Functional Diversity of DNA Methyltransferase Inhibitors Functional Diversity of DNA Methyltransferase Inhibitors.

Abstract:
DNA methylation is catalysed by an enzyme called DNA methyltransferases. Human genome have four DNA methyltransferase genes,DNMT1, DNMT2, DNMT3A, and DNMT3B, still not resolved how these proteins been deregulated through cellular transformation. These proteins will have a big relief for people struggling with the tumours, the first one in the list (5-azacytidine, Vidaza) has been approved as an antitumor agent and the others are in their way of their preclinical and clinical development. They found the most common used DNA methyltransferase inhibitors, 5-azacytidine (5-aza-CR), it’s been characterised 25 years ago. 5-aza-CR need to be incorporated into DNA, this compound need to need extensive modification through metabolic pathways. In this study main focus on the cytosine analogue 5-aza-CR and 5-aza-CdR, both of them been wildly used in clinical trials and have been success to be effective in a variety of hematologic disorders. Generally the drugs been divided into two groups first one 5-aza-CR,5-aza-CdR, and zebularine, these been called nucleoside and the second group called non-nucleoside which contain procaine, EGCG, and RG108. Finally the most favoured drug currently used (5-aza-CdR)had the highest genotoxicity . In spit of cytotoxicity of azanucleoside inhibitors also showed the strongest demethylation effects . In addition to that we found 5-aza-CR and 5-aza-CdR the only drugs capable of significant demethylation and reactivation of the TIMP-3 tumor suppressor gene.

BIOC6006
Name: Ammar Alhassany
ID: 41874259

Global Mapping of DNA Methylation in Mouse Promoters Reveals Epigenetic Reprogramming of Pluripotency Genes

NAME : WOORAM JUNG
ID : 41607448



Abstract


DNA methylation patterns are reprogrammed in primordial germ cells and in preimplantation embryos by demethylation and subsequent de novo methylation. It has been suggested that epigenetic reprogramming may be necessary for the embryonic genome to return to a pluripotent state. We have carried out a genome-wide promoter analysis of DNA methylation in mouse embryonic stem (ES) cells, embryonic germ (EG) cells, sperm, trophoblast stem (TS) cells, and primary embryonic fibroblasts (pMEFs). Global clustering analysis shows that methylation patterns of ES cells, EG cells, and sperm are surprisingly similar, suggesting that while the sperm is a highly specialized cell type, its promoter epigenome is already largely reprogrammed and resembles a pluripotent state. Comparisons between pluripotent tissues and pMEFs reveal that a number of pluripotency related genes, including Nanog, Lefty1 and Tdgf1, as well as the nucleosome remodeller Smarcd1, are hypomethylated in stem cells and hypermethylated in differentiated cells. Differences in promoter methylation are associated with significant differences in transcription levels in more than 60% of genes analysed. Our comparative approach to promoter methylation thus identifies gene candidates for the regulation of pluripotency and epigenetic reprogramming. While the sperm genome is, overall, similarly methylated to that of ES and EG cells, there are some key exceptions, including Nanog and Lefty1, that are highly methylated in sperm. Nanog promoter methylation is erased by active and passive demethylation after fertilisation before expression commences in the morula. In ES cells the normally active Nanog promoter is silenced when targeted by de novo methylation. Our study suggests that reprogramming of promoter methylation is one of the key determinants of the epigenetic regulation of pluripotency genes. Epigenetic reprogramming in the germline prior to fertilisation and the reprogramming of key pluripotency genes in the early embryo is thus crucial for transmission of pluripotency.

Alterations in telomere lengths affect heterochromatin states of telomeres.

Original paper:

Telomere length regulates the epigenetic status of mammalian telomeres and sub- telomeres

Roberta Benetti, Marta Garcı´a-Cao & Marı´a A Blasco

ABSTART:

This article discusses the various changes that are caused in the telomeric and subtelomeric regions by shortening of the telomeric sequences. Telomeres are designed to be highly condensed sequences governed by heterochromatin domains present at the ends of chromosomes. Experiments conducted with early-passage mouse embryonic fibroblasts (MEFs) derived from wild-type, second generation (G2) and fifth generation (G5) telomerase-null mice, suggested a decrease in the telomeric H3K9 and H4K20 trimethylation and CBX3 binding accompanied by increased acetylation. Although, binding of telomere repeat factors was shown to be unaffected, such histone modifications change the heterochromatin structure to a more euchromatinised structure. The article also described changes in subtelomeric DNA methylations due to telomere shortening which further resulted in increased telomeric recombinations. Such heterochromatic domains were shown to regulate telomeric lengths and hence as indispensible modulators in the overall functioning of the eukaryotic genome.

Omkar Patkar

41812822

Long non coding RNAs have an important regulation role in embryonic stem cells
Ayrú Alejandra Rojas. Student number 41873252

Embryonic stem (ES) cells are those derived from the inner mass of the blastocyst, in the early stages of embryo development, and are capable of differentiating into most adult-type lineage-specific cells. Given this property, these cells are able to repair and renew damaged tissues and genetically defective adult organs. For this reason, is necessary to understand the fundamental processes which are essential for the maintenance of pluripotency. In a recent study it has been demonstrated that long non-coding RNAs (ncRNAs) with 200 or more nucleotides, are present thousands of times in the genome of mammalian species, and apparently are involved in the biology and development of embryonic stem cells. These investigators, showed a number of ncRNA which showed a high correlation with well recognized developmental genes, in several stages of ES cells. Additionally, evidence was given, to prove an association between long ncRNAS and trymethylated histones and histones methyltransferase, suggesting a function involving epigenetic regulation.

Reference: Dinger, M., Amaral, P., Mercer, T., Pang, K., Stephen, B., Gardiner, B., Marjan, A.A., Ru, K., Solda, G., Simons, C., Sunkin, S., Crowe, M., Grimmond, S., Perkins, A., Mattick, J. “Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation” (2008).Genome research. 18: 1433-1445

Werner syndrome gene had been epigeneitcally inactivated in human cancer

by Jane Cheung. Student number: 40092869

Werner Syndrome (WS) is a very rare genetic disorder which only occur around three in every one million people worldwide. It is characterized by premature aging and high incidence of cancer. WS is caused by mutations in the WS gene (WRN) and the function of the WRN protein is lost due to the mutation.

CpG islands are a short region of DNA that contains many cytidine and guanosine in the nucleotides. It is located near the promoter region and majority of them are associated with genes that are essential for general cell functions. Under normal conditions, CpG islands will remains unmethylated, allowing expression of the particular gene. In cancer cells, some CpG islands will become hypermethlated and the function of the gene will be inactivated.

In this report by Agerlo et al, it showed that CpG island hypermethylation had inactivated the function of WRN in many tumor cells. This inactivation caused WRN lost its exonuclease activity and chromosomes become more unstable. Furthermore, these hypermethylation-deficient WRN cancer cells will die if they were exposed to topoisomerase inhibitors. They also showed that by adding a DNA-demethylating agent or WRN into these hypermethylation-deficient WRN cancer cells, the growth of the tumor-cell was inhibited and the density of the tumor was reduced. This indicated that WRN has tumor-suppressor gene features. Also, the colon cancer patients with WRN CpG island hypermethylation had a better response to the camptothecin analogue, irinotecan, than the patents without WRN CpG island hypermethylation. Furthermore, WRN CpG island hypermethylation was commonly present in epithelial and mesenchymal tumors by screening a large amount of human tumors. All of these findings further confirmed the close connection between aging and cancer.

References:

Epigenetic inactivation of the premature aging Werner syndrome gene in human cancer

Ruben Agrelo, Wen-Hsing Cheng, Fernando Setien, Santiago Ropero, Jesus Espada, Mario F. Fraga, Michel Herranz, Maria F. Paz, Montserrat Sanchez-Cespedes, Maria Jesus Artiga, David Guerrero, Antoni Castells, Cayetano von Kobbe, Vilhelm A. Bohr, and Manel Esteller

Proc Natl Acad Sci U S A. 2006 June 6; 103(23): 8822–8827.

Discovering the power of methylation

Methylation is a biochemical process that is going on in every cell of our bodies. It is a part of most functions of the body and affects our health, energy and mental state. Methylation also protects and stabilises our DNA against damage which can lead to diseases such as cancer.

Researchers at the University of Wisconsin have developed a new method of detecting how methylation interacts with DNA. This new method promises rapid methylation profiling of DNA compared to existing methods and may lead to new advances in the understanding of diseases and how our bodies function.