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Open Access Research article

Computational prediction and validation of C/D, H/ACA and Eh_U3 snoRNAs of Entamoeba histolytica

Devinder Kaur1, Abhishek Kumar Gupta1, Vandana Kumari1, Rahul Sharma1, Alok Bhattacharya2 and Sudha Bhattacharya1*

Author Affiliations

1 School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

2 School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

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BMC Genomics 2012, 13:390  doi:10.1186/1471-2164-13-390

Published: 14 August 2012

Abstract

Background

Small nucleolar RNAs are a highly conserved group of small RNAs found in eukaryotic cells. Genes encoding these RNAs are diversely located throughout the genome. They are functionally conserved, performing post transcriptional modification (methylation and pseudouridylation) of rRNA and other nuclear RNAs. They belong to two major categories: the C/D box and H/ACA box containing snoRNAs. U3 snoRNA is an exceptional member of C/D box snoRNAs and is involved in early processing of pre-rRNA. An antisense sequence is present in each snoRNA which guides the modification or processing of target RNA. However, some snoRNAs lack this sequence and often they are called orphan snoRNAs.

Results

We have searched snoRNAs of Entamoeba histolytica from the genome sequence using computational programmes (snoscan and snoSeeker) and we obtained 99 snoRNAs (C/D and H/ACA box snoRNAs) along with 5 copies of Eh_U3 snoRNAs. These are located diversely in the genome, mostly in intergenic regions, while some are found in ORFs of protein coding genes, intron and UTRs. The computationally predicted snoRNAs were validated by RT-PCR and northern blotting. The expected sizes were in agreement with the observed sizes for all C/D box snoRNAs tested, while for some of the H/ACA box there was indication of processing to generate shorter products.

Conclusion

Our results showed the presence of snoRNAs in E. histolytica, an early branching eukaryote, and the structural features of E. histolytica snoRNAs were well conserved when compared with yeast and human snoRNAs. This study will help in understanding the evolution of these conserved RNAs in diverse phylogenetic groups.

Keywords:
U3 snoRNA; Guide/ orphan snoRNAs; Entamoeba histolytica