Junk DNA

[hallenrm]

A theory for the genesis of the junk DNA that occured to me after I came across the following research news

 

HOUSTON, Jan. 29, 2007 -- It's a mystery why the speed and complexity of evolution appear to increase with time. For example, the fossil record indicates that single-celled life first appeared about 3.5 billion years ago, and it then took about 2.5 billion more years for multi-cellular life to evolve. That leaves just a billion years or so for the evolution of the diverse menagerie of plants, mammals, insects, birds and other species that populate the earth.

 

New studies by Rice University scientists suggest a possible answer; the speed of evolution has increased over time because bacteria and viruses constantly exchange transposable chunks of DNA between species, thus making it possible for life forms to evolve faster than they would if they relied only on sexual selection or random genetic mutations.

 

"We have developed the first exact solution of a mathematical model of evolution that accounts for this cross-species genetic exchange," said Michael Deem, the John W. Cox Professor in Biochemical and Genetic Engineering and professor of physics and astronomy.

 

The research appears in the Jan. 29 issue of Physical Review Letters.

 

Past mathematical models of evolution have focused largely on how populations respond to point mutations – random changes in single nucleotides on the DNA chain, or genome. A few theories have focused on recombination – the process that occurs in sexual selection when the genetic sequences of parents are recombined.

 

Horizontal gene transfer (HGT) is a cross-species form of genetic transfer. It occurs when the DNA from one species is introduced into another. The idea was ridiculed when first proposed more than 50 years ago, but the advent of drug-resistant bacteria and subsequent discoveries, including the identification of a specialized protein that bacteria use to swap genes, has led to wide acceptance in recent years.

 

"We know that the majority of the DNA in the genomes of some animal and plant species – including humans, mice, wheat and corn – came from HGT insertions," Deem said. "For example, we can trace the development of the adaptive immune system in humans and other jointed vertebrates to an HGT insertion about 400 million years ago."

 

The new mathematical model developed by Deem and visiting professor Jeong-Man Park attempts to find out how HGT changes the overall dynamics of evolution. In comparison to existing models that account for only point mutations or sexual recombination, Deem and Park's model shows how HGT increases the rate of evolution by propagating favorable mutations across populations.

 

Deem described the importance of horizontal gene transfer in the work in a January 2007 cover story in the Physics Today, showing how HGT compliments the modular nature of genetic information, making it feasible to swap whole sets of genetic code – like the genes that allow bacteria to defeat antibiotics.

 

"Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species," Deem said.

 

An organisms comes across many microoranisms during its life time. If the DNA of some of them gets succesfully transfered to the gene bank of the organism, the result is self evident, the genome evolves over time, some of the DNA sequences may be getting assimilated into the genome and in the process some of the residual segments would become junk DNA:)

[maikeru]

My theories about junk DNA, and I'll try avoid points covered by Gribbon, as he's very knowledgeable and has given excellent explanations of those ideas.

 

1. Structural functions, which may determine or influence gene transcription and overall genomic control and expression. Sequences in nucleic acids can often influence shape and function. Shape can in turn influence regulation by influencing interactions with transcription enzymes or how the molecule can bend or twist to bring together different regions of the genome to turn on or off certain genes. C-G rich regions might be more inflexible than A-T rich regions, for example.

 

2. Like Gribbon mentioned, there seem to be a lot of transposons in junk DNA. There are also retroviral elements which act similar to or are transposons, and they make up a significant part of that junk, according to studies:

 

ScienceDaily: Retroviruses Shows That Human-Specific Variety Developed When Humans, Chimps Diverged

 

Or as this scientist puts it: "The widespread presence of these viral elements led Coffin to tell one science magazine that humans probably have 'more viruses in our genes than genes in our genes.'"

 

3. 2% of the DNA codes for proteins, but some other % of junk DNA codes for things like microRNAs (and other unknowns which we'll discover later), which are also important in genomic regulation and expression. Genes that code for miRNAs don't look like protein-coding genes and are harder to recognize.

 

MicroRNA - Wikipedia, the free encyclopedia

 

MicroRNAs are relatively new additions to our view of how the cell and its genome work. There was and is a lot of excitement over their use in research and therapy.

[billg]

Good to see some summaries of the actual science out there. I believe that some DNA on either side of a gene that serves as a recognition area for proteins to bind to may still be categorised as "junk DNA", and DNA coding for microRNA which is generally believed to have a functional role aswell, which means at least some of the "junk DNA" is not junk. However from what I know about viruses and retrotransposons and what-not it seems pretty likely a decent chunk truly is non-functional. Afterall, evolution does not generate perfectly efficient structures as is commonly said, but rather if it happens to produce something efficient enough to survive will not neccessarily evolve a way to get rid of some extra bits...

[gribbon]

The types of junk DNA include introns, (internal segments in genes that are removed at the RNA level) pseudogenes (genes inactivated by an insertion or deletion), mobile and repetitive DNAs, satellite sequences, (tandem arrays of short repeats), and interspersed repeats, (which are longer repetitive sequences mostly derived from mobile DNA elements).

 

Introns

 

An observed mechanism by which introns can regulate gene activity is through the binding of the snipped-out intron RNA to DNA or RNA. There are now a few examples of the role of introns in regulating the genes they are in, as well as other genes. One interesting example is the lin-4 gene intron from the nematode Caenorhabditis elegans. A developmental control gene was found to reside in the intron of another gene.

 

Not only this, but when most eukaryotic genes (and a minority of prokaryotic) have their genes transcribed or copied into RNA, there are segments that are cut out of the messenger RNA (mRNA) before it is used as a template to make a protein. Many of these are later discarded, and so evolutionary theory explains these as being vestigial sequences, or that they are useful only as sites at which recombination can safely take place to reshuffle exons (coding or protein making segments) into new proteins or new forms of these proteins. There are quite a few eukaryotes with these, so there is probably a function. They could be to slow down the rate of translation, (splicing always does take time) and this could make way for greater diversity, as certain exons can be skipped and spliced out to let a different protein be made from the same mRNA, as is seen in some viruses and in the generation of diversity in antibodies. Another example is the CD6 gene, which is involved in T cell stimulation. Variable splicing of exons gives rise to at least five different forms of the protein, which allows regulation of its activity. On human chromosome 22, the 61-kilobase TIMP3 gene, which is involved in macular deterioration, sits within a 268-kb intron of the large SYN3 gene, and the 8.5-kb HCF2 gene lies within a 27.5-kb intron of the PIK4CA gene, showing another example of protein encoding.

 

Another way, which they have been proven to have function, is in creating hairpin loop structures using self-complementary or exon-complementary intron sequences which can bind to each other, allowing the sequence of the RNA to be changed after transcription from the DNA. Beyond this, they may also play a role in mRNA, editing and cause new messages to be formed without altering coding sequences, a procedure where the adenine residues in the mRNA are changed to guanine.

 

The role of introns in gene regulation and chromosome structure is clear, which would remove 8.15% of the junk DNA of the human genome from the so-called junk heap.

 

Pseudogenes

 

These are common in Mammals, but virtually absent in Drosphilia as far as I know. Sometimes when we observe functional genes we find families of genes close by which appear to have been inactivated. Some have movable parts inserted into their “Open Reading Frames” (OFR’s) and others appear to be processed genes, meaning that their RNA looks like it has been used to reverse transcribe. A processed pseudogene precisely lacks the introns, possesses 3'-terminal poly-(A) tracts, and lacks the upstream promoter sequence required for transcription of the corresponding parent gene.I should also note on how many of these genes have additional mutations within them, probably as there is no restraint on how much these can mutate. By binding transcriptional factors that activate the normal gene, some pseudogenes influence cell activity. It seems to me that these can hardly be called junk DNA, though.

 

Retroviruses and retroelements

 

Making up around 35.40% of the “junk heap”, these class I mobile elements reproduce themselves through an RNA intermediate which, in a reversal of the usual DNA to RNA transcription, is reverse transcribed to DNA by the reverse transcriptase enzyme encoded on intact elements. SINEs and LINEs, make up the majority of this class of DNA, with Alu and LINE-1, with the latter used to encode their own reverse transcriptase and also help the spread of SINE’s (which I’m pretty sure lack the enzyme they would need).

 

These have been found to regulate the structure of the genome as well as gene expression in many ways, as transposition can disrupt genes by direct insertional mutagenesis and can negatively affect transcription. They don’t seem to do anything positive, seeing as they have constitutive promoters that muck up genes below them, causing translocations and inversions. Allele shuffling between homologous chromosomes and DNA breaks need to be repaired by recombination, but having promoters in the wrong place never helps. Having said that, if the promoter is in the opposite direction of the gene, RNA corresponding to the mRNA of the gene can be made that can behave as antisense RNA that binds up the mRNA, often changing the translation for the better.

 

Repetitive DNA sequences

 

When these were first discovered, most observations showed that all they did was move around and cause useless or dangerous mutations, but know we can see evidence that these carry important functions. Despite being present in many eukaryote’s and forming a substantial fraction of DNA there, they did not appear to do anything. Their class inlcudes satellite DNA (very highly repetitive, tandemly repeated sequences), minisatellite and microsatellite sequences (moderately repetitive, tandemly repeated sequences), the new megasatellites (moderately repetitive, tandem repeats of larger size) and transposable or mobile elements (moderately repetitive, dispersed sequences that can move about how they like).

We now know them to help in regulating mutations.

 

Satellite sequences

 

Although these do not appear to carry out any function on their own, these highly repetitive sequences do have collective purposes. The actual sequence repeated differs from species to species, and repeats can differ slightly from one another. The number in an array can vary between individuals.

 

The begin with, these types of sequences have a function in organising the centromeres, the constricted sites on each chromosome where the chromosomes attach to cellular tethers and are pulled apart during meiosis and mitosis. These sequences help condense the DNA region they are in into heterochromatin.

 

Beyond this, big expanses of non-coding sequences act as tethers, so that the placement of groups of genes into different zones in the cell nucleus can be co-ordinated properly.

 

The original belief that a large portion of the genome of eukaryotes is comprised of useless material fits with the problem known as the ‘c-value paradox’, ‘c’ meaning the haploid chromosomal DNA content. There is an extraordinary degree of variation in genome size between different eukaryotes, which does not correlate with organism complexity or the numbers of genes that code for proteins.

 

Transposons + Retrotransposons

 

We looked into this earlier, but one thing I should have talked about before was miniature inverted-repeat transposable elements (MITEs). These were discovered relatively recently, (firstly in plants, but latterly in humans, nematodes, mosquitoes and certain fish types) and are 125–500 bp in size, and have short terminal inverted repeats. I don’t know an enormous bit about them, but they have been given some pretty interesting names like “Tourist”, “Stowaway”, “Alien” and “Bigfoot” which is supposed to relate to how they move around the genome in their tens of thousands.

 

Hmmm…

 

One thing I didn’t mention last time, (which we shouldn’t miss), is that the vast majority of these class II transposable elements’ (which move from place to place by replicative transposition, increasing the copy number), appear to have been inactivated by multiple mutations, and furthermore a lot of these seem to be very inspecific in where they insert themselves. (Except for the R2 non-LTR retrotransposon, which often inserts itself into the 28S ribosomal RNA genes of certain insects). Many scientists hypothesise that this allows for gene transfer by means other than normal inheritance between different species and different phyla.

 

In Drospholia, two retroposons, HeTA and TART, are present in multiple copies on the telomeres, and will retropose specifically to the end of the telomere and heal a frayed chromosome. It should also be noted that the number of copies produced varies massively between species, with a mere two copies to be located in Drosophilasechellia, to be juxtaposed with 17,000 in the horn fly Haematobiairritans.

 

 

Miniature inverted-repeat transposable elements (MITEs)

 

These are really just a sub-category of Transposons etc, and belong to the third class of microelements. They are very small (125–500 bp I believe), and have short life-threatening inverted repeats. I *think* that they were first found in plants, but have also been spotted in nematodes, humans, mosquitoes and zebrafish. They’re still being studies intensively, but so far it has been observed that these are DNA elements that cannot move about, and so must be regarded as non-autonomous. Many scientists suspect them to have been mobile in the recent past due to the close analogy between elements in a particular family, and the distinctions in insertion sites distinguished in related species. As far as I know, these have been seen to have an effect on the type of genetic variation, but we need to wait a bit to find out more.

 

On a more frivolous note, vibrant names such as Alien, Tourist, Stowaway and Bigfoot have been added to these, supposedly to reflect their perceptible ability to move about in the genome. :) :cup: ;) :D

 

Hope that was some help....:eek:

[Queso]

Just opened up this thread for the first time and it was one of the best reads in a while.

 

Is it possible that junk DNA is potential?

 

For instance . . is junk DNA always junk DNA? Does it change over time?

 

I bet some people have more DNA activated than others . .

 

Maybe DNA is a biological hourglass and it's showing us we've only just begun . .

 

?

[ErlyRisa]

JUNK DNA --how preposterous! --> yes the left over 98% may have no direct relationship with any traits of growth in our current state... but

 

--IT IS OUR HISTORY!! --they are fall back genes... if the environment gets to a state that our current make up can't handle---it is the fall back information that we end up relying upon...all the way back to protozoan existance. --this biological historic information can be 're-calculated- and used again in whatever form deemed necessary for survival.... eg. the 2% proportion that decides we should have eyes... may not cope if the environment is made up of high intensity UV.... the offspring in the womb can 'fall back' on the information stored in the 98% that can instruct 'UV vsibility' via the outershell.... this type of UV interaction goes back as far as bacteria.

 

--5th Element --the Anciant alians have how many pairs again? --and what did they look like? --and they were even able to be constructed as a 'Lilloo' --a fall back organism, vs thier current state (big italians without even the need to run) --they 'stored' the information in thier big genes, all the way back to the human form....

 

Down Syndrome people are a higher entity!!! (they are trying to store more gene information)

 

--The virus is the most fundamental carrier of information. (carbon based) --and digitally based too! --in the PC the virus is the smallest executable code known, that can interact with it's environment (other code) --a hello world program on the other hand is nothing more than a gene sequence.

[maikeru]

After another excellent Gribbon post on junk DNA, we have this? :hyper:

 

ErlyRisa, could you please put some organization, logic, and evidence into a few of your posts, at least?