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Targeting non-coding RNAs: strategies and what we need to design an oligo

Morpholinos have been used to alter activity of non-coding RNAs. A citation list is here:
http://www.gene-tools.com/node/14474

Targeting non-coding RNAs presents special problems. Ideally, we need to know where on the non-coding RNA an activity is located that we can block. You will need to tell us where you want the oligo targeted and we’ll try to find the best oligo sequence targeting that location.

For targeting miRNAs, we target to alter the stem-loop structure of the pri-miRNA so that it will not be cleaved by the double-strand nucleases needed for maturing the miRNA (e.g. Drosha, Dicer). Our Design Request Website has a selection available for designing Morpholinos targeting miRNA (https://oligodesign.gene-tools.com/request/).

If the non-coding RNA undergoes splicing, then we can potentially modify the splicing with a Morpholino to excise an exon or insert an intron. In some cases this has been used productively to alter the activity of a non-coding RNA. Targeting a Morpholino to splicing of a non-coding RNA follows the same rules as for targeting a pre-mRNA; typically we target mostly-intronic sequence at a splice junction. Our Design Request Website has a selection available for designing Morpholinos targeting splicing.

We can also directly target activities of non-coding RNAs involving complementary sequence interactions, secondary structure or “sponge” activity. For instance, perhaps the non-coding RNA has a sequence motif that is complementary to another RNA and there is an activity caused by the interaction of the non-coding RNA and the other RNA by complementary base pairing; in that case, we can target a Morpholino oligo across that complementary motif the block the interaction of the two RNAs. Perhaps instead the non-coding RNA's activity is due to a region of secondary structure, such as a crucial stem-loop; in that case, we can target a Morpholino to the stem in order to invade the stem structure, displacing one strand of the stem from the other strand and altering the secondary structure and hopefully altering the activity of that region of the non-coding RNA. Perhaps the non-coding RNA is binding a particular protein or miRNA, acting as a "sponge"; covering the binding site of the protein or miRNA with a Morpholino might productively block the interaction of the RNA with its binding partner. Our Design Request Website has a selection available for designing Morpholinos “Other”; this is an appropriate place to submit sequence for non-coding RNA targets.

To block any of these activities with a Morpholino oligo, we need to know where the activity is located on the non-coding RNA. Recall that Morpholinos do not degrade their RNA targets, so randomly targeting a Morpholino to a non-coding RNA is unlikely to alter the activity of the non-coding RNA. The chances are good that a random target will be distant from the site of the non-coding RNA's activity. So, to design a useful Morpholino for a non-coding RNA we need to know where that activity is located in the non-coding RNA sequence (the base-pairing region, the stem-loop, the binding site, etc.). Please send some sequence for the non-coding RNA with the RNA sequence in UPPER CASE and the active region in lower case, like this:

ATCGTCTATTGTTTCAACTTTTTcgtgctttgatacgcgcgtgatGCTAATACGATTTACTACCATATGAG

We'll look for a good oligo sequence complementary to most or all of the lower case region.

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