J Breast Cancer.  2015 Sep;18(3):235-241. 10.4048/jbc.2015.18.3.235.

Expression Patterns of Circular RNAs from Primary Kinase Transcripts in the Mammary Glands of Lactating Rats

• Zhang C
• Wu H
• Wang Y
• Zhao Y
• Fang X
• Chen C
• Chen H

• KMID: 2407570
• DOI: http://doi.org/10.4048/jbc.2015.18.3.235

Abstract

PURPOSE
Circular RNAs (circRNAs), a novel class of RNAs, perform important functions in biological processes. However, the role of circRNAs in the mammary gland remains unknown. The present study is aimed at identifying and characterizing the circRNAs expressed in the mammary gland of lactating rats.
METHODS
Deep sequencing of RNase R-enriched rat lactating mammary gland samples was performed and circRNAs were predicted using a previously reported computational pipeline. Gene ontology terms of circRNA-producing genes were also analyzed.
RESULTS
A total of 6,824 and 4,523 circRNAs were identified from rat mammary glands at two different lactation stages. Numerous circRNAs were specifically expressed at different lactation stages, and only 1,314 circRNAs were detected at both lactation stages. The majority of the candidate circRNAs map to noncoding intronic and intergenic regions. The results demonstrate a circular preference or specificity of some genes. DAVID analysis revealed an enrichment of protein kinases and related proteins among the set of genes encoding circRNAs. Interestingly, four protein-coding genes (Rev3l, IGSF11, MAML2, and LPP) that also transcribe high levels of circRNAs have been reported to be involved in cancer.
CONCLUSION
Our findings provide the basis for comparison between breast cancer profiles and for selecting representative circRNA candidates for future functional characterization in breast development and breast cancer.

Keyword

Circular RNA; Lactation; Mammary gland; Untranslated RNA

MeSH Terms

Animals
Biological Processes
Breast
Breast Neoplasms
DNA, Intergenic
Female
Gene Ontology
High-Throughput Nucleotide Sequencing
Introns
Lactation
Mammary Glands, Human*
Phosphotransferases*
Protein Kinases
Rats*
Ribonucleases
RNA*
RNA, Untranslated
Sensitivity and Specificity
DNA, Intergenic
Phosphotransferases
Protein Kinases
RNA
RNA, Untranslated
Ribonucleases

Figure

• 

  Figure 1 The distribution of circular RNAs in the genome. (A) Rat mammary gland library at day 1 postpartum. (B) Rat mammary gland library at day 7 postpartum. CDS=coding sequences.

• 

  Figure 2 Quantitative regulation of circular to linear isoform. No genome-wide trend between circular expression and linear transcript expression as measured by log PolyA reads per kilobase of exon model per million mapped reads (RPKM). Y axis=RPKM for circular RNA; X axis=log PolyA RPKM of linear isoform.

Reference

1. Patil VS, Zhou R, Rana TM. Gene regulation by non-coding RNAs. Crit Rev Biochem Mol Biol. 2014; 49:16–32.

2. Piao HL, Ma L. Non-coding RNAs as regulators of mammary development and breast cancer. J Mammary Gland Biol Neoplasia. 2012; 17:33–42.

3. Hsu MT, Coca-Prados M. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature. 1979; 280:339–340.

4. Hansen TB, Wiklund ED, Bramsen JB, Villadsen SB, Statham AL, Clark SJ, et al. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J. 2011; 30:4414–4422.

5. Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013; 495:333–338.

6. Kong X, Li G, Yuan Y, He Y, Wu X, Zhang W, et al. MicroRNA-7 inhibits epithelial-to-mesenchymal transition and metastasis of breast cancer cells via targeting FAK expression. PLoS One. 2012; 7:e41523.

7. Yu N, Huangyang P, Yang X, Han X, Yan R, Jia H, et al. microRNA-7 suppresses the invasive potential of breast cancer cells and sensitizes cells to DNA damages by targeting histone methyltransferase SET8. J Biol Chem. 2013; 288:19633–19642.

8. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013; 495:384–388.

9. Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One. 2012; 7:e30733.

10. Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. PLoS Genet. 2013; 9:e1003777.

11. Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu J, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA. 2013; 19:141–157.

12. Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 2014; 15:409.

13. Gartner LM, Morton J, Lawrence RA, Naylor AJ, O'Hare D, Schanler RJ, et al. Breastfeeding and the use of human milk. Pediatrics. 2005; 115:496–506.

14. Kotsopoulos J, Lubinski J, Salmena L, Lynch HT, Kim-Sing C, Foulkes WD, et al. Breastfeeding and the risk of breast cancer in BRCA1 and BRCA2 mutation carriers. Breast Cancer Res. 2012; 14:R42.

15. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9:357–359.

16. St Laurent G, Shtokalo D, Tackett MR, Yang Z, Eremina T, Wahlestedt C, et al. Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics. 2012; 13:504.

17. Clark DP. Molecular Biology: Academic Cell Update. Burlington: Academic Press/Elsevier;2010.

18. Schenten D, Kracker S, Esposito G, Franco S, Klein U, Murphy M, et al. Pol zeta ablation in B cells impairs the germinal center reaction, class switch recombination, DNA break repair, and genome stability. J Exp Med. 2009; 206:477–490.

19. Lange SS, Bedford E, Reh S, Wittschieben JP, Carbajal S, Kusewitt DF, et al. Dual role for mammalian DNA polymerase zeta in maintaining genome stability and proliferative responses. Proc Natl Acad Sci U S A. 2013; 110:E687–E696.

20. Wittschieben JP, Patil V, Glushets V, Robinson LJ, Kusewitt DF, Wood RD. Loss of DNA polymerase zeta enhances spontaneous tumorigenesis. Cancer Res. 2010; 70:2770–2778.

21. Varadi V, Bevier M, Grzybowska E, Johansson R, Enquist K, Henriksson R, et al. Genetic variation in genes encoding for polymerase zeta subunits associates with breast cancer risk, tumour characteristics and survival. Breast Cancer Res Treat. 2011; 129:235–245.

22. Watanabe T, Suda T, Tsunoda T, Uchida N, Ura K, Kato T, et al. Identification of immunoglobulin superfamily 11 (IGSF11) as a novel target for cancer immunotherapy of gastrointestinal and hepatocellular carcinomas. Cancer Sci. 2005; 96:498–506.

23. Köchert K, Ullrich K, Kreher S, Aster JC, Kitagawa M, Jöhrens K, et al. High-level expression of Mastermind-like 2 contributes to aberrant activation of the NOTCH signaling pathway in human lymphomas. Oncogene. 2011; 30:1831–1840.

24. Grunewald TG, Pasedag SM, Butt E. Cell adhesion and transcriptional activity: defining the role of the novel protooncogene LPP. Transl Oncol. 2009; 2:107–116.

25. Ngan E, Northey JJ, Brown CM, Ursini-Siegel J, Siegel PM. A complex containing LPP and alpha-actinin mediates TGFbeta-induced migration and invasion of ErbB2-expressing breast cancer cells. J Cell Sci. 2013; 126(Pt 9):1981–1991.

26. Crippa E, Lusa L, De Cecco L, Marchesi E, Calin GA, Radice P, et al. miR-342 regulates BRCA1 expression through modulation of ID4 in breast cancer. PLoS One. 2014; 9:e87039.

27. Korpal M, Lee ES, Hu G, Kang Y. The miR-200 family inhibits epithelial-mesenchymal transition and cancer cell migration by direct targeting of E-cadherin transcriptional repressors ZEB1 and ZEB2. J Biol Chem. 2008; 283:14910–14914.

28. Yu F, Yao H, Zhu P, Zhang X, Pan Q, Gong C, et al. let-7 regulates self renewal and tumorigenicity of breast cancer cells. Cell. 2007; 131:1109–1123.

29. Bachmayr-Heyda A, Reiner AT, Auer K, Sukhbaatar N, Aust S, Bachleitner-Hofmann T, et al. Correlation of circular RNA abundance with proliferation: exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. Sci Rep. 2015; 5:8057.

30. Li P, Chen S, Chen H, Mo X, Li T, Shao Y, et al. Using circular RNA as a novel type of biomarker in the screening of gastric cancer. Clin Chim Acta. 2015; 444:132–136.