Publication detail

Differential expression analysis of RNA-Seq data for identification of housekeeping genes in Rhodospirillum rubrum DSM 467

JUREČKOVÁ, K. SLANINOVÁ, E. OBRUČA, S. FLEURIOT-BLITMAN, H. ZINN, M. SEDLÁŘ, K.

Original Title

Differential expression analysis of RNA-Seq data for identification of housekeeping genes in Rhodospirillum rubrum DSM 467

Type

abstract

Language

English

Original Abstract

Rhodospirillum rubrum is a bacterium that has gained attention due to its ability to produce and accumulate polyhydroxyalkanoate (PHA) in a form of intracellular granules, which serve as a carbon and energy storage mechanism. Apart from that, PHA is sustainable, biocompatible, biodegradable and also a promising replacement for petrochemical polymers. Rhodospirillum rubrum is currently intensively studied for its metabolic flexibility and diverse biosynthetic strategies, further expanding our understanding of PHA synthesis and its potential applications. Differential expression analysis of transcriptomic data is one the most important tools for understanding gene regulation under specific conditions. Yet, it can also help with identification of genes that are not differentially expressed but maintain stable gene expression and preserve basal metabolism. These housekeeping genes can used as reference genes for normalization of gene expression data obtained by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR), a crucial step for accurate data interpretation. Reference genes should be chosen individually for each particular organism and that can be accomplished by analysis of available transcriptomic data. In our study, we focused on identification of housekeeping genes in Rhodospirillum rubrum DSM 467 by conducting differential expression analysis of available RNA-Seq data using selected tools (empiReS, DESeq2, limma-voom, edgeR). We compared the results with respect to the identification of housekeeping genes. We evaluated how the selection differed among the tools and which tools are the best for identification of the housekeeping genes. Our results will be used to improve our method for identification of novel housekeeping genes based on RNA-Seq data and enable the identification of candidate reference genes for R. rubrum. Subsequently, these candidates will be validated through RT-qPCR experiments.

Keywords

PHA, RNA-Seq, reference genes

Authors

JUREČKOVÁ, K.; SLANINOVÁ, E.; OBRUČA, S.; FLEURIOT-BLITMAN, H.; ZINN, M.; SEDLÁŘ, K.

Released

13. 9. 2023

BibTex

@misc{BUT185435,
  author="Kateřina {Šabatová} and Eva {Slaninová} and Stanislav {Obruča} and Hugo {Fleuriot-Blitman} and Manfred {Zinn} and Karel {Sedlář}",
  title="Differential expression analysis of RNA-Seq data for identification of housekeeping genes in Rhodospirillum rubrum DSM 467",
  booktitle="11th European Symposium on Biopolymer (ESBP)",
  year="2023",
  note="abstract"
}