MicroRNA switches in Trypanosoma brucei

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Abstract

Trypanosoma brucei develops chronic infection in mammalian hosts due to a sophisticated strategy of antigenic variation of variant surface glycoprotein (VSG) coat to escape antibody-mediated lysis. MicroRNAs are a class of non-coding RNAs with presumed post-transcriptional regulatory activity. Homology based informatic approach is used to identify the microRNA (miRNA) genes of T. brucei and their target mRNAs. Our observation reveals a set of microRNAs targeting mRNAs corresponding to VSGs. Further, a number of miRNA hairpins have been found in clusters of multiple identical copies. The target proteins, 20S proteosome, GM6 and GRESAG 4.2 corresponding to these clustered miRNAs play essential role in trypanosomiasis. These snippets can act as genetic switches modulating host–parasite interaction and provide useful clue toward treatment of trypanosomiasis.

Section snippets

Results and discussion

The initiation of our bioinformatic hunt for miRNA genes began with the reference set of genomic sequences from 11 chromosomes of Tb subjected to einverted program which generated an output of 41,033 inverted repeats. The screening procedure at the second stage reduced the output to 8828 unbranched structures (refer Table 1). An attempt to reduce the unlikely precursor candidates and finding the mature ones generated 1889 (not given in table) mature miRNAs.

Materials and methods

Sources. The genomic sequences of the 11 chromosomes of Tb (Taxonomy ID: 185431) [36] are obtained from NCBI database (http://www.ncbi.nlm.nih.gov/). The 3′ UTR (3′ untranslated region) sequences needed for target identification are obtained from UTResource (Release 7.1.3.1) (http://www.ba.itb.cnr.it/UTR/) [37].

Prediction strategy. The input genomic sequence is scanned using einverted program of EMBOSS obtained from www.hgmp.mrc.ac.uk/Software/EMBOSS/ to identify the repeats of length 120 nts

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    These authors have equally contributed.

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