Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopodacave crickets (Orthoptera, Rhaphidophoridae)

Lene Martinsen,Federica Venanzetti,Arild Johnsen,Lutz Bachmann

doi:10.1186/1471-2148-10-3

Abstract

BackgroundThe great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat.ResultsWe assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species.ConclusionsThe phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

Highlights

The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component
It has been demonstrated that small non-coding RNAs can play a crucial role in regulating heterochromatin formation [12] and it has been found that transcripts of tandem repeated non-coding DNA can give rise to dsRNAs [13]
This study showed that ribozymes might act in post-transcriptional regulation of protein coding gene expression in a way that is similar to destabilizing protein factors

Summary

Introduction

The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Transcription of satDNA and other non-coding DNA has been found in many species The function of the vast majority of these transcripts is unclear, but recent studies using RNA interference have documented the role of non-coding RNAs in regulation of gene expression, chromatin organization, and genome functioning (for a review, see [11]). It has been demonstrated that small non-coding RNAs can play a crucial role in regulating heterochromatin formation [12] and it has been found that transcripts of tandem repeated non-coding DNA can give rise to dsRNAs [13]

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Discussion

Conclusion