Tag Archives: retrovirus

Scary stuff

While you were in your mother’s womb, endogenous viruses were moving around the genome in your developing developing brain according to [ Neuron vol. 85 pp. 49 – 59 ’15 ].

The evidence is pretty good. For a while half our genome was called ‘junk’ by those who thought they had molecular biology pretty well figured out. For instance 17% of our 3.2 gigaBase DNA genome is made of LINE1 elements. These are ‘up to’ 6 kiloBases long. Most are defective in the sense that they stay where they are in the genome. However some are able to be transcribed into RNA, the RNA translated into proteins, among which is a reverse transcriptase (just like the AIDS virus) and an integrase. The reverse transcriptase makes a DNA copy of the RNA, and the integrates puts it back into the genome in a different place.

Most LINE1 DNA transcribed into RNA has a ‘tail’ of polyAdenine (polyA) tacked onto the 3′ end. The numbers of A’s tacked on isn’t coded in the genome, so it’s variable. This allows the active LINE1’s (under 1/1,000 of the total) to be recognized when they move to a new place in the genome.

It’s unbelievable how far we’ve come since the Human Genome Project which took over a decade and over a billion dollars to sequence a single human genome (still being completed by the way filling in gaps etc. etc [ Nature vol. 517 pp. 608 – 611 ’15 ] using a haploid human tumor called a hydatidiform mole ). The Neuron paper sequenced the DNA of 16 single neurons. They found LINE1 movement in 4

Once a LINE1 element has moved (something very improbable) it stays put, but all cells derived from it have the LINE1 element in the new position.

They found multiple lineages and sublineages of cells marked by different LINE1 retrotransposition events and subsequent mutation of polyA microsatellites within L1. One clone contained thousands of cells limited to the left middle frontal gyrus, while a second clone contained millions of cells distributed over the whole left hemisphere (did they do whole genome on millions of cells).

There is one fly in the ointment. All 16 neurons were from the same ‘neurologically normal’ individual.

Mosaicism is a term used to mean that different cells in a given individual have different genomes. This is certainly true in everyone’s immune system, but we’re talking brain here.

Is there other evidence for mosaicism in the brain? Yes. Here it is

[ Science vol. 345 pp. 1438 – 1439 ’14 ] 8/158 kids with brain malformations with no genetic cause (as found by previous techniques) had disease causing mutations in only a fraction of their cells (hopefully not brain cells produced by biopsy). Some mosaicism is obvious — the cafe au lait spots of McCune Albright syndrome for example. DNA sequencing takes the average of multiple reads (of the DNA from multiple cells?). Mutations foudn in only a few reads are interpreted as part of the machine’s inherent error rate. The trick was to use sequencing of candidate gene regions to a depth of 300 (rather than the usual 50 – 60).

It is possible that some genetically ‘normal’ parents who have abnormal kids are mosaics for the genetic abnormality.

[ Science vol. 342 pp. 564 – 565, 632 -637 ’13 ] Our genomes aren’t perfect. Each human genome contains 120 protein gene inactivating variants, with 20/120 being inactivated in both copies.

The blood of ‘many’ individuals becomes increasingly clonal with age, and the expanded clones often contain large deletions and duplications, a risk factor for cancer.

Some cases of hemimegalencephaly are due to somatic mutations in AKT3.

30% of skin fibroblasts ‘may’ have somatic copy number variations in their genomes.

The genomes of 110 individual neurons from the frontal cortex of 3 people were sequenced. 45/110 of the neurons had copy number variations (CNVs) — ranging in size from 3 megaBases to a whole chromosome. 15% of the neurons accounted for 73% of of the CNVs. However, 59% of neurons showed no CNVs, while 25% showed only 1 or 2.

We wouldn’t exist if retroviruses weren’t moving around in our genome.

Time for some of the excellent molecular biology I’ve put off writing about while I plow through the new Clayden.  I reached the halfway point today (p. 590) Exactly 2 months and 2 weeks after it arrived.  The chemist might need  some brushing up on DNA and messenger RNA before pushing on.  Pretty much all the background needed is found in https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/ an d https://luysii.wordpress.com/2010/07/11/molecular-biology-survival-guide-for-chemists-ii-what-dna-is-transcribed-into/.

Everyone has heard of the AIDs virus.  It has so far been impossible to cure because it hides in our DNA doing next to nothing.  Tickle it in a variety of unknown ways, and it’s DNA is transcribed into messenger RNA (mRNA), the virus is assembled and goes on to wreak havoc with our immune system.  How does the AIDs virus get into our DNA in the first place?  Its genome is made of RNA, not DNA.  It has an enzyme (reverse transcriptase) which transcribes its RNA into DNA, and another enzyme (the integrate, which is actually a complex of proteins) which patches the DNA copy (called cDNA) into our genome.  That’s why we can’t get rid of it.  That’s also why it’s called a retrovirus — because of retrograde transcription of its RNA into cDNA).

Well, sorry to say, but at least 10% of our DNA is made of retrovirus remnants.  The vast majority of them have been crippled by mutation so their reverse transcriptases  don’t work any more, or there is something wrong with their integrase, etc. etc.  Some of them do make RNA copies of themselves however, but the copies are mutated enough that infectious virus doesn’t form.  But the RNA copies can be reverse transcribed  into cDNA and reinserted back into our DNA, and in a new site to boot.  This is why they are called retrotransposons.

The whole bunch of retroviruses, retrotransposons, and other repetitive elements of DNA have been called ‘junk’ by eminent authority.  Another epithet for them is the selfish gene — which exists only to reproduce itself.  Humans are said to be machines for reproducing human DNA.

Enter  [ Cell vol. 150 pp. 7 – 9, 29 – 38 ’12 ].  Now it’s time for some very human biology The fetus represents an immunologically different graft to the mother.  Half its antigens are tolerated because they are maternal, the paternal half are not likely to be.  Allogeneic means a transplant from a different member of the same species, so the fetus is regarded as semiallogeneic. 

So why doesn’t our immune system attack the placenta surrounding the fetus, which expresses the paternal proteins?  There’s probably a lot more to it but a class of immune cell called a regulatory T cell (Treg) shuts down the immune response wherever they are found, and the placenta has lots of them.

Different cells express different proteins, and Tregs are no exception. A transcription factor is something that binds to the DNA in front of a gene, turning on transcription of the gene,  ultimately increasing production of the protein the gene codes for. Specificity is obtained by the transcription factor binding to particular sequences of DNA, which are found in only in front of a subset of  genes

The transcription factor which turns on genes necessary to turn an immune cell into a Treg is called Foxp3.  Foxp3 is a protein and to have lots of it around the gene for it must be turned on so its mRNA can be made.  Guess what?  This means that other transcription factors must bind in front the Foxp3 gene.
Here’s Jonathan Swift on the subject
So nat’ralists observe, a flea
Hath smaller fleas that on him prey,
And these have smaller fleas that bite ’em,
And so proceed ad infinitum.”

An important protein like Foxp3 is highly controlled.  There are 3 distinct regions in front of the gene were other transcription factors and repressors of transcription bind.  They are called conserved nonCoding sequences (CNSs), an oxymoron, because they are clearly coding for something quite important. The 3 sequences are called CNS1, CNS2 and CNS3.    Technology has progressed to the point where we can remove just about any DNA sequence from the mouse genome we wish (the resultant mice are called knockout mice).  

Anyway if you knockout CNS1 the mice resorb semiallogenic fetuses (where the father and the mother aren’t genetically related), but not allogenic fetuses (where the genomes of the father and the mother are pretty much the same due to inbreeding).  It’s possible to trace Foxp3 far back in evolution.  Only animals with placentas (eutherians) have CNS1 in addition to CNS2 and CNS3. Marsupials, which don’t have placentas, just have CNS2 and CNS3. 

So where do retrotransposons come in?  The structure of CNS1 shows that it is a retrotransposon which moved in front of the Foxp3 gene.  It mutated enough for a new and different set of transcription factors to bind to it and turn on Foxp3 expression in the placenta allowing survival of the fetus.  Some Junk DNA indeed !