A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules

Zsolt Czimmerer, Julianna Hulvely, Zoltan Simandi, E. Várallyay, Z. Havelda, Erzsebet Szabo, Attila Varga, B. Dezső, Maria Balogh, Attila Horvath, Balint Domokos, Zsolt Torok, L. Nagy, Balint L. Balint

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

Short regulatory RNA-s have been identified as key regulators of gene expression in eukaryotes. They have been involved in the regulation of both physiological and pathological processes such as embryonal development, immunoregulation and cancer. One of their relevant characteristics is their high stability, which makes them excellent candidates for use as biomarkers. Their number is constantly increasing as next generation sequencing methods reveal more and more details of their synthesis. These novel findings aim for new detection methods for the individual short regulatory RNA-s in order to be able to confirm the primary data and characterize newly identified subtypes in different biological conditions. We have developed a flexible method to design RT-qPCR assays that are very sensitive and robust. The newly designed assays were tested extensively in samples from plant, mouse and even human formalin fixed paraffin embedded tissues. Moreover, we have shown that these assays are able to quantify endogenously generated shRNA molecules. The assay design method is freely available for anyone who wishes to use a robust and flexible system for the quantitative analysis of matured regulatory RNA-s.

Original languageEnglish
Article numbere55168
JournalPLoS One
Volume8
Issue number1
DOIs
Publication statusPublished - Jan 31 2013

Fingerprint

Assays
quantitative polymerase chain reaction
RNA
Polymerase Chain Reaction
Molecules
stems
assays
Physiological Phenomena
physiological regulation
immunomodulation
Biomarkers
Pathologic Processes
Regulator Genes
regulator genes
Eukaryota
methodology
formalin
Gene expression
Paraffin
alkanes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules. / Czimmerer, Zsolt; Hulvely, Julianna; Simandi, Zoltan; Várallyay, E.; Havelda, Z.; Szabo, Erzsebet; Varga, Attila; Dezső, B.; Balogh, Maria; Horvath, Attila; Domokos, Balint; Torok, Zsolt; Nagy, L.; Balint, Balint L.

In: PLoS One, Vol. 8, No. 1, e55168, 31.01.2013.

Research output: Contribution to journalArticle

Czimmerer, Z, Hulvely, J, Simandi, Z, Várallyay, E, Havelda, Z, Szabo, E, Varga, A, Dezső, B, Balogh, M, Horvath, A, Domokos, B, Torok, Z, Nagy, L & Balint, BL 2013, 'A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules', PLoS One, vol. 8, no. 1, e55168. https://doi.org/10.1371/journal.pone.0055168
Czimmerer, Zsolt ; Hulvely, Julianna ; Simandi, Zoltan ; Várallyay, E. ; Havelda, Z. ; Szabo, Erzsebet ; Varga, Attila ; Dezső, B. ; Balogh, Maria ; Horvath, Attila ; Domokos, Balint ; Torok, Zsolt ; Nagy, L. ; Balint, Balint L. / A Versatile Method to Design Stem-Loop Primer-Based Quantitative PCR Assays for Detecting Small Regulatory RNA Molecules. In: PLoS One. 2013 ; Vol. 8, No. 1.
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