I\'ve read about DNA sequence motifs, but still don\'t understand what makes som

Question

I've read about DNA sequence motifs, but still don't understand what makes some sequence a DNA sequence motif. Is this a well-defined concept? For, example, What are DNA sequence motifs? says:

Sequence motifs are short, recurring patterns in DNA that are presumed to have a biological function. Often they indicate sequence-specific binding sites for proteins such as nucleases and transcription factors (TF). Others are involved in important processes at the RNA level, including ribosome binding, mRNA processing (splicing, editing, polyadenylation) and transcription termination.

For example, I've been working with Recombination Signal Sequences (RSS), which are important in immunology. However, from what I can tell, RSS are not themselves motifs, but they do contain motifs. E.g. Conservation of sequence in recombination signal sequence spacers says

Previously, the RSS has been described as possessing both a conserved heptamer and a conserved nonamer motif.

So, apparently, the heptamer and nonamer component of the RSS are themselves motifs, but the RSS itself is not. Can anyone explain why? Thanks.

Explanation / Answer

Motif means a pattern. For any array of objects to be called a pattern, it has to have at least more than one instance. To define more precisely, a motif should have significantly (statistical) higher occurrence in a given array compared to what you would obtain in a randomized array of same components (expecting at random).

RSS nonamers/heptamers are called a motif because they are a pattern of sequence which a) has more than one occurrence b) the occurrence is significantly higher than a random expectation. Generally in sequence motifs randomization is not usually done because the genome size is too huge. In such conditions if your sequence has >= 2 occurrences throughout the genome it may be considered a motif. Lets assume a 10bp sequence. Its random probability = 1/4

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