Category Archives: Gene Silencing

It’s not over until the RNA sings…

Posted on March 6, 2012 by Nicole Kelesoglu

Epigenetic regulation is accomplished by a series of interdependent systems. It’s overall effect on gene expression is often compared to a musical composition. Today I’m thinking of opera in particular…since I’m proud to say that my uncle Robert Aldridge just won a Grammy for best contemporary classical composition. Bravo Uncle Bob! So you probably know the silly old saying, “It’s not over till the fat lady sings”, right? There are numerous well studied roles in the epigenetic opera….modifications of DNA, chromatin and histones, enzymes activities like DNA and protein methyltransferase, etc….but today let’s think of RNA expression as the grand finale. Once a gene has been physically exposed through modifications to chromatin and histone structural proteins, and expression takes place…those … Continue reading →

Posted in Bioinformatics, Cell Culture Models, Cellular Biology, Gene Regulation, Gene Silencing, Histone Modification Assay, Non-coding RNA, chIP, siRNA | Tagged , , , , | Leave a comment

Identical Twins are Not Identically Imprinted : Epigenome in Context of the Genome

Posted on October 28, 2011 by Nicole Kelesoglu

As is the case with their fingerprints, imprinted genes are NOT identical in identical twins. In fact, methylation levels vary notably, yet randomly, in localized imprinted regulatory regions, between MZ twins. Even cooler, a new epigenetics clue came out of demonstrating this imprinting variability. This month in PloS one, the collaborators from the Garvin Institute, the University of Nijmegen Medical Centre, the Queensland Institute of Medical Research and St. Vincent’s Clinical School, University of NSW, produced the paper Impact of the Genome on the Epigenome Is Manifested in DNA Methylation Patterns of Imprinted Regions in Monozygotic and Dizygotic Twins. by Marcel W. Coolen et al. Blood samples from 128 pairs of identical, and 128 pairs of fraternal teen aged twins, … Continue reading →

Posted in Autism, Bioinformatics, DNA Methylation, Developmental Biology, Divergent Transcription, Gene Regulation, Gene Silencing, Genomewide Methylation Profiling, In Utero, Mass Spec, Methylation Specific PCR, Next Gen Sequencing, Sodium Bisulfite Sequencing, Transcriptome microarray | Tagged , , , | Leave a comment

Epigenetics Aids AML Research

Posted on September 2, 2011 by Nicole Kelesoglu

According to NCI, there are well over 300 ongoing clinical trials for acute myeloid leukemia (AML). AML is an important disease model to our understanding of how epigenetics fits into the multidimensional cancer process.  Please find below a description of AML, and a few recent important studies providing traction on AML sub-type biomarkers and drug targets using epigenetic techniques. AML is a blood and marrow cancer. Myeloid stem cells abnormally propagate and differentiate into non-functional red blood cell, white blood cell, or platelets.  Clinical sub-typing is currently based on the degree of derivation from normal cells microscopically, and by cytogenic methods. Adult AML is diagnosed when 20% or greater leukemia cells appear in the bone marrow. Keep in mind, this … Continue reading →

Posted in Applications, siRNA | Tagged , , , | 2 Comments

No Promoter is an Island: Methylation Affects Transcription Even Without CpG Clusters

Posted on August 26, 2011 by Chris Womack

Last week I stumbled on an interesting finding–or so it seems to me. Even genes whose promoters aren’t near CpG islands can be regulated by DNA methylation. Previous research seemed to point to the idea that CpG islands–short DNA stretches containing lots of two-nucleotide cytosine-guanosine sequences–were necessary for controlling nearby transcriptional promoters. Methylating a CpG island turns a gene off–shutting down RNA transcription from that site–while demethylating the island turns a gene on. And methylating CpGs in a CpG-poor promoter seemed to have little or no effect. About half of promoter sequences don’t have nearby CpG islands, which seems a little strange, since many of these promoters control genes that’re important only for specific tissues. After all, methylation is one … Continue reading →

Posted in DNA Methylation, Gene Regulation, Gene Silencing, Sodium Bisulfite Sequencing | Tagged , , | Leave a comment

Pondering the Evolution of E. coli (0104:H4)

Posted on June 13, 2011 by Nicole Kelesoglu

The trace back investigation in europe appears to have determined the source of the outbreak of the hemorrhagic colitis and hemolytic uremic syndrome causing E.coli strain (0104:H4). Organic bean sprouts are the culprit and the farm field has been identified. This Reuters report makes an interesting point about organic farming.  Regardless, identifying the source is a critical step in stopping an outbreak. For long term planning, we need science that establishes how a pathogenic E. coli strain like this evolves.  That way, chinks in the armor can be identified. Epigenetics has a role to play in the evolution of bacterial virulence factors. It allows the bacteria to respond to various environments faster than by the process of genetic mutations alone. … Continue reading →

Posted in Evolutionary Epigenetics, Gene Silencing, Methylation, Microbial Epigenetics | Tagged | Leave a comment

Cellular Trash to Treasure – Exosomes

Posted on May 27, 2011 by Nicole Kelesoglu

Blood-Based Gene Expression Signatures in Non-Small Cell Lung Cancer.Clin Cancer Res. 2011 May 15 Thomas Zander, Andrea Hofmann, Andrea Staratschek-Jox, et al has been big in the international news recently. The authors are aiming to develop an RNA-stabilized blood test for asymptomatic lung cancer, using gene expression profiles, from what they believe to be immune effector blood cells – not cancer cells. The prognosis for lung cancer once you already have symptoms, is terrible. Their work is great news because this kind of non-invasive diagnostic test is desperately needed. However, there is another promising approach to transcriptome signature diagnostics to be aware of…Microvesicle shuttled RNA. Microvesicles, (MV), were once considered just cellular debris. We now know that blood, and many … Continue reading →

Posted in Applications, Biomarkers, Clinical Studies, Diagnostics, Flow Cytometry, Genetics, History & Trends, Next Gen Sequencing, Oncology, Pathology, Real-time PCR, Virology, microRNA, siRNA | Leave a comment

You Light Up My Methylation — Luminescence Detection for Epigenetics

Posted on May 20, 2011 by Chris Womack

Epigeneticists can only look on in envy as their peers measure ongoing protein-protein interactions and other arcana using luminescent signals and over-engineered cameras. The epigeneticists sigh and turn back to their radioactive methylated DNA, dejectedly removing another aliquot in an endless time-course study. But not for much longer. Researchers Ivan Hemeon and Vern Schramm at Yeshiva University’s Albert Einstein College of Medicine report this month in Analytical Chemistry that they’ve developed a Luciferase-based assay that will allow epigeneticists to measure gene silencing as it occurs–with emitted light. After a DNMT methylates a cytosine in DNA, the assay converts the leftover methyl donating molecule–S-adenosyl-L-homocysteine, or AdoHcy–to adenine using a nucleosidase. Another enzyme converts that to AMP, and yet another makes it … Continue reading →

Posted in DNA Methylation, Gene Silencing, Methyltransferases, New Lab Methods | Tagged , , | Leave a comment

Epigenetics, Eh! to Promote Canadian Collaboration

Posted on April 30, 2011 by Nicole Kelesoglu

Late registration is still available online for Epigenetics Eh!, the Canadian Conference on Epigenetics, which is taking place in London, Ontario from May 4 to May 7th, 2011. Part of the stated mission for this conference is to promote a Canadian Epigenetics Research Network (EPIGENETICS CANADA). The epigenetic research areas of the speakers for this conference include, but are not limited to the following. Diabetes Early detection of cancer Leukemia Pluripotency in ES cells Proteomics to study protein import into the nucleus Genomic CNV and epigenetic changes in Neurobehavioral disorders Chromatin factors in brain development Molecular mechanisms underlying cell fate specification, proliferation, and differentiation of neural stem cells Genomic imprinting X chromosome inactivation Dicer expression and/or microRNA function. ING family … Continue reading →

Posted in Applications, Bioinformatics, Biomarkers, Cellular Biology, Chromatin Structure, DNA Methylation, Developmental Biology, Divergent Transcription, Evolutionary Epigenetics, Gene Regulation, Gene Silencing, Genetics, Hematology, Histone Modifications, Leukemia, Neuroscience, Non-coding RNA, Plant Epigenetics, Reproductive Biology, Stem Cells, Translational Research, chIP, siRNA | 2 Comments