1. Telomere Length Protocol19
1. DNA isolation
Most DNA isolation methods may be used. Our Lab prefers Qiagen DNeasy Kit (#69506) for blood sources. Depending on the source of DNA, such as buccal or other sources, a different isolation method may be used.
2. Primers
All primers are diluted to a stock concentration of 100pmoles/&mu;l in PCR grade water and stored at -20 &deg;C until required. Working stocks o...

Telomere length provides a unique cellular marker to study the stressed and aging cell and offers insights into the mechanisms of aging. Since its role in aging had first been suggested, a multitude of studies have been done relating telomere length to age, longevity, age-related disease, cancers, and stress. For decades, the gold standard of telomere length measurements was terminal restriction fragment analysis using Southern hybridization. However, recently an affordable, quick, and easy to perform method by Ca...

Telomeres are repeating DNA hexamer (TTAGGG) sequences found at the ends of chromosomes. In each cell replication, these chromosome ends are shortened. If they become too short, chromosomes can undergo telomere end fusions, aberrant recombination, and degradation. Thus sufficient telomere length maintenance plays a major role in chromosome stability and cell protection 38. Telomere length maintenance is also crucial for genes found near the ends of chromosomes, since DNA replication cannot continue to the very end of chromosomes 1-2. Consequently, prevention of telomere shortening may improve cell stability.
Numerous studies have reported that telomere length is correlated with an organism's longevity and diseased state, such as in cancer 3-4, diabetes 5, and cardiovascular disease 6,7. Additionally, shortened telomeres have been associated with excessive stress or an unhealthy lifestyle 8, perhaps by promoting premature cell aging and death 9. On the other hand, some studies have found that there is no significant difference between telomere length and longevity and age related disease 39, 40, 41.
One of the cell's innate mechanisms of protection from telomere shortening is by activating its own enzyme telomerase reverse transcriptase (TERT). This enzyme and its subunit, telomerase RNA (TERC), a non-coding RNA, use the telomere as a template to add telomere repeats to chromosome ends 10. Although telomerase activity is absent from several types of cells and other mechanisms are involved in telomere length maintenance, increased telomerase activity is correlated with increased telomere length. Telomerase activation has been established as one of the mechanisms by which cells respond to damage and stress and avoid premature senescence and death. For example, longer telomeres were demonstrated in a population of Ashkenazi Jews with exceptional lifespan 11, mutations in TERC or TERT have been shown to contribute to fatal disease 12, and epigenetic regulation of telomerase has been shown to have an effect on age-related disease 13. Since its discovery, telomere length has been proposed as a biomarker for health status in various animal models as well as in humans, but these early studies were difficult to widely replicate because the method used was tedious, long and expensive. In 2002 and further tuned in 2009, Cawthon proposed and demonstrated a new, accurate, fast and simple PCR based protocol to assess telomere length and further investigate its role in various aspects of cell biology, aging and disease 19.
Choosing the correct telomere measuring method for a study is essential. Currently, there are various methods used to measure telomere length, each with its own advantages and disadvantages. Traditionally, telomere length is measured using Southern Blot analysis of terminal restriction fragments (TRFs), which involves: a. digesting the DNA with restriction enzymes that do not cut in telomere repeats in order to obtain TRFs, b. Southern Blot of these TRFs is done by determining the mean TRF length using a telomeric probe 14, 37. Although this method is highly accurate with a small coefficient of variation, is a direct measure, and can be advantageous for measuring length distribution, TRF analysis is costly, labor intensive and requires at least 3 &mu;g of DNA. This method is also insensitive to short telomeres and length determination can be confounded by subtelomeric DNA, which can be detected by the probe due the (TTAGGG)n like sequences they contain 15, 42.
Another highly accurate method in measuring telomere length is Single Telomere Elongation Length Analysis (STELA), a single molecule PCR based method that only requires a small amount of DNA. In this method, primers are made to recognize the G-rich overhang at the end of chromosomes and to bind to a unique subtelomeric sequence on one chromosome, which amplifies the telomere of a specific chromosome. The resulting amplification is then visualized by Southern Blot. This method has the advantage of being highly accurate and is able to detect short outlier telomeres 16. Unfortunately, since not all chromosomes have G-rich ends and a usable subtelomeric sequence, telomere length can only be measured on specific chromosomes and these measurements may not represent the length of all the telomeres in the cell 15.
Another method that has been practiced is the use of Peptide Nucleic Acid (PNA) probes to detect telomere length. Quantitative Florescence in situ Hybridization (Q-FISH) allows us to visualize telomeres during metaphase, where the staining of telomeres with a PNA probe in proportion to their size permits the comparison of telomeres between specific chromosomes. Although this method can also be used for cells in interphase, here the telomere length for distinct chromosomes cannot be detected, which introduces a limitation when measuring telomere length in senescent or infrequently dividing cells 17. Flow FISH instead uses flow cytometry and is currently the most sensitive method for measuring telomere length of blood cells in the clinical setting, but requires highly skilled technicians 18.
Currently, the standard method for measuring average telomere length in our lab takes advantage of the precision, sensitivity, and ease of quantitative real-time PCR. This method was made possible for measuring telomere length by the development of novel primers that avoid the synthesis of primer dimer-derived products, which would have otherwise been produced in a standard assay due to the repeating nature of telomeres. For this assay, the measurement of telomere length is represented by the T/S ratio, the telomere repeat copy number to single-copy gene number. Since there is a direct proportional relationship between the telomere length and the number of labeled telomere primers binding to the DNA during the beginning stages of PCR, the T/S ratio is directly proportional to telomere length. The T/S ratio is measured by comparing the difference in Ct, the fractional cycle number at which the sample's accumulated florescence crosses a threshold that is several standard deviations above the baseline florescence, between samples with telomere primers and SCG primers 19. This method has been criticized for its indirect measurement of telomere length, which can lead to inaccurate measurements, for example, in the case of chromosome duplications or copy number variations 15. Also, comparison between studies is often difficult, but standard oligomers have been developed to measure absolute telomere length 20. This method was furthered improved upon by Cawthon, using a monochrome multiplex qPCR assay. In this assay, the PCR was run at lower temperatures for the first few cycles to avoid primer-dimer binding and the telomere and control gene were analyzed in the same PCR tube to further avoid error. The resulting telomere length measurements strongly correlated with telomere length measured by Southern blot analysis of TRFs and had higher accuracy 15, 19, 36. At the moment, qRT-PCR is the only convenient method available for testing large sample sizes and only requires a small amount of DNA to carry out. A crucial part of this method is comprehensive quality control measures, so that when it's done properly, this method can provide valuable comparative information about telomere length. Additionally, this method had been adapted for use beyond leukocytes for measuring telomere length in a variety of different tissues 42.
Additionally, in order to further understand the biology behind telomere length maintenance and interactions between the two opposing effects (i.e. telomere shortening during replication and elongation by the telomerase enzyme), we accompanied the telomere length method with an additional assay that measures telomerase activity.
For this purpose, we used a Telomeric Repeat Amplification Protocol, an in vitro assay. Briefly, lysed, preserved, enzymatically active cells synthesized telomeric repeats onto an oligonucleotide substrate using telomerase, and the products were amplified using PCR in the presence of SYBR Green. The results were then analyzed by comparing sample and control Ct threshold values. Since telomerase is a heat-sensitive enzyme, an additional heat treated control is run alongside each sample 21.
While measuring telomere length can provide valuable insight into the possible role of telomere length in the pathophysiology of aging and disease, telomere length is not a static property and more information is needed to understand telomere function. Telomerase activity studies can add information about telomere length regulation mechanisms. For example, the controlled activation of telomerase can maintain telomere length and cell proliferation, but the uncontrolled activation of telomerase can result in cancer. These two inexpensive and straight forward methods combined provided us not only with stronger evidence towards a relationship between telomere length and cell stability, but also further insight into the possible mechanisms of telomere shortening and recovery. With these methods we hope to further elucidate the cell's response to aging and various states of cell proliferation with the ultimate goal of a better understanding of the central mechanisms of cell biology.

<table border="1">
<tbody>
 <tr>
 <td>Name of the reagent</td>
 <td>Company</td>
 <td>Catalogue number</td>
 </tr>
 <tr>
 <td>Quantitative Telomerase Detection </td>
 <td>Allied Biotech </td>
 <td>MT3012 </td>
 </tr>
 <tr>
 <td>Qiagen DNeasy Kit</td>
 <td>Qiagen</td>
 <td>69506</td>
 </tr>
 <tr>
 <td>LightCycler 480 SYBR Green I Master, Ready-to-use hot start reaction mix for SYBR Green I-based real-time PCR using the LightCycler 480 Instrument</td>
 <td>Roche Diagnostics</td>
 <td>4707516</td>
 </tr>
 </tbody>
</table>

telomere length and telomerase activity; a yin and yang of cell senescence

Telomeres are repeating DNA sequences at the tip ends of the chromosomes that are diverse in length and in humans can reach a length of 15,000 base pairs. The telomere serves as a bioprotective mechanism of chromosome attrition at each cell division. At a certain length, telomeres become too short to allow replication, a process that may lead to chromosome instability or cell death. Telomere length is regulated by two opposing mechanisms: attrition and elongation. Attrition occurs as each cell divides. In contrast, elongation is partially modulated by the enzyme telomerase, which adds repeating sequences to the ends of the chromosomes. In this way, telomerase could possibly reverse an aging mechanism and rejuvenates cell viability. These are crucial elements in maintaining cell life and are used to assess cellular aging. In this manuscript we will describe an accurate, short, sophisticated and cheap method to assess telomere length in multiple tissues and species. This method takes advantage of two key elements, the tandem repeat of the telomere sequence and the sensitivity of the qRT-PCR to detect differential copy numbers of tested samples. In addition, we will describe a simple assay to assess telomerase activity as a complementary backbone test for telomere length.

An example of a telomere length qRT-PCR assay is shown in Figure 1. On the top left panel, samples labeled in red and green represent the location of the tested subjects on the 96-well plate. On the top right panel, the amplification curve is demonstrated. Each subject is tested by two assays (Telomere and Single Copy Gene), which is done in triplicates. Due to different DNA copy numbers produced in the two assays of selected individuals, the number of cycles until the florescence detection reache...

Watch this Scientific Journal Video about Telomere Length and Telomerase Activity; A Yin and Yang of Cell Senescence at JoVE.com

Telomere Length and Telomerase Activity; A Yin and Yang of Cell Senescence

An accurate, short, sophisticated and cheap method is described that assesses telomere length in multiple tissues and species using qRT-PCR. In addition, we will describe a simple assay to assess telomerase activity as a complementary backbone test for telomere length.

Telomeres  are repeating DNA sequences at the tip ends of the chromosomes that are diverse  in length and in humans can reach a length of 15,000 base ...