MEME-ChIP results interpretation

[mdok...@fiu.edu]

Hello,

I am analyzing ChIP-Seq data from Illumina using Galaxy web server. I have mapped the reads with bowtie2 tool and did the peak calling with MACS2. I have used the peak regions to find the statistically significant motifs. Then, we also screened for simple repeat sequence and removed them.I have found GAGAGAGAGA repeats sequences in those peak regions. To confirm the results, I have manually checked the sequences of the peaks (binding regions) which fall within the promoter region of the gene as well as peaks with the highest peak score. I have found the same  GAGAGAGAGA repeats sequences.

I did ChIP on protein which lacks DNA binding domain and it has been shown that it binds to other TFs and then bind to DNA. My question is should we go ahead and do DNA immunoprecipitation (DIP-chip) to check whether our protein of interest binds to GAGAGAGA repeats?. Does this GAGAGAGA repeat sequences bear any significance? Could you please help us with this issue. Thank you.

[CharlesEGrant]

It looks like the masking of short repeats was incomplete. You don't mention what tool you used to do the masking, but they typically have multiple command line parameters to control their sensitivity. In particular, many offer some sort of control over the how long a stretch of repeats they will look for (referred to as the period). You may need to increase this, sine it looks like you have some really long stretches of repeats. You may also want to use a tool that specifically deals with tandem repeats like Tandem Repeat Finder.

No one can guarantee you that that stretch of repeats isn't biologically significant, but it seems unlikely, and it's certainly no more likely to be biologically significant then the repeats you've already masked out.