GENOME WIDE SNRNP MOTIFS AND REGULATORY SEQUENCES IN HIV1 ISOLATES

Paushali Roy¹*, Protip Basu², Sayak Ganguli³, Abhijit Datta^4
1DBT-Centre for Bioinformatics, Presidency College, Kolkata, India.
²DBT-Centre for Bioinformatics, Presidency College, Kolkata, India.
³DBT-Centre for Bioinformatics, Presidency College, Kolkata, India.
⁴DBT-Centre for Bioinformatics, Presidency College, Kolkata, India.
* Corresponding Author : paushali.06@gmail.com

Received : -     Accepted : -     Published : 21-12-2009
Volume : 1     Issue : 2       Pages : 14 - 26
Int J Bioinformatics Res 1.2 (2009):14-26
DOI : http://dx.doi.org/10.9735/0975-3087.1.2.14-26

Keywords : Riboswitch, snRNP motifs, HIV-1, gene regulation, RNA processing
Conflict of Interest : None declared

The pathogenesis of HIV-1 is complex and characterized by the interplay of both viral and host factors. Within HIV 1 genome there are several snRNP motifs responsible for pre mRNA splicing and stabilization. By locating these motifs within the genome and disturbing them may result in an impaired ability of the cells to sustain HIV-1 replication. One of such regulatory sequences is riboswitches that regulate the dimerization of HIV-1 RNA, which is an essential step during packaging. The current work was undertaken to identify possible regulatory RNA motifs in the HIV1 genome from different isolates. The current work has successfully identified multiple snRNP motifs in the genome sequences of different strains of HIV-1 isolates. The identification of the multiple snRNP motifs in the genomic sequences of the various isolates lead us to believe that future studies with artificially constructed snRNPs might have the potential to inhibit HIV1 replication. Apart from containing snRNP motifs they also possess regulatory riboswitch motifs. Riboswitches bind metabolites and control the dimerization and packaging of the genome. Thus the occurrence of such motifs further strengthens the idea that apart from serving as a regulatory domain for structural constraints such motifs may also regulate genome integration and production of the necessary products by using the host transcriptional machinery. It is however beyond doubt that such sequence motifs must have originated in the RNA world as they have the power to mediate RNA induced regulation of gene expression.

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