Publication detail

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

HEŘMÁNKOVÁ, K. SEDLÁŘ, K.

Original Title

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

Type

article in a collection out of WoS and Scopus

Language

English

Original 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 over- representation 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

Authors

HEŘMÁNKOVÁ, K.; SEDLÁŘ, K.

Released

24. 4. 2024

ISBN

978-80-214-6231-1

Book

Proceedings I of the 30 th Conference STUDENT EEICT 2024

Edition

1

Pages from

113

Pages to

116

Pages count

4

BibTex

@inproceedings{BUT189094,
  author="Kristýna {Heřmánková} and Karel {Sedlář}",
  title="Co-expression analysis of small RNAs and untranslated regions in Rhodospirillum rubrum",
  booktitle="Proceedings I of the 30 th Conference STUDENT EEICT 2024",
  year="2024",
  series="1",
  pages="113--116",
  isbn="978-80-214-6231-1"
}