Is there any difference in size between two types of mRNAs?

[Eagle9]

As far as I know only 2 % of human genome can make the proteins (protein-coding DNA) while the major part of DNA mainly produces mRNAs that regulate other genes (regulatory RNAs).

I would like to know – are these two kinds of mRNAs comparable in size, that is in the amount of their nucleotides? For example - are the mRNAs producing the proteins longer than those mRNAs that only regulate other genes? Or maybe this in unknown?

And: the size of protein-coding genes (and hence mRNAs) is of course different since they produce various proteins. What about the regulatory RNAs? Are they as miscellaneous in size as protein-coding genes (and hence mRNAs)? Or perhaps they are similar in size?

 

[Ygggdrasil]

A few notes on terminology: the term mRNA (messenger RNA) refers exclusively to mRNAs that encode for proteins. The term for "regulatory" RNAs is ncRNA (non-coding RNA) which refers to all of the RNA molecules that are not translated into protein.

There are a huge variety of ncRNAs, including the transfer RNAs (tRNA) and ribosomal RNAs (rRNA) that play a role in translation, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) that play roles in splicing and RNA processing, and micro RNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) that play roles in gene silencing. Most of these classes of RNAs are considerably smaller than mRNAs and are produced by different polymerases (e.g. Pol I and Pol III) than mRNAs (which are transcribed by Pol II).

A class of regulatory RNA that resembles mRNAs, however, are referred to as long non-coding RNAs (lncRNAs). These RNAs are transcribed by Pol II and undergo capping, splicing and polyadenylation just like mRNAs. Like mRNAs, they also have a pretty wide distribution of sizes.

Here are a couple of good review articles on ncRNAs and lncRNAs in particular:
Cech and Steitz. 2014. The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones. Cell 157: 77. http://dx.doi.org/10.1016/j.cell.2014.03.008

Mattick and Rinn 2015. Discovery and annotation of long noncoding RNAs. Nat Struct Mol Biol 22:5. http://dx.doi.org/10.1038/nsmb.2942

Here's a link to a relevant thread in physics forums about annotating the "dark matter" of the genome: Researchers claim only ~8% of human DNA is functional

 

[Eagle9]

A few notes on terminology: the term mRNA (messenger RNA) refers exclusively to mRNAs that encode for proteins. The term for "regulatory" RNAs is ncRNA (non-coding RNA) which refers to all of the RNA molecules that are not translated into protein.

Yes, I have confused these terms a bit, thanks.

Most of these classes of RNAs are considerably smaller than mRNAs

A class of regulatory RNA that resembles mRNAs, however, are referred to as long non-coding RNAs (lncRNAs). These RNAs are transcribed by Pol II and undergo capping, splicing and polyadenylation just like mRNAs. Like mRNAs, they also have a pretty wide distribution of sizes.

Well, I will tell you why I have actually opened this thread.

So, mRNA encodes proteins and for this purpose this molecule needs to leave the nucleus and depart to ribosomes in cytoplasm. The tRNA and rRNA should also need to leave the nucleus.

But other kinds of RNAs do not need to leave nucleus and they perform their actions there.

You told me that the sizes of these two kinds of RNAs are more or less similar (I mean that some mRNA can be huge or little and the same is true about lncRNAs – they also can vary in size). But why mRNA+ tRNA+ rRNA leave the nucleus and other kinds of RNA do not? What mechanism enables such “segregation” in their movement?

Or maybe regulatory RNA also leaves the nucleus but do not participate in translation because of yet unknown reasons?

 

[Ygggdrasil]

Well, I will tell you why I have actually opened this thread.

So, mRNA encodes proteins and for this purpose this molecule needs to leave the nucleus and depart to ribosomes in cytoplasm. The tRNA and rRNA should also need to leave the nucleus.

But other kinds of RNAs do not need to leave nucleus and they perform their actions there.

You told me that the sizes of these two kinds of RNAs are more or less similar (I mean that some mRNA can be huge or little and the same is true about lncRNAs – they also can vary in size). But why mRNA+ tRNA+ rRNA leave the nucleus and other kinds of RNA do not? What mechanism enables such “segregation” in their movement?

That's a great question. Some lncRNAs are primarily cytoplasmic in their localization and function, some are primarily nuclear in their location and function, and some have even been shown to shuttle back and forth between the nucleus and cytoplasm (see, for example, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819218/). There is certainly a lot of important regulatory mechanisms that control RNA localization (here's a decent review: http://jcs.biologists.org/content/122/12/1933.full), but we probably don't yet have a full understanding of the processes involved, especially those regulating the localization of lncRNAs.

Or maybe regulatory RNA also leaves the nucleus but do not participate in translation because of yet unknown reasons?

Many lncRNAs leave the nucleus. To what extent these are recognized by ribosomes is still unclear. Some do not seem to be translated, but some lncRNAs that were thought to be non-coding were later shown to encode short peptides (whose function may or may not account for functions previously ascribed to the lncRNA). There's probably still a lot of interesting work to be done to see if there are specific mechanisms preventing certain lncRNAs from being recognized for translation.

 

[Eagle9]

There is certainly a lot of important regulatory mechanisms that control RNA localization (here's a decent review: http://jcs.biologists.org/content/122/12/1933.full)

Thanks, I will read this article, seems to be interesting.

Many lncRNAs leave the nucleus. To what extent these are recognized by ribosomes is still unclear. Some do not seem to be translated, but some lncRNAs that were thought to be non-coding were later shown to encode short peptides (whose function may or may not account for functions previously ascribed to the lncRNA).

And are not these short peptides harmful for cell?

 

[Ygggdrasil]

And are not these short peptides harmful for cell?

In a lot of cases, it's unclear since they are fairly newly discovered. They could be a non-functional byproduct of spurrious ribosome activity, they could be harmful, or they could be beneficial and perform some important role in the cell. Many small peptides act as signaling molecules. Somewhat recent research identified some of these peptides as responsible for neurodegeneration in cases of familial ALS (see http://www.sciencemag.org/content/345/6201/1192.long and http://www.sciencemag.org/content/345/6201/1139.long), so it is certainly possible that they can be harmful.