Functioning DNA from an extinct animal

[Ouabache]

So not only are researchers spelling out the genetic sequences of extinct creatures,
they have now successfully inserted some DNA from an extinct animal into a modern day one and observed how that DNA functions. Amazing!

Researchers took tissue from 100yr old museum specimens of a marsupial (Tazmanian tiger) in Australia and inserted some of its DNA into a mouse. The new DNA did function and the resulting expression observed.

See Tasmanian tiger DNA Resurrected from BBC news and Resurrection of DNA Function In Vivo from an Extinct Genome from science publication - PLoS One

 

[Q_Goest]

That is pretty cool! I'm no biology wiz, but I tried to read through the PLoS paper and I did read the BBC article. From them, I don't understand how the researchers could determine if the gene was expressed or not. Is this strictly a molecular study, such that living mouse cells (were they even inside a living mouse?) had their DNA altered with DNA from Tazmanian Tiger (TT) and researchers observed this particular DNA being expressed by the cell, or was something else done to determine the TT DNA was expressed? Can you explain what the researchers did for us mechanical engineers?

 

[BoomBoom]

They attached an enhancer from the TT to lacZ. This is a reporter gene and shows up a certain color when in the presence of X-gal. So they inserted this construct into a developing mouse and grew it up, then examined the tissue of this mouse under a microscope to determine if the reporter was present.

While many adaptive changes throughout evolution have been ascribed to changes within the proteins themselves [8], [9], the high conservation of protein coding regions between mammalian genomes suggests that changes in the open reading frames are unlikely to be the primary cause of the vast differences observed in both form and function [10]–[12]. With the recent release of the ENCODE pilot study [13] it is clear that the majority of the non-coding mammalian genome is transcribed. It appears that rather than changes in the genes themselves, it is subtle differences in their non-coding regulatory elements that control their spatial, temporal and quantitative expression that underpins the variation in the animal kingdom [10]–[12]. Therefore, the non-coding regions of extinct genomes are likely to hold the most important genetic information that defined a species.

^^ LOL ...and they used to refer to this as "junk" DNA! :P ^^

 

[Ouabache]

They attached an enhancer from the TT to lacZ. This is a reporter gene and shows up a certain color when in the presence of X-gal. So they inserted this construct into a developing mouse and grew it up, then examined the tissue of this mouse under a microscope to determine if the reporter was present.

Thanks for jumping in there BoomBoom. This is not my specialty area, however I can understand the jargon to a useful degree. Q_Goest, it is difficult to answer your questions without assuming some familiarity of the vocabulary. Boomboom has given a good explanation, however there are some terms that may not be obvious to those outside the field..

enhancer = A regulatory sequence that can elevate levels of transcription from an adjacent promoter.

lacZ = is a reporter gene that codes for the enzyme $\beta$-galactosidase.

reporter gene = A gene whose phenotypic expression is easy to monitor; used to study promoter activity in different tissues or developmental stages. Recombinant DNA constructs are made in which the reporter gene is attached to a promoter region of particular interest and the construct transfected into a cell or organism.

promoter = A region of DNA to which RNA polymerase binds in order to initiate transcription.

terms in bold print were referenced from --> http://www.everythingbio.com/glos/index.php

X-gal = 5-bromo-4-chloro-3-indolyl-b-D-galactopyranoside (from PLoS article)

in vivo = the research is done within a living organism, in this case a mouse.. If it had been done in a culture outside the organism, in the laboratory, it would be an in vitro study. From the title of the PLoS article, we see that this research was in vivo

One thing Boomboom didn't elaborate on, is that the tissue which took up stain and observed under the microscope, was cartilage. The DNA from an extinct animal directed chondrocyte-specific expression. (chondrocyte = cartilage cell).

 

[Q_Goest]

BoomBoom, Oabache, thanks. Like the comment about junk DNA!

- Found this short video for us biology laymen:
http://gmy.news.yahoo.com/v/7908961 [Broken]

What strikes me is interpretation of DNA. If you think of DNA like a 4 character code analogous to English having a 26 character code (ie: a through z) then we may be led to believe that the genetic code in one species can be interpreted differently by another species just as a word in English may mean one thing, but in another language, the word may mean something else. But that's not the case for any known species on Earth. We all use the same 'code', which the ribosome deciphers.

So in the case of TT genes being transplanted into the mouse, I have to assume the mouse ribosome has no trouble interpreting the gene. But wouldn't that also be true of genetic material that came from a mushroom, or a trilobite? Wouldn't the mouse embryo have done the same thing with ANY gene from ANY living organism?

 

[BoomBoom]

Apologies for my abbreviated explanation and thanks for the elaboration Ouabache. :)

If you think of DNA like a 4 character code analogous to English having a 26 character code (ie: a through z)

Actually, the DNA code is in triplet codons that are translated into an amino acid, so I prefer to think of the "alphabet" as the 20 amino acids rather than the 4 nucleotides.

What would be REALLY interesting IMO, would be to see if some life form from another planet used the same alphabet...(still hoping they find one in my lifetime).

So in the case of TT genes being transplanted into the mouse, I have to assume the mouse ribosome has no trouble interpreting the gene. But wouldn't that also be true of genetic material that came from a mushroom, or a trilobite? Wouldn't the mouse embryo have done the same thing with ANY gene from ANY living organism?

Pretty much, yes...you are correct. This has been done with many genes from many different dpecies.

 

[Charion]

Just a minor correction (and yeah, I know I am nitpicking). Enhancers do not need to be adjacent to a promoter. One of its interesting properties is that it can be several kilobases distant from the promoter it controls. Of course, if the space in-between might be "empty" thus technically they may be adjacent. But often other sequences (e.g. additional promoters) are found there, especially in prokaryotes.

So in the case of TT genes being transplanted into the mouse, I have to assume the mouse ribosome has no trouble interpreting the gene. But wouldn't that also be true of genetic material that came from a mushroom, or a trilobite? Wouldn't the mouse embryo have done the same thing with ANY gene from ANY living organism?

In principal the origin of the DNA is not important, one could also do it with synthetic sequences. However there are some limitations. One is that the DNA might be modified in a different way. This does not change the encoded information per se, but might affect actual expression. Then organisms have a codon bias that is the abundance of certain tRNAs (witha specific anti-codon) might vary. Translation of rare codons can be inefficient and in some cases might not happen at all. And finally, even if expressed and translated, the resulting protein might of course not be modified or folded correctly. And of course certain (very, very distant) organisms may have slightly different genetic codes)

But again, this is just basically nitpicking (partially to take my mind off paper writing for the moment) and for the most part expressing DNA of one organism in another (also termed heterologous expression) is pretty much standard.