Co-expression analysis of small RNAs and untranslated regions in Rhodospirillum rubrum

Heřmánková, Kristýna; Sedlář, Karel

Co-expression analysis of small RNAs and untranslated regions in Rhodospirillum rubrum

Files

113-eeict-2024.pdf(803.26 KB)

Date

2024

Authors

Heřmánková, Kristýna

Sedlář, Karel

Publisher

Vysoké učení technické v Brně, Fakulta elektrotechniky a komunikačních technologií

Abstract

Bacterial small RNAs (sRNAs) are regulatory elements often mentioned in the context of stress response. So are polyhydroxyalkanoates (PHAs), a possible replacement for conventional plastics, are frequently produced by bacteria facing stress conditions. PHAs then serve as the source of the carbon as well as the defense mechanism against further stress. Here, we present sRNA analysis of PHA-producing bacterium Rhodospirillum rubrum, especially the co-expression analysis of inferred sRNA candidates from RNA-Seq data. Weighted correlation network analysis (WGCNA) was used to compute clusters of genes with similar expression profiles, resulting in 28 modules. Further, the functional annotation of genes in each module was applied and the overall functional profiles were mentioned using a ‘guilt by association’ approach. Additionally, functional enrichment of modules was obtained through overrepresentation analysis (ORA). These results provide an overview of regulatory elements and their predicted functions in R. rubrum, which further unveil its dynamic properties and can help with the assessment of its industrial application.

Keywords

RNA-Seq, PHA, sRNA, functional annotation, coexpression analysis

Citation

Proceedings I of the 30st Conference STUDENT EEICT 2024: General papers. s. 113-116. ISBN 978-80-214-6231-1
https://www.eeict.cz/eeict_download/archiv/sborniky/EEICT_2024_sbornik_1.pdf

Document type

Peer-reviewed

Document version

Published version

Language of document

en

Document licence