Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression

Vince Kornél Grolmusz, Eszter Angéla Tóth, Kornélia Baghy, István Likó, Ottó Darvasi, I. Kovalszky, J. Matkó, K. Rácz, A. Patócs

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Background: Previously, drug-based synchronization procedures were used for characterizing the cell cycle dependent transcriptional program. However, these synchronization methods result in growth imbalance and alteration of the cell cycle machinery. DNA content-based fluorescence activated cell sorting (FACS) is able to sort the different cell cycle phases without perturbing the cell cycle. MiRNAs are key transcriptional regulators of the cell cycle, however, their expression dynamics during cell cycle has not been explored. Methods: Following an optimized FACS, a complex initiative of high throughput platforms (microarray, Taqman Low Density Array, small RNA sequencing) were performed to study gene and miRNA expression profiles of cell cycle sorted human cells originating from different tissues. Validation of high throughput data was performed using quantitative real time PCR. Protein expression was detected by Western blot. Complex statistics and pathway analysis were also applied. Results: Beyond confirming the previously described cell cycle transcriptional program, cell cycle dependently expressed genes showed a higher expression independently from the cell cycle phase and a lower amplitude of dynamic changes in cancer cells as compared to untransformed fibroblasts. Contrary to mRNA changes, miRNA expression was stable throughout the cell cycle. Conclusions: Cell cycle sorting is a synchronization-free method for the proper analysis of cell cycle dynamics. Altered dynamic expression of universal cell cycle genes in cancer cells reflects the transformed cell cycle machinery. Stable miRNA expression during cell cycle progression may suggest that dynamical miRNA-dependent regulation may be of less importance in short term regulations during the cell cycle.

Original languageEnglish
Article number412
JournalBMC Genomics
Volume17
Issue number1
DOIs
Publication statusPublished - May 27 2016

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RNA Sequence Analysis
MicroRNAs
Cell Cycle
Flow Cytometry
cdc Genes

Keywords

  • Cell cycle
  • DNA staining
  • Dynamic expression
  • Fluorescence-activated cell sorting (FACS)
  • MiRNA

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression. / Grolmusz, Vince Kornél; Tóth, Eszter Angéla; Baghy, Kornélia; Likó, István; Darvasi, Ottó; Kovalszky, I.; Matkó, J.; Rácz, K.; Patócs, A.

In: BMC Genomics, Vol. 17, No. 1, 412, 27.05.2016.

Research output: Contribution to journalArticle

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abstract = "Background: Previously, drug-based synchronization procedures were used for characterizing the cell cycle dependent transcriptional program. However, these synchronization methods result in growth imbalance and alteration of the cell cycle machinery. DNA content-based fluorescence activated cell sorting (FACS) is able to sort the different cell cycle phases without perturbing the cell cycle. MiRNAs are key transcriptional regulators of the cell cycle, however, their expression dynamics during cell cycle has not been explored. Methods: Following an optimized FACS, a complex initiative of high throughput platforms (microarray, Taqman Low Density Array, small RNA sequencing) were performed to study gene and miRNA expression profiles of cell cycle sorted human cells originating from different tissues. Validation of high throughput data was performed using quantitative real time PCR. Protein expression was detected by Western blot. Complex statistics and pathway analysis were also applied. Results: Beyond confirming the previously described cell cycle transcriptional program, cell cycle dependently expressed genes showed a higher expression independently from the cell cycle phase and a lower amplitude of dynamic changes in cancer cells as compared to untransformed fibroblasts. Contrary to mRNA changes, miRNA expression was stable throughout the cell cycle. Conclusions: Cell cycle sorting is a synchronization-free method for the proper analysis of cell cycle dynamics. Altered dynamic expression of universal cell cycle genes in cancer cells reflects the transformed cell cycle machinery. Stable miRNA expression during cell cycle progression may suggest that dynamical miRNA-dependent regulation may be of less importance in short term regulations during the cell cycle.",
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AU - Likó, István

AU - Darvasi, Ottó

AU - Kovalszky, I.

AU - Matkó, J.

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