On 10 Jan 1998, ipsingh lall wrote:
> Dear Netters,
> I have a general query about the structure of the long terminal
> repeats (LTRs) of the retrotransposons and retroviruses. What is the
> significance of inverted repeats (perfect or imperfect) present at the
> terminals of the LTRs.
The inverted repeats are generated during the reverse
transcription process and are involved in the initiation of transcription
(5') and its termination (3'). Field's Virology gives a good description
of the process.
> Also please advise me how to find out various promoter elements
> present within the LTR sequence as LTRs serve as promoters for the
> retrotransposons (I have cloned a retrotransposon from a plant Cajanus
> cajan; its 5'LTR is of 372 nucleotide long and 3'LTR is 383 nucleotide
> long with an insertion of 11 nucleotides or may be 11 nucleotides have
> been deleted from the 5'LTR) and about other relevent analysis to
> perform to get an idea about its functioning.
The quickest way to check for all possible transcription factor
sites is to 'fetch' the gcg data file 'tfsites.dat'. This is a pretty
extensive list of transcription factors and their recognition sites. Use
this file as a local data file with any of the restriction enzyme mapping
programmes in GCG. This then gives a map of possible transcription factor
binding sites in your sequence. It is important to remember that this is
only a rough list, you may miss degenerate sites and will get alot of
inappropriate matches. Given that you have a short sequence you are
probably best just cloning the whole thing upstream of a reporter gene and
doing deletion analysis.
Hope this helps,