Data analysis - promoter evolution analysis

The importance of promoters

​ The promoter is RNA Polymerase recognition 、 A segment that binds and begins transcription DNA Sequence , It contains RNA A conserved sequence required for polymerase specific binding and transcription initiation , Most of them are located upstream of the starting point of structural gene transcription , The promoter itself is not transcribed . But there are some promoters ( Such as tRNA Starter ) Located downstream of the starting point of transcription , these DNA Sequences can be transcribed . Promoter properties were initially identified by mutations that increase or decrease the rate of gene transcription . Promoters are usually located upstream of the transcription initiation site . The promoter is located in the structural gene 5' Upstream of the end DNA Sequence , Energy activation RNA Polymerase , Match it to the template DNA Accurate binding and specificity for transcription initiation . Promoters themselves do not control gene activity , But through what is called transcription (transcription) This protein of factor (proteins) Combining to control gene activity . Transcription factors are like one side " flag ", Command the enzyme (enzymes)(RNA Polymerase polymerases) The activities of .

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From the web

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Extraction of promoter sequence

Generally, promoter evolution analysis is required , It is known that a large class of genes are in CDS The district is conservative Of , So I want to see if there is the same situation in the promoter area , Therefore, it is necessary to select species first , With wrky Take the family as an example , Can now ensemble plant Make predictions on the website , Look at the evolutionary relationships between different species .

After searching , You can click on the gene tree on the left , Look at the basic evolutionary relationships .

You can choose wrky The promoter sequences were extracted from species with relatively recent gene evolution .

Click on each... On the web page node The promoter sequence can be exported , After knowing the gene number and species information , Extraction is mainly in ensembel On the website .

Mainly in the biomart Extract on , Select the species information first and then , stay filters Inside gene Choose the genes you want , stay attributes Interior selection sequence, And then click sequence, choice flank(gene), Click on upstrean 1000, And then click count, see result Result , If you need to download , Click on go.

The above extracts are in phytozome It's OK to go up , Also in biomart Let's do the same .

Starter motif analysis

The promoter sequences of several species have been obtained , Then we choose tbtools Of fasta merge Merge the sequences , Get all of it fa file .

Conduct motif analysis , Mainly choose MEME On the website meme analysis , I chose 10 individual motif, And then in advance Will each motif The shortest sequence of is set to 15 Base .

Be a promoter motif The main purpose of the analysis is to see whether some sites in the sequence of these promoters are related to some special signal transduction genes we studied , To support the previous experimental results .

Analysis of cis acting elements of promoter

When analyzing cis acting elements , The main choice is plantcare Website , Because I didn't pay attention to this problem when I did the analysis this time , But if it needs to be done , There are many related tutorials on the web , You can follow the tutorial , Then we get a lot of cis acting elements , The latter is to eliminate the focus of your attention , Make a selection .

Construction of promoter phylogenetic tree

Evolutionary analysis is also commonly used MEGA Software analysis .

First, base sequence alignment , I chose muscle Compare the models of , Cut off after comparison 5' End sum 3' A base with a long difference from other sequences , Then the output mega Sequence .

Then we construct the evolutionary tree , First, the model is used for optimal search , Then proceed ML Evolutionary tree building , It is generally selected 500bootstrap.

When you get it , Output netwrik file , Can be in figtree perhaps itol To beautify .

summary

When conducting promoter evolution analysis , A key point is to know the evolutionary conservatism of this type of gene , Because the following contents are basically based on homology analysis , If the homology is too low , The later results are not very accurate . Based on the above results , We can also do some genetic evolution 、 Within species / Collinearity analysis between /WGD situation , These are mainly based on their own research content , Because we are only focusing on these , So I only did this part .