The c-MYC Oncogene Directly Induces the H19 Noncoding RNA by Allele-Specific Binding to Potentiate Tumorigenesis

c-M YC is a family member of transforming genes such as n-MYC and l-MYC.

c-MYC oncogene products in many cancers (breast, lung and fibroblasts) are deregulated and function as regulators of genes transcription.

c-MYC induces the expression of noncoding RNA H19 by binding to the conserved E-box near the imprinting region.

On the contrast it can repress gene transcription by interfering with the function and assemblely mechanism .

As a regulator its involved many gene target that would eventually implement its various biological executions e.g. a apoptosis , cells proliferation etc

c-MYC down regulates the expression of insulin-like growth factor 2 (IGF2), the imprinted gene at H19/IGF2 locus

Finding the genes Target is the main objective in explaining the mechanism of this oncogene in transformation and has attracted the attention of this study

By Solomon Alier

EPIGENETIC MODIFICATION OF SOX-17 - PAVING THE PATHWAY FOR COLORECTAL CANCER DIAGNOSIS AND STAGING?

Is SOX-17 Making us See Red?

Submitted by: Kebaneilwe Lebani

School of Chemistry and Molecular Biosciences
University of Queensland


26 April 2009

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Cancer is a myriad of different diseases in which the cells or tissues of the body gain abnormal function and lose normal growth control mechanisms. The prevalence of cancer is high and its increase is being driven by increased incidences of cancer world wide. Research into cancer etiology and carcinogenesis as well as diagnostic and staging tools are therefore imperative for prognosis and therapeutic purposes.

Colorectal cancer (CRC) is one of the better understood malignancies and as such, it has availed a good model for the study of the mechanisms underlying carcinogenesis. The development of a readily evident precursor lesion as well as the formation of the adenomatous polyp are two unique features that make CRC models advantageous in the study of tumourigenesis (1). Concomitant to the stated features of the CRC model, pre-neoplastic adenomas in the colon have been found to be polyclonal lesions, meaning that genetics events alone cannot explain the hyper-proliferative state of the colon and thus other events in conjunction with genetic alterations are implicated in the progression of the lesions into colorectal carcinomas (2). Epigenetic modifications are one of the mechanisms that have been found to mediate initiation of colorectal carcinogenesis. The complementary effects of the epigenetic changes together with genetic events seem to drive the progression to CRC through oncogenic pathway addiction (3).

Epigenetics refers to heritable changes in gene expression that are facilitated by mechanisms that do not alter the primary DNA sequence (4). The changes in gene expression can be brought about by DNA methylation or histone modification of CpG island-associated promoters of tumour suppressor genes (5). This review shall however, concentrate on DNA methylation as an initiator and progression determinant of CRC. DNA methylation involves the addition of a methyl group to 5’cytosine residues in CpG dinucleotides by DNA methyl transferases (3). CpG islands have an increased quantity of the CpG dinucleotides and as such, susceptible gene promoter regions are prone to aberrant hypermethylation in de novo epigenetic events and thus lead to inappropriate gene silencing that can initiate tumourigenesis either through summative epigenetic modifications or in concurrence with genetic events (3,6). It is pivotal therefore, that tissue and tumour specific DNA methylation patterns be readily identified to aid in the detection and diagnosis of cancers in an effort to provide better therapeutic and prognostic resolutions.

In an effort to identify a tumour-specific molecular marker for CRC, Zhang et al (6) conducted a study in which they investigated the normal function of Sox-17 as well as the effects of epigenetic inactivation of SOX-17 in colorectal cancer models. Sox-17 is a SRY related High Mobility Group (HMG) box transcription factor which together with Sox-7 and Sox-18 constitute the Sox group F genes. Sox-17 plays a critical role in the regulation of development of several cells and tissues. Its role in the formation and development of the gut definitive endoderm and its implication as a tumour suppressor through repression of Wnt pathway signaling, were its identifying factors as a candidate gene for investigation with regard to CRC (6).

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In their research, Zhang et al (6) worked with normal colon samples, 7 CRC cell lines and a CRC cell line called DKO in which 2 methyl transferases had been genetically crippled and they were able to show that;

1. SOX-17 is a candidate for aberrant gene silencing in CRC

This was demonstrated through microarray analysis which identified Sox-17 expression when compared with other genes - including other Sox genes - as having no basal expression in CRC cell lines but more than a 2-fold increase in expression following treatment with a methyl transferase inhibitor. Sox-17 expression was however present in normal colon cells and the DKO cell line and not affected by the presence or absence of a methyl transferase inhibitor.


2. Silencing of SOX-17 is associated with its promoter CpG island hypermethylation

Genomic DNA sequence analysis of CRC cells that showed no basal expression of Sox-17 was compared with normal colon cells and DKO cells. The analysis was made using methylation specific PCR and bisulphate sequencing and it was found that the 5’ regulatory regions of the CRC cell lines exhibited CpG island hypermethylation of the transcriptional start site. No methylation of Sox-17 promoter regions was observed in the normal and DKO cells. Supplementary experiments that examined hypermethylation of SOX-17 promoter regions in varying human colon specimens showed that hypermethylation was present at a frequency of 86% in colorectal adenomas, 100% of stage I CRC, 100% of stage II CRC and 89% of stage III CRC.


3. Restoration of SOX-17 expression suppresses tumour cell growth


Transient transfection of a vector with wild-type SOX-17 cDNA into CRC cells was shown through colony formation assays to significantly suppress tumour growth. The cell colonies that grew however were shown through Western blots that they did not express any detectable SOX-17 protein which was likely due to transfection inefficiency.

4. SOX-17 inhibits β-catenin/TCF-driven transcription

To explore this hypothesis, CRC cells were transfected with reporter constructs as well as wild-type β-catenin expression vector and increasing amounts of wild-type SOX-17 cDNA. Wild-type β-catenin expression invoked a 60-fold activation of TCF which was repressed by a dose-dependent over-expression of SOX-17. These results show that SOX-17 has a tumour suppressive function that prevents nuclear accumulation of β-catenin which together with TCF factors direct the transcription of genes, some of them oncogenic, to result in disheveled Wnt signaling, a hallmark of numerous aggressive human cancers including CRC (7).

The identification of Sox-17 as a candidate gene that can serve as a hypermethylation marker for colorectal cancer is a step of monumental proportion in the quest to develop molecular strategies for CRC staging as well as detection given the implication of aberrant de novo methylation of Sox-17 in early carcinogenesis. Efforts will now have to go towards refining methylation determination methods that can be routinely used for patients undergoing testing for CRC. The bisulfite treatment method used in the research by Zhang et al although accurate, has high analytical technique requirements and as such, robust and easy to use commercial kits will have to be developed to determine Sox-17 hypermethylation. Zhang et al also worked on tumour samples as well normal colon samples but in order to make testing and assessment feasible it is important that non-invasive procedures be used to provide samples for hypermethylation analysis. A possible sample for the analysis could be stool samples in which DNA could be isolated from colon epithelial cells that are regularly sloughed off with stool given the relatively high turnover of gut epithelial cells. Superseding detection of Sox-17 hypermethylation, the research by Zhang et al also opens up avenues for treatment of early CRC. The results of the study showed that tumour cell growth could be curbed by restoration of SOX-17 expression. One of the ways that this was achieved, was through treatment of the cell with DAC, a drug that inhibits DNA methyl transferase (DNMT) mediated hypermethylation of promoter CpG islands. While DNMT inhibition may seem like a rational process that may be applied to early CRC treatment, there are numerous concerns that long term administration of the inhibitors may lead to chromosome instability which could result in inadvertent genetic mutations (8).The resolution therefore relies on the development of possible strategies that can facilitate competent and safe gene re-expression in vivo. Progress is being made and it will probably not be too long until these research findings along with further studies find clinical applications for patients.

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REFERENCES

1. Chung D. The Genetic Basis of Colorectal Cancer: Insights into Critical Pathways of Tumorigenesis. Gastroenterology 2000;119:854-865.
   
   


2. Issa J. The Epigenetics of Colorectal Cancer. Annals of the New York Academy of Science 2000;910:140-53;discussion 153-5.
   
   


3. Jones PA, Baylin SB. The Fundamental Role of Epigenetic Events in Cancer. Nature Reviews 2002;3:415-428.
   
   


4. Baylin SB, Ohm JE. Epigenetic Gene Silencing in Cancer – A Mechanism for Early Oncogenic Pathway Addiction? Nature Reviews 2006;6:107-116.
   
   


5. Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA, Clark S. Epigenetic Remodeling in Colorectal Cancer Results in Coordinate Gene Suppression Across an Entire Chromosome Band. Nature Genetics 2006;5:540-549.
   
   


6. Zhang W, Glockner SC, Guo M, Machida EO, Wang DH, Easwaran H, Van Neste L, Herman JG, Schubel KE, Watkins DN, Ahuja N, Baylin SB. Epigenetic Inactivation of the Canonical Wnt Antagonist SRY-Box Containing Gene 17 in Colorectal Cancer. Cancer Research 2008;68(8);2764-2772.
   
   
   


7. Zhang Y, Huang S, Dong W, Li L, Feng Y, Pan L, Han Z, Wang X, Ren G, Su D, Huang B, Lu J. SOX7, Down-regualted in Colorectal Cancer, Induces Apoptosis and Inhibits Proliferation of Colorectal Cancer Cells. Cancer Letters 2009;277:29-37.
   
   


8. Tooke N, Pettersson M. CpG Methylation in Clinical Studies: Utility, Methods, and Quality Assurance. [Online]. 2004 [Cited 2009 Apr 6]; Available from: URL: http://www.devicelink.com/ivdt/archive/04/11/002.html
   
   

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Transgenerational Germ-line Epigenetic Modification with Nutritional Supplementation

The paper titled “Germ-line epigenetic modification of the murine A^vy allele by nutritional supplementation,” by Cropley et al. was considered to be the “most memorable epigenetic moment of the year” for 2006.It was a groundbreaking paper which published in Proceedings of the National Academy of Science in November (Cropley et al. 2006) because this paper provides the first direct evidence of a mechanism in a transgenerational, epigenetic alteration.

Cropley uses a mutant mouse strain known as viable yellow agouti, or A^vy. . As previous studies shown, mice carrying the viable yellow agouti allele exhibit yellow fur, obesity, type II diabetes, and predisposition to tumors. The epigenotype of the Avy allele is partially stable in the female germline, which lead to weak inheritance of the maternal phenotype. However, the phenotype of offspring is not influence by paternal A^vy epigenotype. Methyl donors would be more likely to alter the epigenotype of A^vy stably in the female germ line. In other words, nutritional supplementation during gestation seemed to cause an epigenetic alteration in phenotypes of offspring.

The germ-line alteration of the Avy epigenotype is definite evidence that an environmental factor can produce a phenotypic effect by inducing an epigenetic modification in the mammalian germ line, and that such a modification can persist through the epigenetic resetting that takes place during gametogenesis and embryogenesis. However, it would be interesting to see if the shift to the agouti phenotype would continue into the F3 and F4 generations, as would be expected if the epigenetic germ line was permanently reprogrammed.

Guo REN

s41358227

Sequence- and target-independent angiogenesis suppression by siRNA via TLR3

Generic, not sequence- or targeted, SiRNA prevents Age Related Macular Degeneration and can potentially treat Angiogenic Disorders.

Posted by: Mondar M. M. Ahmed
Student Number: 41280337
University of Queensland

Choroidal neovasculasation (CNV) is the formation of new blood vessels in the choroidal layer of the eye that leads to blurring of the central vision or age related macular degeneration. The formation of the new vessels is associated with elevated amounts of Vascular Endothelial Growth Factor (VEGF). Photodynamic drugs are used to treat the disease by breaking down the new vessels and preventing neovascularisation. Anti-VEGF drugs are also used. SiRNAs targeting the VEGFA or its receptor VEGFR1 are also being investigated as a potential route to stopping CNV.


SiRNAs are small interfering RNAs which silence genes by RNA interference. Previously it was thought that sequence specific targeted SiRNA prevented CNV by gene silencing. However, this thorough study by Kleinman et. al. has demonstrated that suppression is not mediated by gene silencing using specific SiRNA but rather is a class effect of generic SiRNAs at least 21 nucleotides long. These generic SiRNAs can suppress CNV mediated by toll-like receptor 3 (TLR3) on the cell surface and its adaptor called TRIF with induction of anti-angiogenic innate immunity via IFN-γ and IL-12. The study opens a new avenue for the treatment of angiogenic disorders, that is, it may be possible to treat other forms of angiogenic disorders using the generic SiRNAs which work as well as VEGFA antibodies and are less toxic.

(Click on eye to see animation.)

How does epigenetics affect body size of vertebrates ?

The longitudinal bone growth at the growth place is the key factor for determining the entire body size of vertebrates. With an increase of age, the plate goes through a programmed cell aging, making the longitudinal bone growth gradually to deteriorate. Indirect scientific data shown that stem-like cells have limit to proliferate in the growth plate resting zone and is worn out slowly. The same situation found on replication of different types of animal cells. It was know as the Hayflick phenomenon. In this study, the authors found that the number of population doublings of rabbit resting zone chondrocytes in culture did not depend on the age of the animal from which the cells were harvestedd”. Also, the observation displayed that the level of DNA methylation in resting zone chondrocytes declined in vivo, along with an increase of age. The slow proliferation of resting zone chondrocytes in vivo caused methylation to disappear particularly, whereas this phenomenon was not found in the rapid proliferation of proliferative zone chondrocytes in vivo. Therefore, during growth plate senescence, the level of methylation in DNA is decreased. Consequently, they assumed that the replication of growth plate chondrocytes in vivo is limited due to DNA methylation lost, which could be a natural mechanism that restricts longitudinal bone growth in vertebrates and, importantly, this is employed to determine the overall adult size(Nilsson et al. 2005).





Chang, Cheng-Hung 41858932

Developments in the field of Cancer Epigenetics

The Dawn of a New Diagnostic Marker for Colorectal Cancer?

Submitted by: Kebaneilwe Lebani 41921706

School of Chemistry & Molecular Biosciences

University of Queensland

20 April 2009

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Colorectal cancer (CRC) incidences are high the world over. The US documents colorectal cancer as its second most prevalent cancer and China reports an increase in CRC incidence. Due to the high incidence and prevalence of cancers as a whole, research has increased efforts not only towards therapeutics but also towards diagnostic markers that can be used for early detection of cancer to improve therapeutic options and prognosis. A collaborative study undertaken by Zhang et al in 2008 entitled Epigenetic Inactivation of the Canonical Wnt Antagonist SRY-Box Containing Gene 17 in Colorectal Cancer brings to the fore a gene called Sox 17 that is involved in early development of CRC and has potential of serving as a marker for early colorectal carcinomas.

The promoter region of Sox 17 gene in CRC was found by Zhang et al, to be silenced by an epigenetic phenomenon and DNA hypermethylation was the mechanism through which the epigenetic changes occurred. The Sox 17 gene promoter in normal colorectal tissue is not methylated and the protein product of the Sox 17 gene has a tumour suppressive function that antagonizes the activity of a downstream pathway called the Wnt signaling pathway. Unidentified events that lead to the hypermethylation of the Sox 17 CpG Islands of the promoter region silence the gene, resulting in aberrant Wnt signaling and the development of carcinomas. Zhang et al documented that this process could be identified in 100% of stage I and II CRC. This epigenetic change coupled with genetic changes is what then drives the progression of CRC. Although the transcription repressive mechanism of the Sox 17 promoter requires further elucidation, its implication in early tumourigenesis makes it a suitable candidate as a novel marker for colorectal cancer.

SOURCE

LITERATURE REVIEW

BRAIN PLASTICITY - AN EPIGENETIC EFFECT?

Ever wondered how we learn, retain, remember and apply in our day to day life? What does experience amount to? Why does salt pepper hair indicate age as well as wisdom?
Well , the answer is brain plasticity. It gives us the capacity to respond to our environment with maximising our own resources.

In fact the neonatal brain of cats need environmental visual stimuli for the development of the AES(anterior ectosylvian sulcus) region of its cortex . Wait there is more to it . In the absence of such stimuli, the neurons that were under the control of AEV(anterior ectosylvian visual) area in AES start responding to auditory stimuli and not the usual visual stimuli, thereby increasing the number of neurons responding to auditory cues while reducing the ones responding to visual cues. Such compensatory mechanisms are debated in humans though most beleive that it is possibl e only during early brain development.

Does this mean that once adults we loose our brain plasticity? No, in the adult rat brain its capacity to react to PEPS(pain and emotional stress) even after 2 months proves that brain plasticity is very much active in the adult brain. This is mainly carried out by the acetylation of H4 histone mediated by the process of phosphorylation carried out by Ca+ protein kinase C. Such a secondary chemical signalling pathway allows the effect to be seen even after 2 months contributing to memory. Interestingly, the cure for depression also lies in epigenetic regulation either by acetylation of histone H3 (in chronic depresion) or H4 (in acute depression) in the promoter regions (P3 and P4)of Bdnf (brain derived neurotrophic factor) mRNA.

NAME: ISHITA
STUDENT NUMBER 4187144

Differential Histone 3 Lysine 56 Acetylation in hESC and Somatic Cells.

All the cells in our body, each and every one of them, came from a single cell!! What makes a single cell form so many different body cells that can carry out variety of specialized functions? The capacity of self renewal and differentiation are the two characteristic potentials of Human Embryonic Stem Cell (hESC). All stem cells have the ability to self-renew and the ability to differentiate. Embryonic stem cells are unique in that they are derived from the inner cell mass of the developing blastocyst and, thus, can give rise to all the tissue types of the embryo. Mammalian development requires the specification of over 200 unique cell types from a single totipotent cell. Histones are intimately associated with DNA and are highly conserved proteins. Variety of post-translational modification, amino acid sequences and their three dimensional structures are highly conserved. These modifications can be acetylation, methylation, phosphorylation, ubiquitination, polyribosylation of specific histone residues.
Approximately 1% of histone 3 is acetylated in human cells. Acetylated lysines are recognised by bromodomains of ATPase remodelling complex to promote transcription. Lysine 56 acetylation (K56Ac) in the helical core of H3 differentiates between epigenetic state of pluripotent and somatic cells. The K56Ac targets are gene specific like canonical histone genes which are bound by transcription factors of hESC NANOG, SOX2 and OCT4. Differential K56Ac is observed in human embryonic stem cell and somatic cells. GO analysis revealed that the genes involved in signal transduction, tissue remodelling and organ development show K56Ac in somatic cells. K56Ac relocates during transition from pluripotent cell to differentiated state. Transcript levels of transcription factors NANOG, SOX2 and OCT4 drop drastically in lineage committed cells. The most deacetylated loci that were observed in differentiated cell are the hESC specific miRNA gene grp mir302 which plays a critical role in development and regulation of ESCs, HOX genes on the other hand are most acetylated. K56Ac is observed to be depleted in canonical histone genes (H1, H2A, H2B, H4 & H5) in somatic cells. K56Ac spatial patterns are parallel to spatial binding of NSO proteins and are linked to hESC core transcriptional network. K56Ac marks both active and inactive genes. By marking core transcriptional network of hESC K56Ac can predict new NSO transcriptional regulator targets can be identified

Jayee Patil
41912094

Epigenetic differences arise during the lifetime of monozygotic twins

Epigenetic differences arise during the lifetime of monozygotic twins
By:
Ramya Viswanath Subramanyam(41813016)

Monozygotic twins are considered to be an ideal example for two individuals having same genotype. But it has also been observed that as the pair grows up they become phenotypically dissimilar although having similar genetic makeup.
To identify the reason for their phenotypically differences 80 twins were analyzed out of which 30 were females , rest being males .it was observed that the epigenetic patterns of DNA methyaltion and histone( H3 and H4) complex were different in the twins thus explaining their differential behaviour. These changes can occur due to internal or external factors. Internal factors can be in incapability of cells during somatic division to transfer epigenetic regulators or difficulty in maintaining the epigenetic factors in the cells. All these reasons lead to Epigenetic drift in the two individuals resulting in their diverge phenotypical behaviour. External factors like smoking, drinking, diet may also lead to same result. Another observation was those twins who had spend less time with each other or had different life styles demonstrated huge difference in their physical behaviour. Out of all these, the most important observation was only a small change in the epigenetics of the cells can lead to huge phenotypical differences.
It has been evident from these observations that not only has epigenetics been able to solve the reason behind the difference in the phenotypical behaviour of monozygotic twins but is also the key to many unsolved questions in behavioural science.

Reference:
1. Epigenetic differences arise during the lifetime of monozygotic twins
Mario F. Fraga,* Esteban Ballestar,* Maria F. Paz,* Santiago Ropero,* Fernando Setien,* Maria L. Ballestar,† Damia Heine-Suñer,‡ Juan C. Cigudosa,§ Miguel Urioste,¶ Javier Benitez,¶ Manuel Boix-Chornet,† Abel Sanchez-Aguilera,† Charlotte Ling,∥ Emma Carlsson,∥ Pernille Poulsen,** Allan Vaag,** Zarko Stephan,†† Tim D. Spector,†† Yue-Zhong Wu,‡‡ Christoph Plass,‡‡ and Manel Esteller*§§
§§ To whom correspondence should be addressed. E-mail: mesteller@cnio.es.
Edited by Stanley M. Gartler, University of Washington, Seattle, WA
Received January 17, 2005; Accepted May 23, 2005.

Can we predetect the the metastasis of cancer?

Cancer is a major threat to the health of human beings and is one of the leading causes of death. Metastasis is a key character in the advanced stage of cancer, therefore it is essential in clinical use to find a marker indicating the development of metastasis in the tissues of cancer patient. The research shows that Synuclein-g (SNCG) is a reliable and sensitive indicator in determining the stage of metastasis in cancer. It is a member of a neuronal protein family synuclein, this group of proteins is abundantly expressed in brain tissues. We have studied that SNCG is abnormally expressed in a high proportion (67.5%) of tumor tissues in variable cancer types, such as liver, esophagus, lung, prostate, cervical, and breast cancer, but the expression in tumor-matched non-neoplastic adjacent tissues is pretty low(0.6%). The SNCG proteins expressed in different types of cancer all display stage specific patterns of very low expression in stage I and high expression in stages II to IV.

An Immunohistochemical assay has been developed to detect the SNCG in the sample of tumor tissue and tumor-matched non-neoplastic adjacent tissue. The results reveal that in 160 samples of tumor tissues, there are nearly 67.5% of samples with staining of SNCG protein exclusively in their malignant cells at different expression levels and varies depend on the types of cancer. In contrast, only 0.6% of the tumor-matched non-neoplastic adjacent tissue from the same patient group has detected the labeled antibody.

sharon XIAOXIA SONG

41912973

WE NEED A TITLE AND LINK AND YOUR NAME WITH THIS POST.

Cancer is a major threat to the health of human beings and is one of the leading causes of death. Metastasis is a key character in the advanced stage of cancer, therefore it is essential in clinical use to find a marker indicating the development of metastasis in the tissues of cancer patient. The research shows that Synuclein-g (SNCG) is a reliable and sensitive indicator in determining the stage of metastasis in cancer. It is a member of a neuronal protein family synuclein, this group of proteins is abundantly expressed in brain tissues. We have studied that SNCG is abnormally expressed in a high proportion (67.5%) of tumor tissues in variable cancer types, such as liver, esophagus, lung, prostate, cervical, and breast cancer, but the expression in tumor-matched non-neoplastic adjacent tissues is pretty low(0.6%). The SNCG proteins expressed in different types of cancer all display stage specific patterns of very low expression in stage I and high expression in stages II to IV.
An Immunohistochemical assay has been developed to detect the SNCG in the sample of tumor tissue and tumor-matched non-neoplastic adjacent tissue. The results reveal that in 160 samples of tumor tissues, there are nearly 67.5% of samples with staining of SNCG protein exclusively in their malignant cells at different expression levels and varies depend on the types of cancer. In contrast, only 0.6% of the tumor matched nonneoplastic adjacent tissue from the same patient group has detected the labeled antibody.

Lymphocytic leukemia and epigenetic

As we know, chronic lymphocyte leukemia is a form of leukemia which is the most common form of leukemia in the western countries. It mainly affects people over the age of 50. Patients with CLL are divided into 3 gropes: If the deletion happened at chromosome 13q14, they will have a big chance to survive whereas potions with deletions at chromosomes 11q22-23 and 17p13 will associate with an adverse outcome and finally if the deletion and the mutation happened to the p53 gene, they will have a poor chance to survive.
In human cancer, many interactions between DNA methylene, histone modifications and RNA interference have been implicated. In this research, they used a candidate gene approach to determine the methylation status of 15 cancer-related genes in 32 potions with CLL. And they found that methylation patterns in CLL are disease s-specific, this because that the profile is not similar to other hematopoietic malignancies.


Zainab Almansour
1450764

An epigenetic mechanism to explain the effect of early childhood abuse and neglect

Increased susceptibility to psychiatric illnesses in adults with a history of childhood abuse and neglect may reflect a lasting impact of early maltreatment on epigenetic mechanisms regulating gene expression.
A recent study has explored the dynamic role of DNA methylation (an epigenetic mechanism) in gene regulation and its potential to mediate gene expression in the pre frontal cortex (PFC) and hippocampus. The PFC and hippocampus both play a central role in cognitive defects and aberrant emotional behaviours originating from early-life adversity.
The lasting effect of this epigenetic mechanism on brain derived neurotrophic factor gene (BDNF) on the central nervous system was demonstrated using a rat model. During the first postnatal week, rat neonates were exposed to either a stressed-abusive mother (maltreatment) or positive care giving mother (cross-fostered care) 30 minutes daily. DNA methylation patterns were assessed as well as gene expression throughout their life-span using methylation specific real-time polymerase chain reaction (PCR) (MSP) and other techniques. Furthermore, DNA methylation patterns were assessed in the next generation of infants using the same methods.
The findings of this study come with both expected and unexpected results. Firstly, the study demonstrates that not only do rodents that have experienced abuse grow up and mistreat their own offspring but that their offspring also have significant DNA methylation. There is maintenance of BDNF DNA methylation both within the individual across its lifespan and in passing that altered methylation from one generation to the next.
The study brought up a strikingly unexpected result. It showed the inability of cross-fostering to rescue DNA methylation in rats born to abused rodents which would otherwise, normally occur as a reversible mechanism of DNA methylation.
The challenge of this finding will lie in replication of these results in human experiments which could have spectacular outcomes for treatments of mental illnesses.

Ranjitha Naidu
s4197437

Copy number will not reveal the epigenetic alterations in a damaged copy of gene from father.

Juani Mazmin Husin
41858996


Have you ever seen a baby with small birth weight, and later showed slow neurodevelopment and mild to moderate learning difficulties, starting to gain weight from the age of 2 and later on overeating, short adult stature, incomplete puberty and having difficulties in communicate appropriately? Do you know that the cause of obesity in child is not 100% due to consumption of fast food as claimed in the media? You might have heard about Prader Willi Syndrome(PSW), an extremely rare human genetic disorder which is believed to be the most common genetic cause of obesity. There is a loss of function of genes situated at 15q11-q13 and if the long q arm of one copy from the mother’s chromosome 15 is deleted, Angelman syndrome results. On the other hand, if the father’s copy of the chromosomal arm is deleted, Prader Willi Syndrome results. The mother’s genes in this are “turned off” through a rare phenomenon called genomic imprinting.The standard diagnosis of PSW includes both clinical observations and genetic investigations involving DNA methylation studies and fluorescence in situ hybridization (FISH) analysis. However, there are limitations on these analyses, which lead to a new designed using real-time PCR assay mainly to determine the size of the chromosomal deletions in patients with PWS. (Teresa Munce, et al). Genomic DNA isolated from both peripheral blood leukocytes and buccal epithelial cells were used in this study. Results were 100% concordant with previous FISH assays performed on the same patients, indicating that this assay is reliable and reproducible for detecting homozygous chromosomal detections.
Apart from the assay design, one must noted that a link between gene dosage and expression has not been experimentally determined in brain. A.Hogart et al have revealed that gene expression abnormalities were resulted from alterations in epigenetic regulations. Previous assumption that have been made was extra copy number of genes lead to increased in expressions. However, their study shows that gene expression can be altered in unexpected ways through epigenetic changes and it is likely that gene expression changes beyond the expected maternally expressed imprinted genes contribute to the variability in phenotypes in 15q11-13 duplication syndrome.

Interesting New Findings of DNA Methylation in Human Colon Cancer

Nurrahmi Dewi Fajarningsih
(41916243)

Previous studies of DNA methylation in cancer are mainly focus on CpG methylation and promotor hypermethylation. However, a complete genome-scale analysis of DNA methylation (DNAm) in order to get a comprehensive understanding about variation of normal and cancer cells have not been carried out. To address that, Irizary et al (2009) conducted a comprehensive high-throughput array based relative methylation (CHARM) genome-wide analysis and found some interesting result. The first interesting finding is that most of tissue specific DNAm are not occurred at CpG islands but at ‘CpG island shores’ (located within 2 kb of islands). Second, they also identified that differential methylation regions changes (C-DMRs) in colon cancer are similarly divided between hypomethylation (44%) and hypermethylation (56%). Third, C-DMRs and tissues differential methylation regions (T-DMRs) are both located at CpG island shores and both are 45-65% overlapped. As a result, spesific DNA methylation changes of cancer involving the same DMRs of normal tissue (involve the same site).

A crosstalk between histone methylation and DNA methylation in gene silencing

Anti Damayanti Hamdani
41917325

Histone and DNA methylation are heritable epigenetic modification for programming gene expression profiles. While DNA methylation leads to stable and long-term repression, histone methylation plays a role in readily reversible gene silencing. Though both mechanisms are carried out by different set of chemical reactions, they are actually dependent on one another in directing gene repression patterns. Histone methylation can help to establish DNA methylation patterns and pre-existing DNA methylation may guide the placement of histone modification. This relationship might be accomplished by physical interaction between DNA methyltransferase and histone methyltransferase. The human β-globin locus is used as a model to reveal the crosstalk between arginine methylation of histones and DNA methylation to repress gene expression. Firstly, the protein arginine methyltransferase PRMT5 is symetrically dimethylating histone H4 arginine 3 (H4R3me2s). The repressed histone then serves as an epigenetic mark for direct binding with DNA methyltransferase DNMT3A to subsequently recruit DNA methylation and induce gene silencing. Notably, the knockdown of PRMT5 by short hairpin RNA (shRNA) leads to globin gene activation because the DNMT3A loss the target marks for binding. Thus, in regulating gene repression, DNMT3A provides a direct link between histone and DNA methylation by interpreting repressive marks on histone and inducing DNA methylation.

The development of small interfering RNA (siRNA) as antiviral against Avian Influenza Virus (AIV) infection

Posted by:
Risza Hartawan
41545858

The consequence of widely spread of AIV outbreaks subtype H5N1 in Asia, Africa and Europe has resulted on economic devastation at poultry industries as well as serious threat on public health circumstance. This segmented negative sense RNA virus from family Orthomyxovidae rapidly mutate via either antigenic drift or shift mechanism that have caused limitation of preexisting vaccines or antivirals. The discovery of siRNA activity as antiviral have furnished new perspective against the disease.
Several studies have dedicated to investigate the efficacy of siRNA, which targeted on AIV conserved genes to protect infection against AIV. Tompkins et al. (2004) designed siRNA specific for Nucleoprotein (NP) and Acidic Polymerase (PA) gene and employed oligofectamine as delivery system. By the intravenous (i.v.) administration before infection, they were successful to reduce mortality rate on the mice challenge study with several highly pathogenic strains of AIV (H1N1, H5N1, H7N7, and H9N2). Moreover, Zhou et al. (2007) was also successful to demonstrate inhibitory effect on the AIVs infection in vitro and in vitro using siRNA that targeted on Nucleoprotein (NP) and Matrix 2 (M2) gene using polyethylenimine (PEI) as carrier. Research by Zhou et al. (2008) using siRNA expression plasmids for NP, PA and PB1 gene also generated promising result. In addition, distinctive study was demonstrated by Ge et al. (2004), which administrated siRNA before and after infection. Using PEI as carrier with slow i.v. injection, the siRNA was able to decrease level of virus titer of challenging mice.
To sump up, the administration of siRNA that targeted on AIV conserved genes either before or after infection showed therapeutic effect against broad strain of AIVs. However, the utilization of these siRNAs were still incapable to induce sterile immune on the challenging animal. Moreover, subsequent researches have to be done to determine the best carrier to deliver siRNA into target cells.

Paper referred to:
1. Protection against lethal influenza virus challenge by RNA interference in vivo.
2. Inhibition of influenza virus production in virus-infected mice by RNA interference.
3. Effective small interfering RNAs targeting matrix and nucleocapsid protein gene inhibit influenza A virus replication in cells and mice.
4. RNA interference of avian influenza virus H5N1 by inhibiting viral mRNA with siRNA expression plasmids.

Did you know that deficiency of vitamin B12, B9 and methionine before pregnancy causes health-related disorders in adult offspring?

Lina Rustanti
41917286

Many studies suggest that mothers’ diet during pregnancy will influence their children’s health. However, little is known about the effect of specific nutrients on the timing of prior to pregnancy and around the time of conception.
A recent research proves that specific nutritional supplements exposure during periconceptional period leads to changes of genome associated with clinical phenotypes in offspring. Reduction of vitamin B12, B9 (folate) and methionine to the diet of adult female sheep from 8 weeks preceeding until 6 days after conception reveals epigenetics modification to DNA methylation in the embryo. Folate and vitamin B12 are essential contributors for DNA methylation. DNA methylation is one of several epigenetics mechanisms that play a role in gene silencing during embryogenesis. Aberrant DNA methylation is associated with the pathogenesis of several diseases.
The experiment was conducted by giving vitamin B12, folate and methionine to both treatment and control groups. Compared to the control group, the treatment group was reduced in the methionine diet. Inadequate methionine diet causes deficiency of vitamin B12 and folate in blood plasma. This leads to DNA hypomethylation and causes the increase of adiposity, insulin resistance, altered immune responses and elevated blood pressure in adult offspring. Interestingly, these health-related disorders are mainly found in males. This research provides the requirement of nutritional advice to intending mothers for improvement of their children’s long-term health.

The significance of DNA methylation on the diversity of species

Student name: Thi Thu Huong Nguyen
ID: 41872406

Epigenetic is a term referring to heritable changes in the gene expression. This phenomenon relates to cytosine methylation of DNA molecule and condensation of DNA molecule with proteins. Differences in term of DNA methylation could lead to diversity of species. However, there is a small amount of research in regard to implications of the DNA methylation. This particular article focuses on investigating the level of DNA methylation polymorphism in Brassica oleracea using the methylation sensitive amplification polymorphism (MSAP) technique. After carrying out the analysis of the four morphotypes (kale, cauliflower, broccoli, and cabbage), authors drew a number of conclusions on their study. Firstly, researchers pointed out that there is an inheritance of a large number of MSAP fragments through generations. Secondly, they observed that a higher proportion of MSAP methylation occurs in Brassica oleracea than that in other species. It is probably caused by concentration of heterochromatic regions when sampling MSAP, the polypoid origin of Brassica oleracea as well as the correspondence of the MSAP-methylated markers with transposons. Finally, they concluded that the phenetic classification based on the MSAP fragments does not match which the morphotype classification based on AFLP fragments.

Chromatin Remodeling in Schizophrenia and Bipolar Disorder

Psychiatry is a field which remains limited by the lack of reliable, objective criteria such as blood tests or imaging investigations that can accurately characterize illness and guide treatment. The authors of this article describe an approach which may prove useful, firstly in diagnosis and secondly in selecting patients that are likely to respond to a particular drug therapy, thus minimising the process of medication trial and error. They focussed on epigenetic modification of histone residues which has previously been proposed as a cause of schizophrenia and bipolar disorder. What makes this paper intriguing is that the researchers ran parallel in vitro and in vivo trials in an effort to make their results directly relevant to clinical practice.
In the clinical part of the trial, 11 patients with schizophrenia and 7 with bipolar disorder were given 4 weeks of treatment with VPA - a drug commonly used in bipolar disorder and one which has been shown to inhibit HDAC (histone deacetylase). Blood was taken before and after the treatment period with results indicating that the participants with schizophrenia started with lower levels of H3K9, K14ac (acetylated histone 3) and showed a lesser increase through the study period when compared to the bipolar group. GAD67 (a gene shown to have reduced activity in schizophrenia) mRNA levels increased in 10 of the participants with the serum VPA level rather than initial diagnosis being the strongest predictor of change. These and other results led the researchers to make a number of conclusions : 1/ the chromatin is more restrictive in schizophrenia patients and responds less well to HDAC inhibition; 2/ VPA can influence GAD67 gene expression, probably via the alteration of chromatin; 3/ This experimental model could be used to assess the epigenetic regulation of other genes in a research or clinical scenario; and 4/ There may be a therapeutic use for drugs such as VPA which ‘soften’ the chromatin and may improve the subsequent efficacy of other psychotropic medications.
Potentially, this could revolutionise psychiatric practice as patients could be individually assessed at a chromatin level with the results guiding treatment and helping to reduce the burden of disease.

Joshua Betts
s3308412

PERMANENTLY ALTERATION TO THE DNA METHYLATION OF SPECIFIC CYTOSINES

Post by Shahril Asraf Omar,41858893
Do you aware the aspects of prenatal environment? Do you believe nutrition will alter the phenotype persistently? How the environment and nutrition affect the way mammalian genes?
There is a high possibility that environmental factors could catapult changes at
levels than the genetic information and thus give huge impacts as well. DNA methylation and covalent histone modifications are two important parts which
monitor or control gene regulation could be interfered by environmental and diet factors.
Protein-restricted diet increases glucocorticoid receptor (GR) and PPARα expressionin the liver by inducing hypomethylation and decreases DNA methyltransferase-1 expression. However, by increasing folic acid content could prevent hypomethylation. DNA methyltransferase-1 expression in human umbilical cord is strongly associated with methylation of the GR promoter. The promoter regions of many genes consists several CpG dinucleotides at which caused changes in methylation.
 

Regulation of pregnane X receptor gene by protein arginine methyltransferase 1: new information for drug designs.

Posted by: Thanh Nga Pham
Student number: 41912124
Imagine when you take a drug, how can it be transformed in the body. Infact, there are many xenobiotics, which are foreign compounds, including drugs or poisons, in organism’s body. Understanding the regulation of xenobiotic metabolism, which is a process modifying xenobiotics, can support the development of drugs and therapies. Xenobiotic metabolism is demonstrated to be regulated by a ligand-dependent trascription factor called pregnane X receptor (PXR). The trascription of PXR depends on protein arginine methyltransferase 1 (PRMT1). PRMT1 acts by methylating histone and non-histone proteins and thus being known to play an significant role in regulating expression of many genes. This research aims to discover the role of PRMT1 in the regulation of PXR gene.
The result demonstrated that PRMT1 had close histone methyltransferase (HMT) associated with PXR, and therefore giving evidence that PRMT1 is needed for PXR transcription. Furthermore, this interaction is in a specific ligand-dependent manner. In this interaction, PRMT1 showed inhibiting influence on the PXR transcriptional activity. This inhibition may indicate that the expression of PXR-regulated gene needs the present of PRMT1. However, PXR also showed significant effect on regulation of PRMT1 subcellular localization. PRMT1 was localized in cytoplasm in absence of PXR, while it was localized in nucleus in present of PXR.
To sum up, this reseach proved reciprocal association between PXR and PRMT1, which may be important for the regulation of both PXR and PRMT1 gene expression.
For more information, follow the link to read the full article.

MR RAGHUVEERARAJ DURAIRAJ

Genetic and Genomewide Analysis of Simultaneous Mutations in Acetylated and Methylated Lysine Residues in Histone H3 in Saccharomyces cerevisiae


So far Histone H3 acetylated and methylated lysine residues may functionally interact through interdependent pathways to regulate gene expression, but mutant alleles of the H3 histone will also plays an important role in promoting growth phenotypes..........

Is it easy just to quit overdrinking? The interaction between alcohol and chromatin remodeling in brain cell

Excessive alcohol consuming is one of the major concerns of the health in worldwide. However, quit is not the only concern, the bigger issue is to deal with the withdraw symptom where anxiety is the main one. In this research, with the rat model, authors found that anxiety caused by acute alcohol were related to decreasing of histone deacetylase (HDAC) activity and increasing in acetylation of histones (H3 and H4), also the levels of CREB(cAMP-responsive element binding) binding protein (CBP), and neuropeptide Y (NPY) expression in the amygdaloid brain regions. On the other hand, by using trichostatin A, the HDAC inhibitor to block the HDAC reaction during the withdraw procedure, showing the significant decline of H3 and H4 acetylation and NPY expression in the amygdale, also effectively prevented the anxiety caused by alcohol-withdraw in rats. In this research, authors found the possible mechanism that responsible for anxiety for those during withdraw after chronic ethanol exposure. With the result of the research, it revealed the mechanism of the epigenetic regulation in brain in alcohol addicts and the potential therapeutic role of trichostatin A in treating the alcohol-withdraw symptom.

Student name: Yu-Hsuan Hsieh

Student No.: 41825037