Are non-coding RNAs introns?

Question

I am slightly confused as to what part of the genome codes for non-coding RNAs. Is it the introns? This would make sense to me as to why they are not transcribed as the introns are not transcribed. Or is non-coding RNA actually exons which are simply not transcribed? If so, what are the introns actually for? I cannot seem to find a succinct answer to this. Wikipedia, for example, seems rather vague:

While introns do not encode protein products, they are integral to gene expression regulation. Some introns themselves encode functional RNAs through further processing after splicing to generate noncoding RNA molecules.[18] Alternative splicing is widely used to generate multiple proteins from a single gene. Furthermore, some introns play essential roles in a wide range of gene expression regulatory functions such as non-sense mediated decay[19] and mRNA export.[20]

In either case, does anyone also have any information as to why the ncRNA is not translated? What is the mechanism that prevents it from being translated? My guess is that, for some ncRNAs, it is a matter of them not being able to leave the nucleus as I understand many ncRNAs deal with post-transcriptional gene silencing, although tRNA and rRNA clearly do leave the nucleus...

I would be very grateful for any help about introns/exons/ncRNAs. Thank you :)

Answer 1

While Ankur's answer is correct, it must be noted that not all non-coding RNAs are introns.

An intron must be excised from an mRNA, which therefore means that any non-coding RNA that is not part of an mRNA cannot be an intron.

For example, rRNA and tRNA are all examples of non-coding RNAs that are not introns, since they are not part of mRNA. miRNA may in some instances be produced from introns, but when transcribed separately, they are not introns.

mRNA translation depends on many factors that bind to processed mRNA (a very long process). Other RNA do not undergo this process, and therefore are not reconised by ribosomes and are not translated.

Answer 2

A clarification on introns and exons.

While it is true that introns are not a part of the mRNA as March Ho said, they are essentially transcribed. This may seem trivial but it is important to note. So:

• Both introns and exons arise from the transcribed region
• Exons need not necessarily form the ORF (i.e. be translated to proteins)

Regarding intronic RNAs:

The community does not have a good definition of intronic RNAs. Most of these RNAs have been identified by sequencing and the sequencing experiment can only say which region of the genome a read maps to. It does not give any clue about how the RNA was produced.

So any read mapping to intron of another gene has been classified as intronic RNA which IMO is not fully correct. Only reads that truly arise from the intronic region of the nascent transcript (via RNA processing) are to be considered as intronic RNAs, and not merely based on their genomic overlap. Any independent transcript that overlaps with the intronic region is to be considered an overlapping gene. However, ascertaining the mechanism may not be that simple. miRNAs and some snoRNAs are known to be produced from processing of the intronic region.

A statement such as this (from the cited article [18] in your quotes):

Examining the data for intronic and exonic DNA from the human genome, piRNAs are significantly more likely than expected ($\chi^2_{1df}$ = 1353.2; P < 2.2 × 10⁻¹⁶) to reside in exons rather than introns, given that introns are on average, approximately 15 times larger than exons.
[…]
we found 36 sequences with a perfect match to regions overlapping the exon–exon splice junctions of mRNA, suggesting that these piRNA are produced from mature mRNA.

may be misleading because it just talks about genomic overlap. Most piRNAs are synthesized as a long RNA that is exonucleolytically chopped from the 3' to yield the mature piRNA. Without further experimentation, making such a statement can be dangerous.

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In either case, does anyone also have any information as to why the ncRNA is not translated? What is the mechanism that prevents it from being translated?

Apart from your reasoning on nuclear retention (many ncRNAs are cytoplasm-localized), there can be many other reasons, chiefly the absence of an intact ORF. Even if an ORF is present, translation initiation requires other features like Kozak consensus sequence etc. Having said that, some reads mapping to lncRNAs have been found to be associated with ribosomes (Guttman et al. 2013). Whether or not they translate is not really known.

Answer 3

Yup - in a lot of cases the transcription of non-coding RNAs is from introns. Some of them are within genes (intragenic) and others are intergenic (between genes). In humans, a large number of both have been documented http://www.nature.com/ng/journal/v47/n3/full/ng.3192.html

Coming to your question about why they are not transcribed - it again comes down to the same histone marks and promoters that regulate the transcription of coding genes; there is nothing fundamentally special about the transcription of ncRNA ; differences emerge later when mRNA is capped and polyadenylated, and therefore prone to less degradation.

Also, lots and lots of ncRNAs are transcribed , but are less abundant. Some of the interesting roles they play include interacting with chromatin modifying enzymes, regulating DNA methylation along with the traditionally known functions involving gene silencing by antisense transcripts or miRNA-driven suppression of expression.