Detail publikačního výsledku

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

HEŘMÁNKOVÁ, K.; SEDLÁŘ, K.

Originální název

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

Anglický název

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

Druh

Stať ve sborníku mimo WoS a Scopus

Originální abstrakt

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.

Anglický abstrakt

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.

Klíčová slova

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

Klíčová slova v angličtině

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

Autoři

HEŘMÁNKOVÁ, K.; SEDLÁŘ, K.

Vydáno

24.04.2024

ISBN

978-80-214-6231-1

Kniha

Proceedings I of the 30 th Conference STUDENT EEICT 2024

Edice

1

Strany od

113

Strany do

116

Strany počet

4

Plný text v Digitální knihovně

http://hdl.handle.net/

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"
}