Circular RNA of cattle casein genes are highly expressed in bovine mammary gland

Journal of Dairy Science

Volumn 99, Issue 6, 2016, Pages 4750-4760

  Zhang, ChunLei ^a   Wu, Hui ^a   Wang, YanHong ^a   Zhu, ShiQi ^a   Liu, JunQiang ^a   Fang, XingTang ^a   Chen, Hong ^a  

^a JIANGSU NORMAL UNIVERSITY   (China)

Author keywords

Casein biosynthesis; Circular RNA; Lactation

Indexed keywords

CASEIN; MESSENGER RNA; MICRORNA; RNA; RNA, CIRCULAR;

ANIMAL; BIOSYNTHESIS; BOVINE; CHEMISTRY; FEMALE; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; LACTATION; METABOLISM; MILK; PUERPERIUM; REPRODUCIBILITY; SEQUENCE ANALYSIS; STATISTICAL MODEL; UDDER;

ANIMALS; CASEINS; CATTLE; FEMALE; GENE EXPRESSION REGULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; LACTATION; LINEAR MODELS; MAMMARY GLANDS, ANIMAL; MICRORNAS; MILK; POSTPARTUM PERIOD; REPRODUCIBILITY OF RESULTS; RNA; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA;

EID: 84962076199     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2015-10381     Document Type: Article

References (45)

1. Agarwal V., Bell G.W., Nam J., Bartel D.P. Predicting effective microRNA target sites in mammalian mRNAs. eLife 2015, 4:e05005.
2. Bai W.L., Yin R.H., Jiang W.Q., Ajayi O.O., Zhao S.J., Luo G.B., Zhao Z.H., Imumorin I.G. Molecular analysis of αs1-, β-, αs2- and κ-casein transcripts reveals differential translational efficiency in yak lactating mammary gland. Livest. Sci. 2013, 152:74-78.
3. Benjamini Y., Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 2001, 29:1165-1188.
4. Bevilacqua C., Helbling J.C., Miranda G., Martin P. Translational efficiency of casein transcripts in the mammary tissue of lactating ruminants. Reprod. Nutr. Dev. 2006, 46:567-578.
5. Bian Y., Lei Y., Wang C., Wang J., Wang L., Liu L., Liu L., Gao X., Li Q. Epigenetic regulation of miR-29s affects the lactation activity of dairy cow mammary epithelial cells. J. Cell. Physiol. 2015, 230:2152-2163.
6. Bionaz M., Loor J.J. Identification of reference genes for quantitative real-time PCR in the bovine mammary gland during the lactation cycle. Physiol. Genomics 2007, 29:312-319.
7. Cocquerelle C., Mascrez B., Hétuin D., Bailleul B. Mis-splicing yields circular RNA molecules. FASEB J. 1993, 7:155-160.
8. Conn S.J., Pillman K.A., Toubia J., Conn V.M., Salmanidis M., Phillips C.A., Roslan S., Schreiber A.W., Gregory P.A., Goodall G.J. The RNA binding protein quaking regulates formation of circRNAs. Cell 2015, 160:1125-1134.
9. Cosenza G., Pauciullo A., Coletta A., DiFrancia A., Feligini M., Gallo D., DiBerardino D., Ramunno L. Short communication: Translational efficiency of casein transcripts in Mediterranean river buffalo. J. Dairy Sci. 2011, 94:5691-5694.
10. DeKruif, C. G., and C. Holt. 2003. Casein micelle structure, functions and interactions. Pages 233-276 in Advanced Dairy Chemistry: 1. Proteins, part A. P. F. Fox and P. L. H. McSweeney, ed. Kluwer Academic/Plenum Publishers, New York, NY.
11. Djuranovic S., Nahvi A., Green R. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 2012, 336:237-240.
12. Dubin R.A., Kazmi M.A., Ostrer H. Inverted repeats are necessary for circularization of the mouse testis Sry transcript. Gene 1995, 167:245-248.
13. Elzoghby A.O., AboEl-Fotoh W.S., Elgindy N.A. Casein based formulations as promising controlled release drug delivery systems. J. Control. Release 2011, 153:206-216.
14. Fan X., Zhang X., Wu X., Guo H., Hu Y., Tang F., Huang Y. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 2015, 16:148.
15. Gao Y., Wang J., Zhao F. CIRI: An efficient and unbiased algorithm for de novo circular RNA identification. Genome Biol. 2015, 16:4.
16. Hansen T.B., Jensen T.I., Clausen B.H., Bramsen J.B., Finsen B., Damgaard C.K., Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature 2013, 495:384-388.
17. Hartmann R., Meisel H. Food-derived peptides with biological activity: From research to food applications. Curr. Opin. Biotechnol. 2007, 18:163-169.
18. Huang D.W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
19. Ivanov A., Memczak S., Wyler E., Torti F., Porath H.T., Orejuela M.R., Piechotta M., Levanon E.Y., Landthaler M., Dieterich C., Rajewsky N. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals. Cell Reports 2015, 10:170-177.
20. Jabed A., Wagner S., McCracken J., Wells D.N., Laible G. Targeted microRNA expression in dairy cattle directs production of β-lactoglobulin-free, high-casein milk. Proc. Natl. Acad. Sci. USA 2012, 109:16811-16816.
21. Jeck W.R., Sorrentino J.A., Wang K., Slevin M.K., Burd C.E., Liu J., Marzluff W.F., Sharpless N.E. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 2013, 19:141-157.
22. Jin W., Ibeagha-Awemu E.M., Liang G., Beaudoin F., Zhao X., Guan L.L. Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles. BMC Genomics 2014, 15:181.
23. Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R., Salzberg S.L. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14:R36.
24. Kitts D.D., Weiler K. Bioactive proteins and peptides from food sources. Applications of bioprocesses used in isolation and recovery. Curr. Pharm. Des. 2003, 9:1309-1323.
25. Lasda E., Parker R. Circular RNAs: Diversity of form and function. RNA 2014, 20:1829-1842.
26. Li F., Zhang L., Li W., Deng J., Zheng J., An M., Lu J., Zhou Y. Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/β-catenin pathway. Oncotarget 2015, 6:6001-6013. a.
27. Li Z., Huang C., Bao C., Chen L., Lin M., Wang X., Zhong G., Yu B., Hu W., Dai L., Zhu P., Chang Z., Wu Q., Zhao Y., Jia Y., Xu P., Liu H., Shan G. Exon-intron circular RNAs regulate transcription in the nucleus. Nat. Struct. Mol. Biol. 2015, 22:256-264. b.
28. Liang D., Wilusz J.E. Short intronic repeat sequences facilitate circular RNA production. Genes Dev. 2014, 28:2233-2247.
29. Memczak S., Jens M., Elefsinioti A., Torti F., Krueger J., Rybak A., Maier L., Mackowiak S.D., Gregersen L.H., Munschauer M., Loewer A., Ziebold U., Landthaler M., Kocks C., leNoble F., Rajewsky N. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013, 495:333-338.
30. Pasman Z., Been M.D., Garcia-Blanco M.A. Exon circularization in mammalian nuclear extracts. RNA 1996, 2:603-610.
31. Pellegrino L., Masotti F., Cattaneo S., Hogenboom J.A., Noni I. Nutritional quality of milk proteins. Advanced Dairy Chemistry. Vol. 1A: Proteins: Basic Aspects 2013, 515-538. Springer, New York, NY. 4th. P.L.H. McSweeney, P.F. Fox (Eds.).
32. Rhoads R.E., Grudzien-Nogalska E. Translational regulation of milk protein synthesis at secretory activation. J. Mammary Gland Biol. Neoplasia 2007, 12:283-292.
33. Ricci-Cabello I., Herrera M.O., Artacho R. Possible role of milk-derived bioactive peptides in the treatment and prevention of metabolic syndrome. Nutr. Rev. 2012, 70:241-255.
34. Robinson J.T., Thorvaldsdottir H., Winckler W., Guttman M., Lander E.S., Getz G. Integrative genomics viewer. Nat. Biotechnol. 2011, 29:24-26.
35. Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
36. Rybak-Wolf A., Stottmeister C., Glažar P., Jens M., Pino N., Giusti S., Hanan M., Behm M., Bartok O., Ashwal-Fluss R., Herzog M., Schreyer L., Papavasileiou P., Ivanov A., Öhman M., Refojo D., Kadener S., Rajewsky N. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol. Cell 2015, 58:870-885.
37. Salzman J., Chen R.E., Olsen M.N., Wang P.L., Brown P.O. Cell-type specific features of circular RNA expression. PLoS Genet. 2013, 9:e1003777.
38. Sanger H.L., Klotz G., Riesner D., Gross H.J., Kleinschmidt A.K. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc. Natl. Acad. Sci. USA 1976, 73:3852-3856.
39. Schaafsma G. The protein digestibility-corrected amino acid score. J. Nutr. 2000, 130:1865S-1867S.
40. Taulli R., Loretelli C., Pandolfi P.P. From pseudo-ceRNAs to circ-ceRNAs: A tale of cross-talk and competition. Nat. Struct. Mol. Biol. 2013, 20:541-543.
41. Trapnell C., Williams B.A., Pertea G., Mortazavi A., Kwan G., van Baren M.J. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 2010, 28:511-515.
42. Westholm J.O., Miura P., Olson S., Shenker S., Joseph B., Sanfilippo P., Celniker S.E., Graveley B.R., Lai E.C. Genome-wide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. Cell Reports 2014, 9:1966-1980.
43. You X., Vlatkovic I., Babic A., Will T., Epstein I., Tushev G., Akbalik G., Wang M., Glock C., Quedenau C., Wang X., Hou J., Liu H., Sun W., Sambandan S., Chen T., Schuman E.M., Chen W. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat. Neurosci. 2015, 18:603-610.
44. Zhang X.O., Wang H.B., Zhang Y., Lu X., Chen L.L., Yang L. Complementary sequence-mediated exon circularization. Cell 2014, 159:134-147.
45. Zhang Y., Zhang X.O., Chen T., Xiang J.F., Yin Q.F., Xing Y.H., Zhu S., Yang L., Chen L.L. Circular intronic long noncoding RNAs. Mol. Cell 2013, 51:792-806.