A recent study has shown that hypermethylation of the regulatory sequences of the erythropoietin (EPO) gene is often seen in tumors and that this abnormal methylation activates epigenetic silencing of EPO in cancer cells.
By utilizing real-time PCR technology, researchers involved in this study were able to demonstrate reduced expression of the EPO gene. The study, conducted by Steinmann and his colleagues from the Institute for Genetics in Justus-Liebig University (Giessen, Germany), used a combination of bisulfite sequencing and quantitative PCR to ascertain the expression levels of this particular gene in cancer cell lines. The German researchers analyzed the epigenetic regulation of EPO discovering that CpG islands in its promoter and enhancer were hypermethylated in most tumor cell lines and tumor tissue samples. This hypermethylation correlated with reduced EPO expression and thus a reduction in the protein expression of EPO.
Although erythropoietin is a hormone known for its potent ability in the regulation of blood cell production, the new research seems to indicate a role for this cytokine in the suppression or inhibition of cancer cells. However, it should be noted that the research has revealed suppression of this gene in cancer cell lines, rather than direct evidence for the biological activity of EPO in cancerous cells.
The researchers looked at numerous forms of cancer, as they often have different mechanisms of self propagation and survival. The results were mixed, as some cancers failed to show hypermethylation of the EPO gene, whilst others even demonstrated enhanced proliferation under ectopic EPO expression. It is clear that further research is needed to fully understand the role of this complex cytokine in cancer biology.
The researchers conclude that “although the data only address the epigenetic regulation of EPO in cancers, this could be a way that cancers regulate many other growth-promoting genes”.
Source: Steinmann K, Richter AM, Dammann RH. Epigenetic silencing of erythropoietin in human cancers. Genes Cancer 2(1), 65–73 (2011).
The original team from the University of North Carolina (NC, USA) who discovered the sixth DNA base, 5-hydroxymethylcytosine (5-hmC), have released information regarding their new discovery of an additional two bases derived from cytosine analogs. The new bases were discovered in the process of understanding the biological role of the previously discovered 5-hmC.
The University of North Carolina team utilized restriction enzymes in conjunction with thin-layer chromatography conditions, discovering that Tet proteins were capable of creating these novel intermediates. This led to the discovery of two new substances, 5-formylocytosine (5fc) and 5-carboxylcytosine (5caC), which Tet proteins produced from the original base 5-methylcytosine in an enzymatic activity-dependent manner.
5-methylcytosine in DNA is an essential tool, which plays a part in gene expression, genomic imprinting and in the suppression of transposable elements. However the activity and biological effect of 5-hmC, and now, 5fc and 5caC remains unknown.
It has been suggested that this revelation could result in the advancement of stem cell research. Chemical groups, through demethylation, could be removed thereby enabling the reprogramming of adult cells so that they may share the same characteristics as stem cells. Regarding cancer, the finding could provide scientists with the opportunity of reactivating tumor suppressor genes that have been silenced by DNA methylation.
The researchers are currently searching for a missing enzyme that transforms 5caC into unmethylated cytosine. Tet proteins are unable to do this unassisted.
“Before we can grasp the magnitude of this discovery, we have to figure out the function of these new bases”, comments the senior study author of the study Yi Zhang, professor of biochemistry and biophysics at University of North Carolina and an Investigator at the Howard Hughes Medical Institute. “Because these bases represent an intermediate state in the demethylation process, they could be important for cell fate reprogramming and cancer, both of which involve DNA demethylation”.
Source: Ito S, Shen L, Dai Q et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333(6047), 1300–1303 (2011).
Dr Andreas Hochwagen and his team from the Whitehead Institute (MA, USA) believe that they have discovered a mechanism in yeast, which allows them to defend against meiotic DNA recombination. The researchers explain that heterochromatin border regions are at a high risk of recombination during meiosis. However, this region is protected by two proteins working in unison to prevent this action, namely pachytene checkpoint protein 2 and origin recognition complex subunit 1.
The human genome is placed under risk during meiosis due to numerous programmed double strand breaks that initiate meiotic recombination. In the repetitive ribosomal DNA array of the yeast Saccharomyces cerevisiae, the meiotic double strand break formation is partially prevented due to the formation of Sir2-dependent heterochromatin. The researchers studied the highly repetitive DNA that make up yeast ribosomal DNA and concluded that it is protected from unsuitable recombination through a previously undiscovered mechanism.
Previous research into this topic indicated that heterochromatin prevents chromosome breakage in repetitive DNA. However, in their paper Dr Vader and Blitzblau suggest that defensive heterochromatin creates a transition zone between the repetitive and nonrepetitive DNA, resulting in an increased level of fragility.
“We had previously seen very little chromosome breakage in large regions close to repetitive DNA”, explains Blitzblau. “The finding that the borders of heterochromatin are particularly fragile helps us to understand why the cell invests in specifically protecting these regions”.
Yeast may not be the only organism which utilizes this form of protection. “In mice and flies repetitive DNA is also packaged into heterochromatin, and there is evidence that very few breaks happen in these regions during meiosis”, concludes Vader. “So it is possible that this type of protection is a general phenomenon”.
Source: Vader G, Blitzblau HG, Tame MA, Falk JE, Curtin L, Hochwagen A. Protection of repetitive DNA borders from self-induced meiotic instability. Nature 477(7362), 115–119 (2011).
Researchers from the John Innes Centre (Norwich, UK), funded by the Biotechnology and Biological Sciences Research Council, have recently published a study in Nature that identifies a Polycomb-based switch in Arabidopsis thaliana responsible for regulating epigenetic memory. The paper explores how an organism can create an epigenetic memory of variable conditions, such as the quality of nutrition or changing temperatures, which it is exposed to during its lifetime. The study, led by Professor Martin Howard and Professor Caroline Dean from the John Innes Centre, explains the mechanism by which this memory is created epigenetically in Arabidopsis and how it can also be inherited by future generations.
Speaking to Epigenomics, lead author of the paper Professor Howard explained the significance of the work, “We showed both theoretically and experimentally that an increasing period of winter cold is recorded through an increasing fraction of cells where a particular gene (FLC) is stably silenced after the removal of the cold stimulus. FLC in each individual cell can only be either fully activated or fully repressed, as only such states can be stably maintained. The quantitative memory comes from the fraction of cells that become fully silenced”. When asked about the implications of the study, Howard stated, “Our work also suggests a mechanism by which the epigenetic state of a cell, as determined by appropriate histone modifications across a locus can be altered: the idea is to nucleate a patch of an opposing histone mark and then allow these marks (through the action of recruited enzymes) to flip the epigenetic state of the whole locus”.
The researchers used a combination of experimental analysis and mathematical modeling techniques to elucidate the mechanism that causes the key gene FLC to either be switched ‘off‘ or ‘on‘ in any one cell and how this occurs in its progeny. From their experiments, the researchers suggested that this was due to reprogramming of epigenetic memory, where during the longer cold periods, FLC was switched off in the majority of cells. This then delayed flowering during the cold periods.
Commenting on the wider implications of the study, Howard explained that “Although the study is specific to quantitative epigenetic silencing in plants and their response to winter cold, the mechanism is potentially valid for any epigenetic system that acts to preserve the memory of a continuously varying but transient stimulus”.
Regarding what the researchers would like to do next, Howard concluded: “The next steps are to understand how the cold is perceived and measured during the cold period itself (as opposed to how the memory of the cold is preserved after return to the warm). We also need to critically test more aspects of the model, particularly with respect to the existence of opposing histone modifications and whether additional elements are required to maintain silencing”.
Source: Angel A, Song J, Dean C, Howard M. A Polycomb-based switch underlying quantitative epigenetic memory. Nature 476(7358), 105–108 (2011).