Question: Biology question: repetitive sequences?
1
gravatar for dah124
7 months ago by
dah12410
dah12410 wrote:

Wikipedia says there are three main types of repetitive regions (https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)), terminal repeats, tandem repeats, and interspersed repeats. However, I am wondering if promoter regions and other transcription factor binding sites will also be exactly the same between different genes? In some cases the exact enzymes that are recruited are exactly the same, making the recruitment regions also identical or at least very similar? We are working with whole genome metagenomic data from the surface of the eye and most of the reads that have multiple alignments are from similar strains/repetitive/low complexity sequences -- so what I'm asking about doesn't seem to be a problem, but I'm wondering why it isn't? Thanks.

Daniel

ADD COMMENTlink modified 7 months ago • written 7 months ago by dah12410

I suspect that if promoters and TF binding sites were identical, they would be much easier to find. Usually you get TF binding motifs that are enriched for certain bases at certain positions, but not identical.

ADD REPLYlink written 7 months ago by mastal5111.7k

True, and in addition those sequences are rather short and therefore less easy to find. If a read is sufficiently longer than the repeat element, multi-mapping won't occur.

ADD REPLYlink written 7 months ago by WouterDeCoster20k

I see, thank you both for your responses. A follow-up question, what accounts for the differences in promoters/TF binding sites that recruit similar/the same enzymes? Are there small differences that may relate to transcriptional regulation, or do some of the differences not make a huge impact?

ADD REPLYlink written 7 months ago by dah12410
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