I recently gave a lab session on using dot matrix plots to detect interesting sequence patterns using Dotlet to some students in genetics. A group showed an interesting palindrome from Tetrahymena pigmentosa rDNA, about 250bp long. I did a quick check and found out some interesting things about this organism (such as it is a protozoa, which I didn’t know). It appears to be a well-studied model, attracting attention of people working the J.Craig Venter Institute. Interestingly, one species actually comes from Malacca (T.malaccensis). In 1991, Yasuda and Yao elucidated a mechanism for the production of long palindromes in Tetrahymena that depends on the presence of short inverted repeats. Here’s a diagram showing the result of a dot plot for the Tetrahymena thermophila macronuclear extrachromosomal rRNA gene (GenBank ID: M11155). The sequence is 1935 bases long, and the palindromic sequence is located at position 1200. The complete palindrome is 42 bases long. Note the presence of a repeat upstream.
It is rewarding to be stimulated by students in this way.
Reference: Yasuda, L.F. & Yao, M-C. (1991). Short inverted repeats at a free end signal large palindromic DNA formation in Tetrahymena. Cell, 67:505-516.