Hi Neslihan,

ok, a good way to find out some informations on your target would be to go to the UCSC website (https://genome.ucsc.edu), choose the genome browser tool, choose the genome and build (I guess humans and hg19) and fill the search tool with the gene name.

you'll arrive in the genome browser with your gene (you can configure the page to see better, it depends on your screen (just search "configure").

once you can see your gene, just have a look at the optional tracks where you'll find enough data. in the page, you can zoom in or or...

there are lot of interesting stuffs on this site, an example, go on top/view and you'll see the sequence of your target.

take some time on this site, it will always help you in your research.

fred

You can use the Ensembl website to look at potential protein binding sites within genomic regions of interest, which is what I've done before. Click here and you will see the last exon and 3' UTR regions of the human FOSL1 gene: http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000175592;r=11:65891050-65894231 You can alter the view by zooming in and out, scrolling etc., but at the bottom of the page where it says 'motif features', you can see a lot of grey and some black bars. The black ones are experimentally verified binding sites, whereas the grey ones are computationally predicted, but not verified yet. If you click on each of them, it will tell you what transcription factors bind at those regions and if you zoom in far enough, then you can see the DNA sequences of the motifs too. However, seeing as this is the 3' UTR of your gene, it is unlikely that these transcription factor binding sites will affect the expression of the FOSL1 gene.

You said that you used CRISPR-Cas9 to cleave the DNA within the last exon and 3' UTR of the FOSL1 gene - have you created mutations within the coding region of the last exon as a result of this cleavage? If so, then perhaps you have destroyed an miRNA binding site, or created a new one. If the locus you have targeted is at the 5' end of the last exon, then have you checked if this has altered the splice site or generated a premature termination codon? That could lead to your mRNA being degraded (and of course reduce translation as a consequence).

Check the predicted miRNA binding sites in the 3' UTR of human FOSL1: http://www.mirdb.org/index.html (other useful websites also exist). Cross-reference these predicted binding sites to the sequence which you targeted with CRISPR-Cas9 and see if they are mutated - that might explain why your gene expression has decreased.

There are many options and possibilities - best of luck!

Jonathan Whitchurch thank you very much for your effort and this very detailed answer ! It helped me a lot!!

Frederic Lepretre thank you very much for your help and your answer !