I want to study the promoters evolution, but I have no idea how to research except for sequences alignment, constructing phylogenetic trees and finding the differences of TF binding sites. Could you give me some advises?
Well, I understand your question but the problem lies in forward sequence. if you design correctly then the a good PCR you expect. When you have good number of sequence in your hand, you may compare more preciously. first of all you have to have a quality of promoter base knowledge in COX sequencing.
Quiang, you can do:
a) comparison of several diverse bioinformatic methods for promoter sequence recongnition and analysis in the genome of your interest, incuding promoter recombination
b) study of functional role and evolution of genes under your promoters
c) place different promoter sequences into vector with reporter gene and study effect of changes on the gene expression
Some useful ideas are in
1: Behrens S, Vingron M. Studying the evolution of promoter sequences: a waiting
time problem. J Comput Biol. 2010 Dec;17(12):1591-606. doi:
10.1089/cmb.2010.0084. PubMed PMID: 21128851; PubMed Central PMCID: PMC3119604.
2: Raijman D, Shamir R, Tanay A. Evolution and selection in yeast promoters:
analyzing the combined effect of diverse transcription factor binding sites. PLoS
Comput Biol. 2008 Jan;4(1):e7. doi: 10.1371/journal.pcbi.0040007. PubMed PMID:
18193940; PubMed Central PMCID: PMC2186363.
3: Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M. CpG
deamination creates transcription factor-binding sites with high efficiency.
Genome Biol Evol. 2011;3:1304-11. doi: 10.1093/gbe/evr107. Epub 2011 Oct 19.
PubMed PMID: 22016335; PubMed Central PMCID: PMC3228489.
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis