Correlation Between Intron Length And Presence Of Intronic Tfbs?

Question

[14134125465346445]

Related to this question:

http://biostars.org/post/show/43765/why-do-transcription-factors-bind-to-intronic-regions-downstream-of-the-transcription-start-site/#43827

I would like to ask if anybody has tried to find a correlation between gene intron size and presence of TFBSs in introns. This is, do genes with longer introns contain TFBSs for the same TF they also have in their TSS region more often than expected? Even after correcting intron length by the background distribution of intron lengths and total length of gene.

[Jeremy Leipzig]

interesting question, and worth investigating. Just be aware that the most highly expressed genes in animals are pretty short with few introns. Those might also be the ones most likely to have a known TFBS, due to "research bias". So you might get answer that only applies to a subset of genes, none of which should stop you.

[Larry_Parnell]

One would also need to look at this by distance to the TSS and by intron number. I see more TFBS in intron one, but I don't know if that is because it is intron 1 or because it is close(r) to the TSS.

[Frenkiboy]

I found this paper, maybe it can be of some help:

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003093

Answer 1

[klaugo]

I think this April 5 publication may be of interest to you: LOESS correction for length variation in gene set-based genomic sequence analysis. The authors found a notable correlation between a gene's noncoding sequence length (i.e., total upstream, downstream, and intronic sequence) and its CRM score in several different CRM/TFBS discovery algorithms. See linked figure CRM length-dependence artifact.

Answer 2

[Frenkiboy]

You can try do divide the promoters in different classes and check for different types of regulation. I think that mostly cpg island containing promoters have long distance input (intronic and intergenic) - specially the developmental genes.

An interesting question is whether the TFs that bind introns regulate transcription, splicing, or some other posttranscriptional process and whether it is possible to discriminate between them..