Turning on pseudogenes

Researchers have discovered a role for pseudogenes – which are thought to be dead genes – in regulating the immune response.
22 August 2013

Interview with 

Howard Chang




Chris -   Within the human genome are large numbers of what are called pseudogenes.  These closely resemble real genes that actually make proteins.  But they've been written off as derelict DNA sequences that have lost their original functions and are no longer needed.  But this is not so says, Stanford's Howard Chang who's found that certain stimuli turn these so-called dead genes back on.  And they appear to have a major role to play as he explained to Kat Arney.

Howard -   So, we were interested in the gene expression programme, just the set of genes that will react when cells are exposed during inflammatory stimulus.  So, inflammation is a very sort of common, universal response of tissue to injury or infection.  That's when if you hit your knee then it gets swollen and red, that's inflammation.  And so, we wanted to understand what kind of genes would turn on or turn off when cells are exposed to signals related to inflammation.

Kat -   And so, how did you go about looking at that?  What sort of cells were you using and what techniques did you try?

Howard -   Using the kind of cell type called fibroblast, they're kind of what makes up what is called the connective tissue.  We use the method that can basically count the different kinds of RNA molecules that a cell would make.  And so, every RNA molecule was sequenced.

Kat -   And an RNA, that's like the message that's made when a gene is switched on?

Howard -   That's right.  So, the genetic information in this DNA is turned into RNA, when the cell wants to use a particular bit of information.  And so, by looking at which RNA molecules are made, you can tell which genes are being turned on.

Kat -   What did you find?

Howard -   Well, what's surprising was that in addition to the usual large number of protein coding genes, so-called messenger RNAs, there were a large number of RNAs that were not coding for proteins.  These are called long, non-coding RNAs.  So, this is a class of newly recognised genes which is actually fairly large.  So, there are probably over 10,000 of these long non-coding RNAs in the human genome.

Kat -   So, these are messages that are written out from the DNA, but they don't tell it to make a protein.  They just do something else.

Howard -   That's right.  Only a very small number of these RNAs have really been studied.  And so, there's a lot of questions about, really, what are full set of long non-coding RNAs and when do they even come on, what kind of signals they respond to, and what they might do.  So, one part of the work was to characterise these long non-coding RNAs that will respond to inflammatory signal.  And a further surprise was that we noticed that there was a set of these long RNAs that come from the so-called pseudogenes.  So, these are genes, are thought to be basically dead genes.  Genes found their ways to becoming molecular fossils if you will.

Kat -   That's really weird because it was thought that these pseudogenes did nothing at all.

Howard -   That's right.  So first of all, I was so surprised and so, we looked more carefully at a particular pseudogene and also, some of the other long non-coding RNAs that were turned on in response an inflammatory signal.  And the further surprise was that now, with the pseudogene turned on in response to let's say a signal, but the response was exquisitely specific.  A certain kind of inflammatory signal let's say for bacteria will turn on the pseudogene.  Therefore, the set of long non-coding RNAs including pseudogenes was so specific that they were like an internal reflection of what the cell was seeing on the outside.  You could tell what the cell was being bombarded with, what kind of infectious or inflammatory signals are coming in by looking at the pattern of these non-coding transcripts.

Kat -   And there was one in particular you studied.  Tell me a bit about that one.

Howard -   This is a pseudogene RNA that we focus on because first, it came out in our screen that it was induced by inflammatory signal and there are other qualities that are interesting in these RNA was made but it was almost entirely in the nucleus, it didn't go into the cytoplasm. And then we noticed that this RNA actually have a role in controlling the inflammatory response.  It turns out that those RNA, when it comes on, the pseudogene RNA is actually a part of the process of damping inflammatory response back down.  It's part of the normal feedback to kind of shut the whole response down again.  We call this RNA Lethe after the Greek 'river of forgetfulness'.  So, they underworld analogy is because of pseudogenes being essentially dead genes.  So, we're both from the idea of the underworld.  But there's also this idea that, let's say, the cell encounter some sort of inflammatory response or some sort of infection and it's gone through this battle and fighting it off.  And now, it's time to go back to your normal life, to move on new life and you had to forget about this inflammation.  And so, you have to turn the whole response down and Lethe is part of that process.  So basically, in the absence of Lethe, the cell will basically keep going forward with the inflammatory response.  It doesn't forget even if the battle is over.

Kat -   Do you think that there are other pseudogenes lurking the genome that have this kind of roles that are actually not drunk and not dead, and could be very active and important?

Howard -   Yes, indeed.  So, I think over the last several years, the other investigators have found have resembled from the ENCODE project that many pseudogenes are actually being transcribed, that they're made.  They're evidence of their activation and that work was led by a Professor Mark Gerstein from Yale.  More recently, other people have realised that pseudogenes because they're copies of normal genes, they have many of the same regulatory sequences embedded in them.  And so, when the pseudogenes are made, because of these regulatory sequences, compete for different cellular factors.

Kat -   Where do you go next for this research?  How are you taking it forward?

Howard -   Well, so a very interesting and unexpected was that we found that the pseudogene regulation actually changes organismal age.  And so, some prior work we had done has shown that as organisms get older, some of the gene regulatory systems involved in inflammation are just activated and stays on over time.  And we didn't know why that was the case.  So, it turns out that the pseudogene, Lethe, that those activated Lethe actually decreases with organismal age.  So somehow, this negative feedback system is gradually lost where organisms get older.  So, this is a very tantalising clue for how, perhaps, the whole system of inflammation and genes regulation aging could break down.  And now, there's a surprising clue that this might actually have to do with pseudogenes.

Chris -   Stanford's Howard Chang.  He was speaking with Kat Arney. 


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