Question for Geneticists & Biologists about DNA sequence nomenclature?

[Henry]

A thread in d20 Systems got me thinking abut something, and I was hoping a poster familiar with the science of Genetics (either a professional or a student) would help point me in the right direction.

I was wondering how certain Genes and DNA sequences in a Genome are properly named and described. I have absolutely no clue, but I know that there has to be a proper I.D. system for identifying a certain gene or DNA sequence in a genome, especially since so much work has now been done on identifying parts of the human genome.

Can someone either help point me in the right direction for such information, or if the ID system is far simpler than I realize, could they brief me on it?

I got to thinking that this knowledge would be useful for GM's looking to inject a bit of pseudo-realism in any of their Modern or Genetech-type games.

Thank you in advance!

 

[Piratecat]

I got to thinking that this knowledge would be useful for GM's looking to inject a bit of pseudo-realism in any of their Modern or Genetech-type games.

Thank you in advance!

Whoo hoo - you know he's a moderator, 'cause he knows how to make a thread gaming-related and keep it in General!

 

[Wrath of the Swarm]

Well, I'm not a professional....

To the best of my knowledge, all genes are known to be preceeded and followed by special codon sequences that signal the cell when to begin and stop transcribing. If you wanted to know whether a particular stretch of DNA represents a gene or not, you could just check for the presence of these sequences.

See

http://www.gene.ucl.ac.uk/nomenclature/
http://www.accessexcellence.org/AE/AEPC/NIH/gene11.html

 

[diaglo]

i'll take a shot at what i think you are asking:

The correlation between a gene defect and a disease at the molecular level may not always involve a mutation in the coding sequence of a gene; changes can occur in the regulatory regions of a gene or a the splice junctions between exons and introns. Once a disease causing gene has been identified, it is often possible to develop diagnostic tests and, more important, to learn more about the molecular basis of the disease, with the goal of devising therapeutic measures.

Gene: A segment of nucleic acid that encodes a functional protein or RNA. The unit of inheritance.

 

[Darklone]

Gattaca

 

[(Psi)SeveredHead]

A thread in d20 Systems got me thinking abut something, and I was hoping a poster familiar with the science of Genetics (either a professional or a student) would help point me in the right direction.

I was wondering how certain Genes and DNA sequences in a Genome are properly named and described. I have absolutely no clue, but I know that there has to be a proper I.D. system for identifying a certain gene or DNA sequence in a genome, especially since so much work has now been done on identifying parts of the human genome.

Can someone either help point me in the right direction for such information, or if the ID system is far simpler than I realize, could they brief me on it?

I got to thinking that this knowledge would be useful for GM's looking to inject a bit of pseudo-realism in any of their Modern or Genetech-type games.

Thank you in advance!

I can give a bit of info. Most genes are named after mutations, which means a gene usually does the opposite of what it's supposed to do

An example is the gene egl-1, which is found in nematodes. A worm with the mutation egl-1- cannot lay eggs, but can still mate (many are hermaphrodites). Egl-2 is a gene with a very different function, but it was discovered through a mutation that prevents a worm from laying eggs. There are something like 9 egl genes; maybe more.

Each mutation can have it's own name, so egl-1- 13 might be a very specific deletion, and egl-1- 14 might be a point mutation. Usually this is more detailed than the researcher needs to know, especially if they're more interested in treating a genetic disease than looking at the underlying genetics.

A gene consists of (this is a simplification) an operator, promoter and one or more transcription sequences. A repressor can attach to the operator, preventing the gene from functioning. The promoter ensures that the DNA is transcribed, but it must be exposed and the operator must be clear.

 

[Henry]

I think (Psi)SeveredHead is hitting closer to the mark of what I'm looking for; basically, if I were spouting off some pseudobabble in-game about "X gene sequence" causing a mutation that causes him to see in the dark, or "DNA sequence X through Y causing those claws growing out of his arms", then what I was looking for was specific nomenclature where someone could find a specific DNA sequence, as if someone were referring to it in a madical paper.

Or is our understanding of genetic sequencing nowhere near that precise yet?

 

[kamosa]

Genes get named in several different ways.

1) Often the gene is named after the gentic mutation it is associated with. For example if a wing causes a fly to have curly wings then its called crl The reasoning is that this makes the gene name more memorable.

2) Genes are named something cool or silly sounding. My particular favorite is cheap date- a gene that affects a fly's behavioral response to alcohol. Sometimes the gene or structure can be named after the professor or student that discovered it.

3) With more modern sequencing of whole genomes, we have whole genomes that are named by the sequencing results. Thus every potential gene is named in the genome in some formulaic manner. ex: every gene that is on this chromosome will begin with ylr, the direction of the reading frame is indicated with a w or c (for watson and crick) and then the genes are number 1,2,3... , so you can end up with the really memorable gene names such as ylr219w.

 

[Conaill]

You would think there's such a standard, wouldn't you? Well, you'd be mostly wrong. In fact, biology has a big problem with a lack of formal nomenclature, or differences in nomenclature between organisms.

Ok, so perhaps it's not quite as bad as that, but for someone like me who has entered this field from a more computational side, it can be quite frustrating.

For human gene names (gene symbols actually, the names are the long form of the name, like "UDP glycosyltransferase 1 family, polypeptide A1", for UGT1A1) have to be upper case letters and numerals, preferably no longer than six characters long, and must not duplicate any existing genes in the human or mouse database. Here's a link for the offcial Human Gene Nomenclature Guidelines

Other organisms have very different rules. For example, egl-1 would not be avalid name for a human gene. The fruitfly community for example has a tradition for coming up with very imaginative and funny names such as "sonic hedgehog" etc. Typically named after how the flies or their embryos look like after mutating the gene.

Here's an excellent collection of links on gene names:
Clever Gene Names

 

[(Psi)SeveredHead]

Basically, if I were spouting off some pseudobabble in-game about "X gene sequence" causing a mutation that causes him to see in the dark, or "DNA sequence X through Y causing those claws growing out of his arms", then what I was looking for was specific nomenclature where someone could find a specific DNA sequence, as if someone were referring to it in a madical paper.

Or is our understanding of genetic sequencing nowhere near that precise yet?

Yes and no If the gene has already been discovered then you could that.

However, there are two points I should make:

1) Don't believe the hype of the Human Genome Project. They know where all the genes are on the chromosomes, but they don't know what they all do. As a result, scientists still have to find out what these genes do.

2) Some mutations are simple, and some are very complex. I tend to look at things from the developmental point of view. For instance, I got somewhat upset when reading the Star Trek books based on the Eugenics Wars, because they would just inject someone with gorilla DNA (I presume the genes for musculature) and, voila, you get a strong embyro!

Of course, humans and gorillas share nearly all the same DNA including the genes for actin and myosin (the active ingredients in muscle), so gorilla muscle genes wouldn't make you stronger. Instead, non-muscle genes used to regulate how muscle is packed together would do the trick. Of course, no one knows how these work yet in enough detail to create stronger human embryos... this information may be available in the future.

Perhaps you could invent a portable full-DNA scanner for your campaign, and either set it some time in the future or have this technology "covert". A supercomputer to do all the calculations would also help (although you could just mention claw-1+ when asked for details ).