The most interesting paper I’ve read this year

We all know what the estrogen receptor is and what it does.  It’s a large protein with 3  functional components.  Actually there are several estrogen receptor proteins, but I’m going to discuss just one — Estrogen Receptor alpha (ERalpha).

Here are the components:

a DNA binding domain (which binds to stretches of bases called the Estrogen Response Element (ERE))

a domain which binds estrogen changing the conformation of the third domain which is —

a domain which binds to RNA polymerase II activating it so it transcribes genes into mRNA.

Given the complexity of the hormonal cycles, it is far from surprising that the estrogen receptor controls the levels of 15% of all annotated protein coding genes < Cell vol. 145 pp. 622 – 634 ’11 >.

Given its importance in breast cancer, ERalpha has been intensively studied for years.

Now various regions of proteins have been assigned function, the SH2 domain binds to phosphotyrosine in proteins, SH3 binds to proline rich motifs, RNA Binding Domains (RBDs) bind to (what else?) RNAs.  Each of them has a characteristic sequence of amino acids allowing them to be picked out from DNA sequences.

Enter Cell vol. 184 pp. 5086 – 5088, 5215 – 5229 ’21 where ERalpha was found to bind to over 1,200 messenger RNAs (mRNAs).   It was not supposed to do that as it doesn’t contain any RBDs (well at least the RBDs we knew about — back to the drawing board on that one).  Even more interesting is the fact what most of the mRNAs bound by ERalpha aren’t from the genes whose ERE ERalpha binds.

Life is said to have originated in the RNA world.  We all know about the big 3 important RNAs for the cell, mRNA, ribosomal RNA and transfer RNA.  But just like the water, sewer, power and subway systems under Manhattan, there is another world down there in the cell which doesn’t much get talked about.  These areRNAs, whose primary (and possibly only) function is to interact with other RNAs.

The RNA world is still alive and well in all our cells.  It’s like DOS still out there under Windows, or Unix and its command line under the Apple interface. We studied proteins and DNA because they were (relatively) easy to study.

The papers go on to study how ERalpha RNA binding affects cancer (which it does).

But there are far larger questions the work brings forth.

l. ERalpha is just one nuclear hormone receptor and Estrogen is just one hormone.  Do the nuclear hormone receptor for other hormones also bind RNA? Have we been missing some of their actions inside cells and if so there are mechanisms to exploit?

2. Why stop at nuclear hormone receptors?  ERalpha binds RNA with no RNA binding  domains (RBDs) in sight.  Do other proteins also bind RNAs and if so what does it mean?

Fantastic stuff.  There is a whole world of possibilities opening before our eyes thanks to these papers.

It reminds me of what an anatomy professor told us when we were studying neuroanatomy — ‘unfortunately everything is connected to everything else’.

Forgotten but not gone — take III

It’s pretty clear that life originated in the RNA world.  Consumed by thinking of proteins, enzymes, DNA etc. we tend to forget that there is a lot of RNA out there doing things we didn’t suspect.  Here are two more examples, one of which may explain why even genes coding  for proteins are relatively free of codons transcribed into amino acids.  The champ of course is dystrophin, discussed in the last post — https://luysii.wordpress.com/2019/05/05/duchenne-muscular-dystrophy-a-novel-genetic-treatment/.  The gene is a monster with  2,220,233 nucleotides coding for just 3,685 amino acids, meaning that less than 1/200th of the gene is actually coding for protein. The work below should make us think about just what else the 199/200th of dystrophin might be doing,

Unsuspected use of RNA #1.   [ Neuron vol. 102 pp. 507 – 509, 553 – 563 ’19 ]  The Tumor protein p53 inducible nuclear protein 2 (Tp53inp2) gene codes for a low complexity protein of 222 amino acids, all in one exon.  However the ‘3 untranslated region (3’UTR)  of the RNA for it is nearly 5 times longer (3,121 nucleotides) vs. 666 amino acid coding nucleotides.  The protein is made from the mRNA in some cells, but not in sympathetic neurons, even though the mRNA for Tp53inp2 is the most abundant RNA in the axons of these neurons.

Why do animals lick their wounds?  Because their saliva contains nerve growth factor (NGF) among other things.  NGF is crucial for the growth of sympathetic neuron axons, and their very survival in embryonic life.  It is a protein, which binds to a receptor for it (TrkA) on the axon membrane.  The receptor/NGF complex is then internalized and transported back to the nucleus turning on the genes necessary for axon growth and cell survival.

Even though the mRNA for Tp53inp2 is NOT translated into protein in the axon, it is crucial for the internalization of TrkA/NGF.

People have studied proteins whose function it is to bind RNA for years.  They are called RBPs (RNA Binding Proteins), and our genome has 750 of them.  200 RBPs are associated with genetic disease.  This work turns everthing on its head.  Here is an RNA whose function it is to bind a protein (e.g. TrkA).

How many more mRNAs have nonCoding (for protein) parts with other functions?

Unsuspected use of RNA #2. Circular RNAs had been missed for years (although known since 1976).  The classic sequencing methods isolate only RNAs with characteristic tails (such as polyAdenine).  Circular RNAs don’t have any.    They are formed by back splicing of 3′ end of exon N to the 5′ end of exon N.  Fortunately this is only 1% as efficient as the normal way.

So what?  Circular RNAs are crucial in the innate immune response to microbial invaders.  Double stranded DNA belongs inside the nucleus.  When it gets into the cytoplasm when some organism brings it there,it binds to Protein Kinase R (PKR) activating it so it phosphorylates eukaryotic initiation factor 2 (eiF2) bringing protein synthesis to a screeching halt.

This means that the cell needs a mechanism to keep PKR quiet.  This is where circular RNAs come in   [ Cell vol. 177 pp. 797 – 799, 865 – 880 ’19 ].  If the nucleotides in the circle can reach across the circle and base pair with each other forming a duplex of any length, it will bind to PKR inhibiting it.  Most circular RNAs are expressed at only a handful of copies/cell, the cell containing just 10,000 of them.

The work found that overexpression of a single circular RNA able to form duplexes (dsRNA) inhibits PKR.  Over expression of linear RNA of the same sequence does not, nor does overexpression of circular RNA which can’t form dsRNA.

So when an invader with dsDNA or dsRNA gets into the cell, RNAase L, a cytoplasmic endonuclease is activated, cleaving circular RNA, and uninhibiting PKR.

So it’s back to the drawing board for mRNA and those parts (introns, 3’UTRs) we didn’t think were doing anything.  Perhaps that’s why there are so many of them, and why they take up more room in mRNA and genes than the ones coding for amino acids.  Also it’s time to look at RNAs as protein binders and modifiers, rather than the other way around as we have been doing.

Here’s a link to an earlier member of the series — https://luysii.wordpress.com/2019/04/15/forgotten-but-not-gone-take-ii/xa

Forgotten but not gone — take II

The RNA world from whence we sprang strikes again, this time giving us a glimpse into its own internal dynamic.  18 months ago I wrote the following post — which will give you the background to follow the latest (found at the end after the (***)

Life is said to have originated in the RNA world.  We all know about the big 3 important RNAs for the cell, mRNA, ribosomal RNA and transfer RNA.  But just like the water, sewer, power and subway systems under Manhattan, there is another world down there in the cell which doesn’t much get talked about.  These areRNAs, whose primary (and possibly only) function is to interact with other RNAs.

Start with microRNAs (of which we have at least 1,500 as of 12/12).  Their function is to bind to messenger RNA (mRNA) and inhibit translation of the mRNA into protein.  The effects aren’t huge, but they are a more subtle control of protein expression, than the degree of transcription of the gene.

Then there are ceRNAs (competitive endogenous RNAs) which have a large number of binding sites for microRNAs — humans have a variety of them all with horrible acronyms — HULC, PTCSC3 etc. etc. They act as sponges for microRNAs keeping them bound and quiet.

Then there are circular RNAs.  They’d been missed until recently, because typical RNA sequencing methods isolate only RNAs with characteristic tails, and a circular RNA doesn’t have any.  One such is called CiRS7/CDR1) which contain 70 binding sites for one particular microRNA (miR-7).  They are unlike to be trivial.  They are derived from 15% of actively transcribed genes.  They ‘can be’ 10 times as numerous as linear RNAs (like mRNA and everything else) — probably because they are hard to degrade < Science vol. 340 pp. 440 – 441 ’17 >. So some of them are certainly RNA sponges — but all of them?

The latest, and most interesting class are the nonCoding RNAs found in viruses. Some of them function to attack cellular microRNAs and help the virus survive. Herpesvirus saimiri a gamma-herpes virus establishes latency in the T lymphocytes of New World primates, by expressing 7 small nuclear uracil-rich nonCoding RNAs (called HSURs).  They associate with some microRNAs, and rather than blocking their function act as chaperones < Nature vol. 550 pp. 275 – 279 ’17 >.  They HSURs also bind to some mRNAs inhibiting their function — they do this by helping miR-16 bind to their targets — so they are chaperones.  So viral Sm-class RNAs may function as microRNA adaptors.

Do you think for one minute, that the cell isn’t doing something like this.

I have a tendency to think of RNAs as always binding to other RNAs by classic Watson Crick base pairing — this is wrong as a look at any transfer RNA structure will show. https://en.wikipedia.org/wiki/Transfer_RNA.  Far more complicated structures may be involved, but we’ve barely started to look.

Then there are the pseudogenes, which may also have a function, which is to be transcribed and sop up microRNAs and other things — I’ve already written about this — https://luysii.wordpress.com/2010/07/14/junk-dna-that-isnt-and-why-chemistry-isnt-enough/.  Breast cancer cells think one (PTEN1) is important enough to stop it from being transcribed, even though it can’t be translated into protein.

*****

[ Proc. Natl. Acad. Sci. vol. 116 pp. 7455 – 7464 ’19 ] The work reports a fascinating example of that early world in which the function of one denizen (a circular RNA called cPWWP2A) binds to another denizen of that world (microRNA 579 aka miR-579) acting as a sponge sopping up so it can’t bind to the mRNAs for angiopoetitin1, occludin and SIRT1.

So what you say?  Well it may lead to a way to treat diabetic retinopathy. How did they find cPWWP2A?  They used the Shanghai BIotechnology Company Mouse Circular RNA microArray which measures circular RNAs.  They found that 400 or so that were upregulated in diabetic retinopathy and another 400 or so that were downregulated.  cPWWP2A was on of the 3 top upregulated circular RNAs in diabetic retinopathy.  cPWWP2A comes from (what else?) PWWP2A, a gene coding for a protein which specifically binds the histone protein H2A.Z.

Overexpression of cPWW2PA or inhibition of miR-579 improves retinal vascular dysfunction in experimental diabetes.

So here is all this stuff going on way down there in the RNA world, first interacting with other players in this world and eventually reaching up to the level we thought we knew about and controlling gene expression.  It’s sort of like DOS (Disc Operating System) still being important in Windows.

How much more stuff like this is to be discovered controlling gene expression in us is anyone’s guess

Why drug development is hard #30 — more new interactions we had no idea existed

We’re full of proteins which bind RNA wrangling it into a desired conformation.  The ribosome (whose enzymatic business end is pure RNA) has a mere 80 proteins doing this.  Its mass is 4,300,000 times that of a hydrogen atom.  However the idea that RNA could return the favor was pretty much unheard of until [ Science vol. 358 pp. 993 – 994, 1051 – 1055 ’17 — http://science.sciencemag.org/content/358/6366/1051 ].

As is often the case, viruses and the RNA world continue to instruct us.  In order to survive, some viruses induce cells to express a long (2,200+ nucleotides) nonCoding (for protein that is) RNA called lncRNA-ACOD1.   It binds to a protein enzyme (called GOT2, for Glutamic acid OxaloAcetic Transaminase 2) increasing its catalytic efficiency.  This shifts cellular metabolism around making it more favorable for virus proliferation, as GOT2 is found in mitochondria being used to replenish tricarboxylic cycle intermediates — e.g. making more energy available to the virus.

lncRNA-ACOD1 is induced by a variety of viruses, most importantly influenza virus in man, and vaccinia, herpes simplex 1, vesicular stomatitis virus in mice.  Exactly how viruses induce it isn’t clear, but the transcription factor NFkappaB is involved.

Viruses continue to teach us.  The amino acids of GOT2 (#15 – #68) and the interacting sequence of nucleotides in lncRNA-ACOD1 (#165 – #390) are well conserved across species.  This might be a primordial mechanism from the RNA world (forgotten but not gone) to produce ATP production to compe with metabolic stress.   The RNA/protein binding site is close (4.2 Angstroms) to the substrate binding site.

The fun is just starting as several other lncRNAs are induced by viruses.  You can only imagine what they will tell us.  Another set of drug targets perhaps, or worse, the cause of peculiar side effects from drugs already in use.