Comparative RNA Genomics

Methods Mol Biol. 2024:2802:347-393. doi: 10.1007/978-1-0716-3838-5_12.


Over the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large-scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible non-coding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of non-coding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.

Keywords: Alternative splicing; Chromatin; Evolution; RNA secondary structure; long non-coding RNA.

MeSH terms

  • Computational Biology* / methods
  • Genomics* / methods
  • Humans
  • Nucleic Acid Conformation
  • RNA / genetics
  • RNA, Untranslated / genetics
  • Sequence Analysis, RNA / methods


  • RNA
  • RNA, Untranslated