I am working on Secondary metabolites, I have identified the gene clusters using the AntiSmash bioinformatics tools, now I am interested to find the Silent Biosynthetic gene cluster. can we identify these silent gene clusters using transcriptomics ?
If you can't find the mRNA of any of the genes in the cluster then it is silent.
(I have not done micro-array or transcriptomic analysis)
If you are working with the lab strains, there might be many gene clusters which are silent and do not express in normal conditions. Therefore, in the normal transcriptomics it "should not" be visible.
For the analysis of silent gene clusters, either you need to have genetic modifications and over expression experiments and than transcriptomics analysis or genomic data analysis could give you some insight.
As said, microarrays will only show mRNA from genes expressed. You can activate them under a strong promoter. Now my question, why do you need transcriptome analysis? the cluster product (PKS, NRPS, ect...) is the only way to prove its function. Genes expression is not a hint.
Loubna Youssar I am actually designing my projects, which is related to Invivo activation of silent biosynthetic gene clusters using CRISPR/CAS9, however before that i need to know which genes are silent. For that i have to do transcriptomic analysis at different culture conditions and different time points.. But i am not sure how i can link the transcriptomic data to gen clusters activity.
If antiSmatch predicted clusters involved in secondary metabolism, you can select one gene of each and run RT-PCR. The result of the PCR will give you a hint whether the gene of that cluster is active. If you are interested on the product then construct, as suggested, the genes of that cluster under a strong promotor and check the product by LC-MS. I don t think transcriptomic approach is required in your case.
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