Saturday, April 4, 2009
LINES and SINES and other fun things
Explain what LINES and SINES are. Why do LINES and SINES survive from generation to generation? How can we use LINES and SINES to determine ancestral relationships between species, and why does a similarity in LINES and SINES indicate a relationship between species? Use an example of a relationship between a human and another species found using LINES and SINES. Have a nice last day of Spring Break!
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Both LINES and SINES are interspersed repetitive DNA. They are repetitive DNA that have "copies" located throughout the genome that are very similar but not identical. As for mammalian DNA, they make up 25-40% of the genome, are 100-10,000 base pairs in length, and are repeated 1-10 million times (Campbell 357). Most of the interspersed repetitive DNA are "junk DNA" but 5% of them are known as Alu elements. Alu elements are 300 nucleotide pairs long and are transcribed into RNA molecules - their function, however, is unknown. These interspersed elements make up what Carroll refers to as LINES and SINES (long and short respectively). LINES and SINES survive from generation to generation because natural selection is relaxed upon them. They have no real function, or known function as of yet, in organisms and thus my prediction would be that natural selection has relaxed on them just as it has upon fossil genes. However, the LINES and SINES would still be susceptible to mutations, like all other genes and genetic codes. As Carroll states, "Once a SINE or LINE is inserted, there is no active mechanism for removing it. The insertion of these elements marks a gene in a species, and is then inherited by all species descended from it," (99). The way SINES and LINES occur in DNA has to do with the idea of transposons. In effect, SINES and LINES are transposons that move within the genome, or retrotransposons. A retrotransposon is transcribed into RNA which is translated into reverse transcriptase (encoded in the retrotransposon in itself). Reverse transcriptase then adds a complementary DNA strand. Then reverse transcriptase replaces the RNA strand with a DNA strand and the insertion of the new retrotransposon occurs somewhere else in the genome (Campbell 360). We can use LINES and SINES to determine ancestral relationships between species through the following steps:
ReplyDelete1. Identifying a set of SINES/LINES
2. Use Gel Electrophoresis and DNA typing
3. Visually determine the relative position of bands of DNA.
To understand the process even further: Carroll p. 101.
Researchers surveyed a set of SINES in a human test subject and then found other SINES similar in length to that of the human. Using gel electrophoresis, the bands of DNA of SINES were separated. Visually determining the evolutionary tree was simple after the electrophoresis (view figure 4.3 on Carroll 100). The relationship found that humans were closely related to chimps and bonobos compared to owl monkeys. The owl monkeys had no SINES that were similar to the test subject, while the chimps and bonobos had the SINES similar to the human test subject (again, figure 4.3). Thus this issue relates to the biological theme of heritable information in that genetic elements, such as LINES and SINES, were passed through different genealogical lines and trees to the current, modern-day organisms.
SINEs, short interspersed elements (<500 bases), and LINEs, long interspersed elements, are chunks of junk DNA. In primates, the most common SINEs are known as Alu sequences. SINEs are thought to be transposable elements that originated from reverse transcribed RNA molecules. Although scientist currently believe that LINEs and SINEs have no function, the fact that SINEs originated from RNA transcripts have led some to speculate that SINEs do have a function. These biologists believe that SINEs might be the answer to some unsolved problems in biology.
ReplyDeleteAlthough the molecular function of SINEs and LINEs are debatable, molecular biologists use SINEs and LINEs to determine the relationship between species. This is possible because “once a SINE or LINE is inserted, there is no active mechanism for remove it” (Carroll 99) and it is passed down from generation to generation. Thus, SINEs and LINEs function as genetic markers on DNA that determine the degree of relatedness between two organisms. Organisms that diverged earlier would share less SINEs and LINEs than organisms that diverged later. For example, if two organisms share a unique SINE or LINE, it would mean that these two species shared the common ancestor more recently than with any other species.
Biologists can use a gel electrophoresis to compare SINEs of different species. Organisms who share the same SINEs all have a band of DNA the same distance from the loading well. By studying SINEs, scientists have realized that while chimpanzee might be human’s closest relative, humans are certainly not the chimpanzee’s closest relative. Humans, chimps, and bonobo all share a common SINE which shows that these three organisms shared a recent common ancestor. However, chimps and bonobos also share a SINE that is not found in humans. This shows that bonobos are actually the chimp’s closest relatives.
Using SINEs and LINEs as genetic markers to map out evolution relationships remind us that although live forms are diverse, we care still connected to all life forms through our universal genetic code (Theme 7). The SINEs and LINEs in our genome are proof of the common ancestry we share with all of Earth’s creatures.
Here is an after thought:
The RNA origin of SINEs bares an uncanny resemblance to retrovirus. Retrovirus, such as HIV, have mRNA as their genetic information and use the enzyme reverse transcriptase to “transcribe DNA from an RNA template” (Campell 335) and then integrate this DNA into the hosts genome. Is it possible that SINEs are remnants of retrovirus DNA that stayed in the lysogenic phase?
Here is the source to my response
ReplyDeleteSource: http://genomicron.blogspot.com/