If you could zoom in and look at the DNA on the tip of one of your chromosomes, what would you see? You might expect to find genes, or perhaps some DNA sequences involved in gene regulation.
Instead, what you'd actually find is a single sequence –TTAGGG – repeated over and over again, hundreds or even thousands of times.
Telomeres appear as the bright spots at the ends of each chromosome in the picture shown above. Image credit: "Telomere caps," by U.S. Department of Energy Human Genome Program (public domain).
Repetitive regions at the very ends of chromosomes are called telomeres, and they're found in a wide range of eukaryotic species, from human beings to unicellular protists. Telomeres act as caps that protect the internal regions of the chromosomes, and they're worn down a small amount in each round of DNA replication.
In this article, we'll take a closer look at why telomeres are needed, why they shorten during DNA replication, and how the enzyme telomerase can be used to extend them.
The end-replication problem
Unlike bacterial chromosomes, the chromosomes of eukaryotes are linear (rod-shaped), meaning that they have ends. These ends pose a problem for DNA replication. The DNA at the very end of the chromosome cannot be fully copied in each round of replication, resulting in a slow, gradual shortening of the chromosome.
Why is this the case? When DNA is being copied, one of the two new strands of DNA at a replication fork is made continuously and is called the leading strand. The other strand is produced in many small pieces called Okazaki fragments, each of which begins with its own RNA primer, and is known as the lagging strand. (See the article on DNA replication for more details.)
In most cases, the primers of the Okazaki fragments can be easily replaced with DNA and the fragments connected to form an unbroken strand. When the replication fork reaches the end of the chromosome, however, there is (in many species, including humans) a short stretch of DNA that does not get covered by an Okazaki fragment—essentially, there's no way to get the fragment started because the primer would fall beyond the chromosome end1start superscript, 1, end superscript. Also, the primer of the last Okazaki fragment that does get made can't be replaced with DNA like other primers.
In general, DNA polymerases can't start a new strand of DNA from scratch, even if they are given a template. That's because the polymerization reaction they catalyze involves attaching the phosphate group of an incoming nucleotide to the hydroxyl group of an existing nucleotide (one that's already part of the strand), as shown at right. Without this hydroxyl group to use as a "hook," a DNA polymerase has nothing to attach nucleotides to and cannot catalyze its reaction to make new DNA.
Most primers that start Okazaki fragments can be replaced without a problem. That's because the hydroxyl at the end of the neighboring Okazaki fragment can be used as a starter by the DNA polymerase, allowing it to replace the primer with DNA. At the end of the chromosome, however, there is no neighboring Okazaki fragment to provide the needed hydroxyl, resulting in incomplete replication of the chromosome end.
Thanks to these problems, part of the DNA at the end of a eukaryotic chromosome goes uncopied in each round of replication, leaving a single-stranded overhang. Over multiple rounds of cell division, the chromosome will get shorter and shorter as this process repeats.
A real eukaryotic chromosome would have multiple origins of replication and multiple replication bubbles, but the end-replication problem would be the same as shown above. Image modified from "Telomere shortening," by Zlir'a, public domain.
In the last panel of the diagram above, the leading strand end of the chromosome is shown as being blunt (having no overhang). Although the leading strand end is, in fact, initially blunt, it's later processed by enzymes in the cell produce an overhang of about 3030 bp1start superscript, 1, end superscript.
The production of this overhang is important for chromosome end protection, as discussed in the section below. It also contributes to the progressive shortening of the telomeres over multiple rounds of cell division.
In human cells, the last RNA primer of the lagging strand may be positioned as much as 7070 to 100100 nucleotides away from the chromosome end2start superscript, 2, end superscript. Thus, the single-stranded overhangs produced by incomplete end replication in humans are fairly long, and the chromosome shortens significantly with each round of cell division.
To prevent the loss of genes as chromosome ends wear down, the tips of eukaryotic chromosomes have specialized DNA “caps” called telomeres. Telomeres consist of hundreds or thousands of repeats of the same short DNA sequence, which varies between organisms but is 5'-TTAGGG-3' in humans and other mammals.
Telomeres need to be protected from a cell's DNA repair systems because they have single-stranded overhangs, which "look like" damaged DNA. The overhang at the lagging strand end of the chromosome is due to incomplete end replication (see figure above). The overhang at the leading strand end of the chromosome is actually generated by enzymes that cut away part of the DNA1start superscript, 1, end superscript.
In some species (including humans), the single-stranded overhangs bind to complementary repeats in the nearby double-stranded DNA, causing the telomere ends to form protective loops3start superscript, 3, end superscript. Proteins associated with the telomere ends also help protect them and prevent them from triggering DNA repair pathways.
The repeats that make up a telomere are eaten away slowly over many division cycles, providing a buffer that protects the internal chromosome regions bearing the genes (at least, for some period of time). Telomere shortening has been connected to the aging of cells, and the progressive loss of telomeres may explain why cells can only divide a certain number of times4start superscript, 4, end superscript.
Some cells have the ability to reverse telomere shortening by expressing telomerase, an enzyme that extends the telomeres of chromosomes. Telomerase is an RNA-dependent DNA polymerase, meaning an enzyme that can make DNA using RNA as a template.
How does telomerase work? The enzyme binds to a special RNA molecule that contains a sequence complementary to the telomeric repeat. It extends (adds nucleotides to) the overhanging strand of the telomere DNA using this complementary RNA as a template. When the overhang is long enough, a matching strand can be made by the normal DNA replication machinery (that is, using an RNA primer and DNA polymerase), producing double-stranded DNA.
The primer may not be positioned right at the chromosome end and cannot be replaced with DNA, so an overhang will still be present. However, the overall length of the telomere will be greater.
Telomerase is not usually active most somatic cells (cells of the body), but it’s active in germ cells (the cells that make sperm and eggs) and some adult stem cells. These are cell types that need to undergo many divisions, or, in the case of germ cells, give rise to a new organism with its telomeric “clock” reset5start superscript, 5, end superscript.
Interestingly, many cancer cells have shortened telomeres, and telomerase is active in these cells. If telomerase could be inhibited by drugs as part of cancer therapy, their excess division (and thus, the growth of the cancerous tumor) could potentially be stopped.
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Chow, T. T., Zhao, Y., Mak, S. S., Shay, J. W., and Wright, W. E. (2012). Early and late steps in telomere overhang processing in normal human cells: The position of the final RNA primer drives telomere shortening. Genes Dev., 26(11), 1167.
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