Rahul Sharma1, Devinder kaur1, Vandana Kumari1, Abhishek Kumar Gupta1, Alok Bhattacharya2, Sudha Bhattacharya1
1School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
2School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
Small nucleolar RNAs (snoRNA) plays a vital role in biogenesis of pre ribosomal RNA by guiding the chemical modifications required for generation of mature ribosomal RNA. snoRNAs can be categorized into two major families on the basis of conserved sequence and structural motifs and the modifications that the snoRNAs bring about. The two families are called CD-Box and H/ACA box snoRNAs. CD-box is responsible for the 2′-O-ribose methylation and H/ACA box is responsible for the pseudouridylation of pre-rRNA molecules. Entamoeba histolytica is an anaerobic parasitic protozoan, and causative agent of amoebiasis in human beings. Little work has been done on the noncoding RNA of this parasite till date. In this study we have computationally predicted and validated 24 guide CDBox, 42 orphan CD-Box, 18 Guide H/ACA-Box snoRNA and 38 Orphan H/ACA-Box snoRNAs of E.histolytica using the already existing computational tools Snoscan and snoSeeker respectively. We have determined the genomic localization of these snoRNAs, and checked whether they are coming from introns, intergenic region or genic region and we have also checked their structural features which play a vital role in the modification process. Finally we have confirmed the expression of these predicted snoRNAs using small RNA data of this parasite obtained by us using Next generation sequencing techniques (Illumina). Confirmation of their existence and expression verification is also done by using biochemical methods like RT-PCR and Northern blotting which shows the resemblance of Eh H/ACA snoRNAs with that of trypanosomes. Read more…