Researchers discover how the ticking ‘cellular clock‘ signals the approach of cellular oblivion by causing global changes in the chromatin landscape.
A study published in the October 2 2010 issue of the journal, Nature Structural and Molecular Biology, has shed light on the biological phenomenon of aging. Researchers from the Salk Institute for Biological Studies, CA, USA discovered that while primary cells enter the countdown to senescence and telomere wear down, the packaging of DNA undergoes significant alterations which result in ‘aging‘.
Team leader Dr Jan Karlseder, explains the gravitas of this discovery: “Prior to this study we knew that telomeres get shorter and shorter as a cell divides and that when they reach a critical length, cells stop dividing or die”, the associate professor at the Molecular and Cell Biology Laboratory went on to speculate that “something must translate the local signal at chromosome ends into a huge signal felt throughout the nucleus. But there was a big gap in between”.
Closing this gap, Dr Karlseder and fellow researcher Dr Roddy O‘Sullivan compared the levels of histones present in ‘young cells‘ (cells that had divided 30 times), with those present in ‘late middle-aged‘ cells (cells that had divided 75 times) that were nearing senescence (reached at 85 divisions).
Remarking on the results of the study, Dr O‘Sullivan explained: “We were surprised to find that histone levels decreased as cells aged. These proteins are required throughout the genome, and therefore any event that disrupts this production line affects the stability of the entire genome”.
The changes in histone abundance were observed alongside the activation of the DNA damage response machinery. The age-dependent reprogramming was found to progressively destabilize the telomeric chromatin, causing an increase of telomere-associated DNA damage response with each successive cell cycle.
In order to confirm the marked differences observed in the primary cells in histone abundance and variety during replicative aging, exhaustive ‘time-lapse‘ comparisons of histones in young versus aging cells were performed. Young cells were found to have a default pattern that Dr O‘Sullivan described as “happy, healthy chromatin”. By contrast, aging cells appeared to experience stress upon chromosomal duplication, and had difficulty restoring a ‘healthy‘ chromatin pattern after cell division. In addition, the team engineered aging cells to express telomerase enzyme and witnessed these cells become rejuvenated exhibiting histone levels reminiscent of younger chromatin.
The histone trends observed in cell lines were also found mirrored in cells from an old (92 years old) versus a young (9 year old) subject. “These key experiments suggest that what we observe in cultured cells in a laboratory setting actually occurs and is relevant to aging in a population”, explained Dr Karlseder.
It is well known that DNA damage lies at the heart of many age-associated diseases, however, these findings suggests that aging itself is infinitely complex; that signals emitted by shortening telomeres drive epigenetic changes that hasten chromosomal aging. Preventing the erosion of telomeres however is not the key to longevity: “The flip side of elongating telomeres is that you enable cells to grow for much longer periods and can generate what are called immortal cells”, explains Dr Karlseder. “That takes you one step closer to cancer cell development”.
Asked what future plans of the researchers are: “We will continue to examine epigenetic changes in cells at different ages,” reveals Dr Karlseder. “We now want to determine if histone changes follow a linear process or whether they kick in as we age”.
Source: O‘Sullivan RJ, Kubicek S, Schreiber SL, Karlseder J: Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat. Struct. Mol. Biol. 17(10), 1218–1225 (2010).
Researchers from the Cancer Research UK Institute for Cancer Studies, Birmingham, UK, have, for the first time, published direct evidence proving that taking up smoking causes epigenetic changes linked to cancer development. The findings were presented in October 2010 at the 35th Congress of the European Society for Medical Oncology (ESMO) held in Milan, Italy, by head researcher at the Institute, Dr Yuk Ting Ma.
It is widely known that smoking is the world‘s number one cause of cancer, and that carcinogenic substances in cigarettes are damagers of DNA. “Until now, however, there has been no direct evidence that smoking induces DNA methylation in humans”, Dr Ma highlights. “Cross-sectional surveys restricted to patients with cancer have revealed that aberrant methylation of several tumor suppressor genes is associated with smoking. But such surveys cannot distinguish those epigenetic changes that are a consequence of the disease process from those which are directly attributable to smoking”.
The relationship between methylation and smoking was studied in a cohort of 2011 healthy young women, ranging from 15 to 19 years of age, who tested negative for human papillomavirus. Researchers used cervical smears to compare methylation levels of the tumor suppressor molecule, p16, between women who started smoking upon study commencement, and those who had never smoked. The Birmingham researchers found that women who took up smoking during the study were over 3 times more likely (with an odds ratio of 3.67) to acquire p16 methylation.
On what lies ahead, Dr Ma concludes that: “the next step is now to show that women who acquire such smoking-induced methylation have an increased risk of developing malignancy”.
Source: European Society of Medical Oncology Press Release: www.esmo.org/no_cache/view-news.html?tx_ttnews%5Btt_news%5D=934&tx_ttnews%5BbackPid%5D=585
A team from the University of Pittsburgh School of Medicine, Baltimore, (MD, USA) has shed light on the origin of chromosomal errors and gene diversity. The research, which was published in the 14th October 2010 issue of the journal, Nature, discovered a novel chromatin factor, X nondisjunction factor 1 (xnd-1), which dictates where genetic material is swapped between maternal and paternal chromosomes during germ cell creation.
Senior author Dr Judith Yanowitz, assistant professor of obstetrics, gynecology and reproductive sciences at the Pittsburgh School of Medicine, explains: “When germ cells form, segments of DNA are exchanged, or recombined, between maternal and paternal chromosomes, leading to greater diversity in the daughter cells. Our research reveals a protein that plays a key role in choosing where those crossovers occur”.
Studying the genome of the tiny round worm Caenorhabditis elegans, the Pittsburgh team revealed that xnd-1 exerts its effects independently of genes required for X chromosome-specific gene silencing, and in the process revealed a novel pathway capable of distinguishing the X chromosome from autosomes in the germline. These effects of xnd-1 on meiotic crossovers were shown to be modulated, in part, by fluctuating levels of H2A lysine 5 acetylation.
Commenting on the importance of crossover fidelity, Yanowitz explains “Crossing over is essential for the correct movement, or segregation, of chromosomes into the germ cells. Failure to exchange DNA properly can lead to offspring with the wrong number of chromosomes and, in humans, defects in this process are a leading cause of infertility”.
The Pittsburgh researcher went on to speculate that the ‘crossover landscape‘, was altered in worms that carried a mutation in the xnd-1 protein, whereby the occurrence of crossovers was limited to the gene-rich, central areas of the chromosomes, and crossovers on the X chromosome were absent.
“This is the first gene in any system that is specifically required for the segregation of single chromosomes,” Yanowitz stated. “The fact that this is the X chromosome is interesting because the sex chromosomes play a unique role both in germline and general development”.
Source: Wagner CR, Kuervers L, Baillie DL, Yanowitz JL: xnd-1 regulates the global recombination landscape in Caenorhabditis elegans. Nature 467, 839–843 (2010).
A collaborative study between the Beth Israel Deaconess Medical Center (BIDMC), Boston, (MA, USA) and the Broad Institute, Cambridge, (MA, USA) has brought to light two new transcription factors – SRF and PLZF – that regulate adipocyte formation. The findings, which appear in the 1st October 2010 issue of the journal, Cell, have the potential to impact the treatment of metabolic diseases such as obesity and Type 2 diabetes.
“These findings help to demonstrate the power of epigenomic mapping when it comes to gleaning key insights into fat cell formation”, explains senior author Dr Evan Rosen, an investigator in the Department of Endocrinology, Diabetes and Metabolism at BIDMC and Associate Professor of Medicine at Harvard Medical School (MA, USA). “We found two new transcription factors involved in fat cell development”, Rosen went on to remark: “We have essentially demonstrated how an epigenomic ‘road map‘ can be used to identify biology that could not have been predicted through any other means”.
In order to better understand how fat cells control the genes imparting specialized functions on lipid and glucose balance, researchers generated genome-wide chromatin state maps in mouse and human cells. Unlike previous studies, which have investigated fat cells at a single static time point, this new study mapped several histone modifications throughout the course of the fat cell development, using chromatin immunoprecipitation followed by massively parallel sequencing.
Commenting on the importance of the models used, Rosen explained: “Our study looked at both mouse cells and human cells. This is key because each cell type can accumulate histone marks that actually have nothing to do with fat cell differentiation. Consequently, by comparing two different cell models, we were able to sift through and focus on the epigenetic marks that appeared in both cell types”.
The location of these marks differed between the two models and were determined by sequence analysis and a reporter assay. What emerged was a ‘core‘ set of histone modifications that formed the basis of a ‘road map‘ for the scientists to follow, and eventually, discover the two transcription factors.
Subsequent experiments confirmed the role of the transcription factors in adipocyte formation – upon depletion of either SRF or the PLZF – fat cells were generated at a faster rate and, equally, upon increase of either protein, adipocyte formation ceased.
“Although these particular studies were focused on the development of fat cells, we have reason to think that SRF and PLZF may be involved in the workings of mature fat cells as well”, noted Rosen, adding that these new findings, therefore, have the potential to impact a plethora of metabolic diseases.
“The huge costs of obesity and metabolic disease, both in terms of health and from a financial standpoint, are making adipocyte biology increasingly important”, he adds. “With these new findings we now have a better understanding of normal fat cell development, and going forward, we can compare normal fat cells to fat cells in disease states. If we can better understand why fat cells behave as they do, then we can work to develop therapies for obesity or diabetes”.
Source: Mikkelsen TS, Xu Z, Zhang X et al.: Comparative epigenomic analysis of murine and human adipogenesis. Cell 143(1), 156–169 (2010).