Sunday, March 22, 2009
SINES and LINES
On page 99, Carroll talks about how lots of our DNA is made up of short interspersed elements (SINES) and long interspersed elements (LINES). These elements are noncoding "chunks of junk DNA" that are created by accidental insertions. Carroll states that these rare DNA elements are important as landmarks to trace genealogy and to prove that two species of organisms came from a single common ancestor. Besides helping scientists track evolutionary relationships, why is long noncoding "junk DNA" such as SINES and LINES beneficial to organisms? Is it necessary for organisms to have noncoding DNA interspersed in their genome?
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In “SINEs of the perfect character”, David M. Hillis used the same detection of SINEs and LINEs within the genetic code to prove that hippopotamuses are the closest extant relative to whales. Through the use of phylogenetic estimates, and the use of SINE and LINE data, a complete tree for artiodactyl mammals was completed. The scientists used these insertion studies because of the apparent low levels of homoplasy (a correspondence between parts as a result of similarity of environment rather than common heredity) and the irreversible nature of the characters. It was useful because of the predicted close genetic relatedness between species. Other than the use of SINE/LINE comparison data for the discovery of lineage between closely related species, it is possible that these “meaningless” codes do not observe an expressed purpose, more likely that they serve as “breathing room” for error and mutations that may occur within the DNA of any organism. SINE copes have been linked with the changing of chromatin structure, DNA recombination, replication and transcription, and the effect of these sequences in mRNAs effect the splicing and editing during the translation process.
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ReplyDeleteAlu elements are the most common type of noncoding DNA, and they are apart of the SINE DNA (short interspersed repeated sequence). Alu elements can change places with RNA, and they must borrow other elements, LINES (long interspersed repeated sequences). These are not as common, but they are larger in size (20% of human DNA compared to SINE's 13%). Alu elements are 280 base pairs long and do not have any coding sequences. They can be recognized by Alul, the restriction enzyme.
ReplyDeleteThe research began into this "junk DNA" because they discovered that there was RNA transcripts from SINE elements. SINEs were discovered to control gene expression by aiding in transcripts of SINEs for a messenger RNA, and start DNA replication. In addition, these elements may create diversity, a possible selective advantage, by moving into a DNA sequence or they may be a disadvantage if it interrupts an essential gene and changes the protein. Also, SINEs have been considered as the origin for DNA replication. SINES were originally transcribed by RNA polymerase III into tRNA, rRNA, and other RNAs.LINES are a more recent discovery so there is little information about the,, but they are mobile like SINEs are. Both SINEs and LINEs play a large role in gene evolution, structure, and transcription.
http://genomicron.blogspot.com/2008/02/quotes-of-interest-sines-and-lines.html
http://en.wikipedia.org/wiki/Retrotransposon
http://network.nature.com/people/trgregory/blog/2008/02/18/mashing-junk-dna
There is no conclusive reason how “junk” DNA appeared in the genomes of organisms and why it still remains. However, there are many hypotheses of their origins and why they remain. One hypothesis is that “junk” DNA may become functional genes in the future after duplication and insertion/deletion of nucleotides. By changing the nucleotide sequence, the new gene may code for a functional protein that could be advantageous to the organism. Also, “junk” DNA can act as spacer material that can allow enzyme complexes of DNA polymerase and other proteins to bind more easily to the beginnings of functional genes and aid in their replication. This spacer material would therefore also help the binding of RNA polymerase and transcription factors to help the transcription of DNA into mRNA. Another hypothesis could be that the “junk” DNA that appears to have no specific function may actually code for genes of unknown functions. Since the genomes of some organisms are still somewhat unknown, some genes could have functions that we don’t know of yet.
ReplyDeleteThere are two types of “junk” DNA. One is called pseudogenes, or fossilized genes. As described elaborately by Carroll, pseudogenes are now-dysfunctional genes that were functional in other organisms. However, do to relaxed selection on these genes after mutation if the genes are no longer needed (ex. Human olfactory genes), then the genes can eventually lose their function. The other type of “junk” DNA is repeated sequences, such as SINES and LINES, that have no function in the genome. Some of these sequences are called transposons and can amplify themselves inside the genome. This can be beneficial to an organism, as an increase in “junk” DNA can act as more spacer material between functional genes.
An example of how noncoding repetitive DNA is important in organisms is the benefits of telomeres at the end of chromosomes. Telomeres are regions of repetitive DNA at chromosome ends and prevent the end of the chromosome from degradation. These DNA sequences are needed because of the end replication problem in eukaryotes. On the lagging strand during replication, the last site where the last RNA primer was placed cannot be replaced by DNA nucleotides because a primer cannot be placed in front of it. Therefore, our DNA becomes smaller and smaller after each round of DNA replication. If telomeres are located at the end of the chromosomes, then it is okay if the chromosome ends are constantly becoming shorter because no functional DNA is become erased. For this reason and the reasons mentioned earlier, “junk” DNA is in fact not really “junk”, as it plays vital roles in our genomes.
Sources:
http://www.psrast.org/junkdna.htm