0
$\begingroup$

I was having a look at lncRNAdb and its help says:

The ENCODE project gene annotation list, GENCODE, has predicted that the human genome contains 14,470 lncRNAs whereas only a small proportion of these have been shown to have function.

We have examined thousands of publications in order to find and manually annotate lncRNAs that have been shown to be functional by overexpression or knockdown experiments.

What is meant by Overexpression of a Non-coding RNA here? Even if you have a look at any lncRNA in the DB, its entry has a column for "Expression":

enter image description here

$\endgroup$
1
$\begingroup$

They queried publications dealing with the lncRNA that studied whether it was functional through over-expression or knockdown. Cells do something measurable in their normal state, that can be observed through microscopy, qPCR, microarray, etc. You use the data as a control which to compare experimental results against.

For an over-expression study, for example, you can transfect your cells with a vector that will transcribe a lot of your ncRNA. Whether the transfection need be stable or transient will depend on a number of other factors. So the methods you used to collect data as a control, apply these to the transfected group. If there are statistically significant changes to anything when you have more of the ncRNA, you can say in part that your ncRNA is functional. It's doing something observable.

The opposite is true for knockdown. You can maybe use CRISPR to do the job but lentiviral transduction with say a doxycycline-inducible promoter is among other possibilities. The goal now is to make the gene, or the expression of the gene go away. You do the same experiment, and see if an absence of the ncRNA does anything to the cell.

Now in the database you're looking at, expression is being used to show you in what tissues has BX118339 been detected? It basically says BX118339 is expressed in testis and the fetal brain.

$\endgroup$
3
$\begingroup$

With many non-coding RNAs, the RNA is the functional endpoint. Therefore, ncRNA "expression" simply refers to the production of that functional component. Similarly to with proteins, this involves looking at differential tissue production of that noncoding RNA (i.e. in which tissues the RNA is produced).

Gene expression is defined in the Oxford Dictionary of Biology as:

The manifestation of the effects of a gene by the production of the particular protein, polypeptide, or type of RNA whose synthesis it controls.

In other words, gene expression means the same thing whether the functional product is a protein or a noncoding RNA. Of course, there is no translational component to expression of ncRNA.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.