Hello every one
I am dealing with gene that produce protein , the UCSC show the presence of active transcription binding region in the middle of the gene ,it say that this gene should have two isoform ,but on the mRNA didn't show the expected isoform.
So i start to think this region may produce anther product like microRNA ?! what do you think ?and how I can know if there is micro RNA produced ?!
thank you :)
Hi Abrar,
Can you clarify a little your description of your locus? When you say "active transcription binding region", do you mean that there is an exon defined in transcriptome annotations? Or that you see density of e.g. Pol II by ChIP-Seq? Or, for example, a density of reads from RNA-seq experiments? Answers to these questions will make possible explanations for your observations much clearer.
It is certainly possible that you have distinct RNA species within a protein-coding genes, and that these units may be controlled by TF binding within a gene - TF binding throughout the length of a gene is very common, and can control not just transcriptional initiation but also, for example, exon skipping/inclusion, transcriptional silencing, fine-tuning transcription etc. etc..
Re: miRNAs: many pri-miRNAs are of course transcribed from TF-bound promoters as their own units; however, a class of them - known as miRtrons - are positioned within the introns of protein-coding genes, and are transcribed as parts of these ORFs then processed separately. It's also worth considering that there are numerous other possible RNA species that can be found in introns of protein-coding genes - in particular, snRNAs. Examination of the sequence of your region of interest (and comparison to known miRNAs/snRNAs curated in online databases) may provide you with some guidance on this.
However, it's important to remember that, while you may see two annotated "isoforms" of an mRNA with different exon arrangements, you will not necessarily see both isoforms in all cells/tissues. There are many spicing isoforms that are expressed in tight spatial/temporal/developmental control and may only be seen in certain cells/tissues/developmental stages etc. etc.. To get some insight into this, you can look at the GTEx database (http://gtexportal.org/home/) which has data on tissue-specific expression for different splicing forms for humans.
I hope that all helps! Let me know if you have more information/questions.
Cheers,
Dan
I suggest to analyze the complete sequence (5'UTR, Exons, Introns, 3'UTR) of the gene of interest and aligning it against several microRNAs to determine the presence of any possible match, and then take the flanking regions of the microRNA finded to determine if the sequence is able to form stem-loop structures that are characteristic of the microRNA precursors.
Regards
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