Using microarrays - (Dec/16/2007 )

NtcA is a transcriptional activator required for heterocyst differentiation. using microarray techniques, how could u determine which genes are affected (up or down regulated) by the presence of NtcA?

---

You could compare gene expression between NtcA+/+ and -/- cells. I did this with a transcription factor and found many direct target genes.

---

It seems, you can compare samples with different activities of your transcription factor. If NtcA(-/-) phenotype is not available it would be logic to activate or suppress NtcA by a treatment with chemicals. You need to find out what stimulates DNA-binding activity and what reduces it. Unfortunately, this is not my field and I can't suggest you the names. The obvious way to figure it out is to search in PubMed.

Then, you need to confirm that your cells respond to the treatments. For a transcription factror, I would run EMSA and check whether its binding to DNA changed.

Then, you can prepare the desired samples (samples with different NtcA binding) for the microarray and compare the lists of genes.

---