Secretion of prolactin and luteinizing hormone at oestrus in the ewe. J Endocrinol 54: pp. 207-213 CrossRef
    57. Zhao, WM, Liu, WF, Tian, DM, Tang, BX, Wang, YQ, Yu, CX, Li, RJ, Ling, YC, Wu, JY, Song, SH, Hu, SN (2011) wapRNA: a web-based application for the processing of RNA sequences. Bioinformatics 27: pp. 3076-3077 CrossRef
    58. Friedlander, MR, Mackowiak, SD, Li, N, Chen, W, Rajewsky, N (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucl Acid R 40: pp. 37-52 CrossRef
    59. Robinson, MD, McCarthy, DJ, Smyth, GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: pp. 139-140 CrossRef
    60. Livak, KJ, Schmittgen, TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 25: pp. 402-408 CrossRef
    61. Langmead, B, Trapnell, C, Pop, M, Salzberg, SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: pp. R25 CrossRef
    62. Rosenkranz, D, Zischler, H (2012) proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics 13: pp. 5 CrossRef
  • 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
  • 出版者：BioMed Central
  • ISSN：1471-2164
文摘
Background Seasonal estrus is a critical limiting factor of animal fecundity, and it involves changes in both ovarian biology and hormone secretion in different seasons. Previous studies indicate that two classes of small RNAs (miRNAs and piRNAs) play important regulatory roles in ovarian biology. To understand the roles of small RNA-mediated post-transcriptional regulation in ovine seasonal estrus, the variation in expression patterns of ovarian small RNAs during anestrus and the breeding season were analyzed using Solexa sequencing technology. In addition, reproductive hormone levels were determined during ovine anestrus and the breeding season. Results A total of 483 miRNAs (including 97 known, 369 conserved and 17 predicated novel miRNAs), which belong to 183 different miRNA families, were identified in ovaries of Tan sheep and Small Tail Han (STH) sheep. Compared with the three stages of the breeding season, 25 shared significantly differentially expressed (including 19 up- and six down-regulated) miRNAs were identified in ovine anestrus. KEGG Pathway analysis revealed that the target genes for some of the differentially expressed miRNAs were involved in reproductive hormone related pathways (e.g. steroid biosynthesis, androgen and estrogen metabolism and GnRH signaling pathway) as well as follicular/luteal development related pathways. Moreover, the expression of the differentially expressed miRNAs and most of their target genes were negatively correlated in the above pathways. Furthermore, the levels of estrogen, progesterone and LH in ovine anestrus were significantly lower than those in the breeding season. Combining the results of pathway enrichment analysis, expression of target genes and hormone measurement, we suggest that these differentially expressed miRNAs in anestrus might participate in attenuation of ovarian activity by regulating the above pathways. Besides miRNAs, a large and unexpectedly diverse set of piRNAs were also identified. Conclusions The miRNA profiles of ovine ovaries in anestrus were presented for the first time. The identification and characterization of miRNAs that are differentially expressed between ovine anestrus and the breeding season will help understanding of the role of miRNAs in the regulation of seasonal estrus, and provides candidates for determining miRNAs which could be potentially used to regulate ovine seasonal estrus.
NGLC 2004-2010.National Geological Library of China All Rights Reserved.
Add:29 Xueyuan Rd,Haidian District,Beijing,PRC. Mail Add: 8324 mailbox 100083
For exchange or info please contact us via email.