Sunday, February 26, 2006
Repetitive Elements and Genome Function
Two of my favorite biologists, Sternberg and Shapiro, have teamed up to co-author a paper! The paper is Why repetitive DNA is essential to genome function. They also have coauthored another paper that focuses on retroelements, but I have not gotten around to reading it yet.
Their main thesis is that DNA is essentially a cell's storage mechanism, and that repetitive elements are used to help organise the genome for proper access and function. The repetitive elements serve many functions, including being "generic signals so that operational hardware can locate and process the stored information". They also point out that formatting signals are more-or-less required to have less informational content than the signal, in order to function as formatting signals. Think about a carrier wave versus the data contained therein. Without the carrier wave, it would not be possible to locate the data, but the carrier wave itself does not contain interesting information.
As for the repetitive nature of repetitive elements, they point out that robust systems have redundant components. A minimum is required for function, but excesses are compatible with normal operation.
They also point out that genome size is related to the life cycle length, and that repetitive element size is related to genome size. I _think_ that the point was that larger genomes need more formatting.
They also point out that the ratio of repetitive elements to protein can have phenotypic effects. They use that to indicate that the ratio is "flexible but not adaptively neutral".
They separate storage into "long-term" (DNA codes), "intermediate-term" (epigenetic effects through protein, RNA, and DNA complexes), and "short-term" (DNA, RNA, and protein complexes that are lifecycle-dependent).
They also list several functions genomes are required to perform besides coding for proteins. This includes:
They then discuss the idea that repetitive elements hierarchically organize the genome into series of folders for indexing and access. They did not elaborate this point much, but mostly pointed to other literature.
They discuss at length the interactions of proteins and DNA and their reliance on repetitive elements to work. It helps regulate transcription in response to specific cell states. They relate the function of such repetitive elements to a "multi-layered fuzzy logic system".
As for transposable elements. They say that they allow the cell to "have the ability to introduce a pre-organized constellation of functional signals into any location in the genome". So, transposons are basically a collection of functionality that can be deployed to modulate specific parts of genome function.
Finally, they point out that repetitive elements are highly taxonomically restricted. They say, "Operationally, it is much easier to identify the species of origin of a DNA, cell culture or tissue sample by examining reptitive DNA than coding or unique sequences". This indicates that different types of animals have different cell architectures. The repetitive elements are the primary ways of knowing the cell architectures. They point out that E. Coli and Bacillus subtilis both monitor external glucoses, they each use different mechanisms with repetitive elements to connect the monitoring systems to the genomic repression systems.
They criticize the classical view of the genome (the selfish DNA hypothesis) by proposing a more "systems" view of biology:
The paper also included a fabulous table documenting the various types of repeat elements and some of the functions they are known to play within the genome. Having these descriptions of repeat element types and their functions is worth the price of the article itself.
This is all very interesting for creationists. It implies that genomes have semantics. Viewing the genome's architecture holistically rather than historically seems to be a prime example of a creationist research endeavor. Likewise, it would be interesting to look at how well repetitive elements are able to differentiate baramins, if at all, and also to look and see if these genome restructurings that Shapiro and Sternberg point to in almost every paper involve changes in repetitive elements, or if the repetitive elements remain somewhat static. This may also be a key (or may not be) to Wood's biological similarity problem.
Their main thesis is that DNA is essentially a cell's storage mechanism, and that repetitive elements are used to help organise the genome for proper access and function. The repetitive elements serve many functions, including being "generic signals so that operational hardware can locate and process the stored information". They also point out that formatting signals are more-or-less required to have less informational content than the signal, in order to function as formatting signals. Think about a carrier wave versus the data contained therein. Without the carrier wave, it would not be possible to locate the data, but the carrier wave itself does not contain interesting information.
As for the repetitive nature of repetitive elements, they point out that robust systems have redundant components. A minimum is required for function, but excesses are compatible with normal operation.
They also point out that genome size is related to the life cycle length, and that repetitive element size is related to genome size. I _think_ that the point was that larger genomes need more formatting.
They also point out that the ratio of repetitive elements to protein can have phenotypic effects. They use that to indicate that the ratio is "flexible but not adaptively neutral".
They separate storage into "long-term" (DNA codes), "intermediate-term" (epigenetic effects through protein, RNA, and DNA complexes), and "short-term" (DNA, RNA, and protein complexes that are lifecycle-dependent).
They also list several functions genomes are required to perform besides coding for proteins. This includes:
- Regulating the timing of coding sequence expression
- Regulating coding sequence expression itself
- Coordinating protein expression for proteins that need to function together or in a sequence
- Packaging DNA for retrieval within the cell
- Restructuring the genome (either as part of the cell life cycle, or in response to stress)
- In mitosis, to structure the genome division and copying process
They then discuss the idea that repetitive elements hierarchically organize the genome into series of folders for indexing and access. They did not elaborate this point much, but mostly pointed to other literature.
They discuss at length the interactions of proteins and DNA and their reliance on repetitive elements to work. It helps regulate transcription in response to specific cell states. They relate the function of such repetitive elements to a "multi-layered fuzzy logic system".
As for transposable elements. They say that they allow the cell to "have the ability to introduce a pre-organized constellation of functional signals into any location in the genome". So, transposons are basically a collection of functionality that can be deployed to modulate specific parts of genome function.
Finally, they point out that repetitive elements are highly taxonomically restricted. They say, "Operationally, it is much easier to identify the species of origin of a DNA, cell culture or tissue sample by examining reptitive DNA than coding or unique sequences". This indicates that different types of animals have different cell architectures. The repetitive elements are the primary ways of knowing the cell architectures. They point out that E. Coli and Bacillus subtilis both monitor external glucoses, they each use different mechanisms with repetitive elements to connect the monitoring systems to the genomic repression systems.
They criticize the classical view of the genome (the selfish DNA hypothesis) by proposing a more "systems" view of biology:
As we enter the era of 'systems biology', it is useful to recall that a system is more than a collection of components. Those components need ot integrate functionality so they can accomplish ssystemic tasks requiring cooperative action. One way to state our argument is to say that repetitive DNA elements provide the physical basis within the genome for functional integration. As Britten and Davidson realized, dispersed regulatory sites connect unlinked coding sequences into coordinately controlled subsystems. Similarly, replication and genome transmission processes are organised by generic signals that determine origins, telomeres, centromeres and other nucleoprotein complexes involved in genome maintenance...distributed sites for attachment to cellular or nuclear structures provide a dynamic overall physical organisation of the genome that we are just beginning to comprehend.
The paper also included a fabulous table documenting the various types of repeat elements and some of the functions they are known to play within the genome. Having these descriptions of repeat element types and their functions is worth the price of the article itself.
This is all very interesting for creationists. It implies that genomes have semantics. Viewing the genome's architecture holistically rather than historically seems to be a prime example of a creationist research endeavor. Likewise, it would be interesting to look at how well repetitive elements are able to differentiate baramins, if at all, and also to look and see if these genome restructurings that Shapiro and Sternberg point to in almost every paper involve changes in repetitive elements, or if the repetitive elements remain somewhat static. This may also be a key (or may not be) to Wood's biological similarity problem.
Permanent Link posted by crevo @ 6:49 PM 
