RESEARCH PAPER
Evaluation of methods for the detection of low-abundant snoRNA-derived small RNAs in Saccharomyces cerevisiae
1
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
Submission date: 2016-01-26
Acceptance date: 2016-02-18
Publication date: 2016-04-20
BioTechnologia 2016;97(1):19-26
KEYWORDS
TOPICS
ABSTRACT
In recent years, there are a growing number of studies demonstrating the existence of small RNAs derived from snoRNAs (sdRNAs) in multiple eukaryotic organisms. Such RNAs have been initially observed in high throughput sequencing studies and assumed to be processed by miRNA machinery. Recently, we have identified sdRNAs that are associated with ribosomes in yeast Saccharomyces cerevisiae. Although sdRNAs were detectable in sequencing data, their low abundance hampered their detection by other methods. Here, we present the results of our survey for optimized experimental method for sdRNA detection. We have compared two extraction procedures of total RNA from S. cerevisiae : MasterPureTM kit and Trizol with two methods resulting in enrichment in small RNA fraction and MasterPureTM with selective isopropanol precipitation and bulk tRNA isolation methods. Also the sensitivity of three methods for sdRNA detection was verified: a northern blot using standard or LNA probes and stem-loop reverse transcription followed by PCR (SL-RT-PCR). Our results reveal that Trizol isolation method combined with SL-RT-PCR is the most effective in the detection of low-abundant sdRNAs.
REFERENCES (30)
1.
Brameier M., Herwig A., Reinhardt R., Walter L., Gruber J. (2011) Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucl. Acids Res. 39: 675-686.
2.
Cavaille J., Buiting K., Kiefmann M., Lalande M., Brannan C.I., Horsthemke B., Bachellerie J.P., Brosius J., Hüttenhofer A. (2000) Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl. Acad. Sci. USA 97: 14311-14316.
3.
Chen C., Ridzon D.A., Broomer A.J., Zhou Z., Lee D.H., Nguyen J.T., Barbisin M., Xu N.L., Mahuvakar V.R., Andersen M.R., Lao K.Q., Livak K.J., Guegler K.J. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucl. Acids Res. 33: e179.
4.
Ender C., Krek A., Friedländer M.R., Beitzinger M., Weinmann L., Chen W., Pfeffer S., Rajewsky N., Meister G. (2008) A human snoRNA with microRNA-like functions. Mol. Cell. 32: 519-528.
5.
Falaleeva M., Stamm S. (2013) Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs. Bioessays 35: 46-54.
6.
Hüttenhofer A., Kiefmann M., Meier-Ewert S., O'Brien J., Lehrach H., Bachellerie J.P., Brosius J. (2001) RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J. 20: 2943-2953.
7.
Hutzinger R., Feederle R., Mrazek J., Schiefermeier N., Balwierz P.J., Zavolan M., Polacek N., Delecluse H.J., Hüttenhofer A. (2009) Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathog. 5: e1000547.
8.
Houseley J., Tollervey D. (2008) The nuclear RNA surveillance machinery: the link between ncRNAs and genome structure in budding yeast? Biochim. Biophys. Acta 1779: 239-246.
9.
Jady B.E., Kiss T. (2000) Characterisation of the U83 and U84 small nucleolar RNAs: two novel 2N-O-ribose methylation guide RNAs that lack complementarities to ribosomal RNAs. Nucl. Acids Res. 28: 1348-1354.
10.
Kim Y.K., Yeo J., Kim B., Ha M., Kim V.N. (2012) Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol. Cell. 46: 893-895.
11.
Kishore S., Khanna A., Zhang Z., Hui J., Balwierz P.J., Stefan M., Beach C., Nicholls R.D., Zavolan M., Stamm S. (2010) The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum. Mol. Genet. 19: 1153-1164.
12.
Kishore S., Stamm S. (2006) The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311: 230-232.
13.
Krichevsky A.M., King K.S., Donahue C.P., Khrapko K., Kosik K.S. (2003) A microRNA array reveals extensive regulation of microRNAs during brain development. RNA 9: 1274-1281.
14.
Li W., Saraiya A.A., Wang C.C. (2011) Gene regulation in Giardia lambia involves a putative microRNA derived from a small nucleolar RNA. PLoS Negl. Trop. Dis. 5: e1338.
15.
Li Y., Kowdley K.V. (2012) Method for microRNA isolation from clinical serum samples. Anal. Biochem. 431: 69-75.
16.
Lim L.P., Glasner M.E., Yekta S., Burge C.B., Bartel D.P. (2003) Vertebrate microRNA genes. Science 299: 1540.
17.
Michel C.I., Holley C.L., Scruggs B.S., Sidhu R., Brookheart R.T., Listenberger L.L., Behlke M.A., Ory D.S., Schaffer J.E. (2011) Small nucleolar RNAs U32a, U33, and U35a are critical mediators of metabolic stress. Cell. Metab. 14: 33-44.
18.
Monier R., Stephenson M.L., Zamenick P.C. (1960) The preparation and some properties of a low molecular weight ribonucleic acid from baker's yeast. Biochim. Biophys. Acta 9: 1-8.
19.
Monleau M., Bonnel S., Gostan T., Blanchard D., Courgnaud V., Lecellier C.H. (2014) Comparison of different extraction techniques to profile microRNAs from human sera and peripheral blood mononuclear cells. BMC Genomics 15: 395.
20.
Pall G.S., Hamilton A.J. (2008) Improved northern blot method for enhanced detection of small RNA. Nat. Protoc. 3: 1077-1084.
21.
Pircher A., Bakowska-Zywicka K., Schneider L., Zywicki M., Polacek N. (2014) An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol. Cell. 54: 147-155.
22.
Podolska A., Kaczkowski B., Litman T., Fredholm M., Cirera S. (2011) How the RNA isolation method can affect micro- RNA microarray results. Acta Biochim. Pol. 58: 535-540.
23.
Saraiya A.A., Wang C.C. (2008) snoRNA, a novel precursor of microRNA in Giardia lamblia. PLoS Pathog. 4: e1000224.
24.
Tang F., Hajkova P., Barton S.C., Lao K., Surani M.A. (2006) MicroRNA expression profiling of single whole embryonic stem cells. Nucl. Acids Res. 34: e9.
25.
Tyczewska A., Bąkowska-Żywicka K., Gracz J., Twardowski T. (2016) Stress responsive non-protein coding RNAs. [In:] Abiotic and biotic stress in plants – recent advances and future perspectives. Ed. Shanker A., InTech: 153-181.
26.
Valleron W., Laprevotte E., Gautier E.F., Quelen C., Demur C., Delabesse E., Agi rre X., Prósper F., Kiss T., Brousset P. (2012) Specific small nucleolar RNA expression profiles in acute leukemia. Leukemia 26: 2052-2060.
27.
Válóczi A., Hornyik C., Varga N., Burgyán J., Kauppinen S., Havelda Z. (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucl. Acids Res. 32: e175.
28.
Varkonyi-Gasic E., Wu R., Wood M., Walton E.F., Hellens R.P. (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Meth. 3: 12.
29.
Vitali P., Royo H., Seitz H., Bachellerie J..P, Huttenhofer A., Cavaillé J. (2003) Identification of 13 novel human modification guide RNAs. Nucl. Acids Res. 31: 6543-6551.
30.
Zywicki M., Bakowska-Zywicka K., Polacek N. (2012) Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucl. Acids Res. 40: 4013-4024.
| eISSN: | 2353-9461 |
| ISSN: | 0860-7796 |
We process personal data collected when visiting the website. The function of obtaining information about users and their behavior is carried out by voluntarily entered information in forms and saving cookies in end devices. Data, including cookies, are used to provide services, improve the user experience and to analyze the traffic in accordance with the Privacy policy. Data are also collected and processed by Google Analytics tool (more).
You can change cookies settings in your browser. Restricted use of cookies in the browser configuration may affect some functionalities of the website.
You can change cookies settings in your browser. Restricted use of cookies in the browser configuration may affect some functionalities of the website.
