Abcam’s Epigenetics and Stem Cells Conference was held in Copenhagen, Denmark. EpiGenie reader Ahmad Khalil made the journey across the pond to take in the event, and report back to us on all of the exciting epigenetic happenings that went on. Read on to see how his trip went.
After a 9 hour trans-atlantic fight, we finally landed in Copenhagen, Denmark. As it turns out Copenhagen may have been the ideal location for this meeting as a neutral ground after several neighboring European countries battled it out for the world-cup. In fact, just outside of the BRIC (Biotechnology and Research Innovation Center) building where the meeting took place one could see the Danish youth playing soccer, perhaps practicing for the next world-cup. The meeting was, as expected, action packed with hot topics and here are the highlights:
The Warburg Theory and Epigenetic Effects of Glucose Levels
Mina Bissell, Lawrence Berkeley National Laboratory, USA
Dr Bissell came back to visit the Warburg theory which was proposed several decades ago but at the time was given little attention. This theory states that cancerous cells are more glycolytic than normal cells. To that end Dr Bissell drew on her years of scientific experience to test this hypothesis and found that transformed cells have a higher rate of glycolysis than normal cells, they found out that this is due to the fact that transformed cells are better at glucose uptake than normal cells (so maybe we all should be careful next time we order our favorite dessert). To get to the bottom of this the Bissell team used the mammary gland as a system to study how the environment can affect our cellular function. One of the striking discoveries was that when milk-producing mammary glands were grown in culture, they lost their milk-producing ability. Using several approaches they found that Laminin-1 function was disrupted in the cells grown in culture and this was sufficient to affect their function. Using this system they also discovered that extracellular glucose levels can affect signaling pathways within cells which ultimately affect gene expression through epigenetic alterations. These results emphasize the importance of the environment in the control of our Epigenome.
EMSY Regulation of microRNAs
Tony Kousarides, University of Cambridge
Tony and his team are no strangers at epigenetic conferences and they once again had some breakthroughs to share. Over a decade ago the K-team found through a two-hybrid screen a strong interacting protein with BRCA2 which they call EMSY. EMSY has a repressive domain that interacts with HP1 and more importantly this gene is amplified breast and ovarian cancer. EMSY amplification is strongly associated with a negative outcome in breast cancer. One of their hypotheses (based on published work by Robert Weinberg, MIT) is that EMSY maybe regulating microRNAs. Through siRNA knockdowns and over-expression of EMSY they indeed found that EMSY regulates miR-31 by directly binding to the promoter of miR-31. To regulate miR-31, EMSY interacts with the histone demethylase KDM5B to remove H3K4me from miR-31 promoter and therefore repressing the expression of this critical miRNA gene.
Tet Proteins and DNA Demethylation
Kristian Helin, BRIC- University of Copenhagen
Kristian is another familiar face at the meeting and also one of the organizers of this event. He and his team became recently interested in DNA demethylation. Unlike histone demethylation, we still have yet to uncover the enzymes that are responsible for this process. Several proteins known as Tet1, Tet2, and Tet3 have recently been implicated in DNA demethylation. These enzymes convert 5-methyl-cytosine to 5-Hydroxymethyl cytosine. Interestingly, Tet1 is known to form a fusion protein with MLL in acute myeloid leukemia. Kristian and his team found through ChIP-Seq that Tet-1 binds to 8,037 gene promoters in ES cells and the majority of these target genes are enriched with H3K4me and many of these target genes are involved in development, proliferation and gene expression. They also identified Sin3A as a novel interacting protein with Tet-1. Further work by KH and his team should provide more insights on this important protein.
AML1-ETO Binding in Acute Myeloid Lymphoma (AML)
Henk Stunnenberg, Nijmegen Centre for Molecular Life Sciences, Netherlands
Stunnenberg and his s team have been studying acute myeloid leukemia (AML). In 15% of AML cases there is an AML1-ETO fusion. To figure out how this translocation plays a role in AML, they used several antibodies to the AML1-ETO fusion protein and carried out ChIP-Seq to pinpoint the localization of this fusion protein to the genome. They found a 1,000 AML-ETO binding sites which also highly overlap with Erg/Fl1 binding sites. Importantly, Erg is thought to make chromatin more accessible to AML1-ETO. Further work should shed more light on how this fusion protein is involved in AML.
Transcription Factor Binding in ES Cells
Huck Hui Ng, Genome Institute of Singapore
Dr Ng and his lab are interested on how ES cells maintain their identity. To that end they used ChIP –Seq to map 13 transcription factors binding sites to chromatin in these cells. Of course these included proteins with well known function in ES cells including Oct4, Nanog, Sox2 as well as Smad1, Stat3, Zfx, n-Myc, c-Myc. They were able to obtain high resolution mapping of these proteins which allowed them to identify octamer motifs. They were also able to identify ES cell specific “Enhancesomes” which they define as regions densely bound by multiple transcription factors. Then they used this wealth of knowledge to compare human and mouse ES binding sites of these transcription factors. Surprisingly, they found that Oct-4 and Nanog binding sites, for example, only share 5% conservation between human and mouse. They attribute this low conservation of binding sites to the fact that many of Oct4 and Nanog binding sites are located within repeat regions. However, among all of his data, I found his most intriguing finding is the identification of Nr5a2 as a reprogramming factor that replaces Oct4 to reprogram mouse embryonic fibroblasts to iPS cells. Stay tuned to more breakthroughs from this team on the understanding of pluripotency and reprogramming.
Comparing ES and iPS Cells
Konrad Hochedlinger, Massachusetts General Hospital
Dr Hochedlinger discussed the ongoing debate in the literature to whether ES and iPS cells are similar or different from each other. He presented evidence that iPS can show differences based on their cell of origin. Furthermore, iPS cells seem to retain transcriptional memory of their cell of origin. They also found that longer passaging of iPS cells results in similar transcriptional programs (this is of course counterintuitive because passaging of other cell types in culture is known to produce abnormal changes in their genomes and epigenomes) but iPS maybe the exception to the rule. Stay tuned to find other surprises that may come from studying iPS cells.
Large Non-coding RNA Regulation of Chromatin-modifying Complexes
Ahmad Khalil, Harvard Medical School
One of the main interests of our lab is how the human body which consists of more than 10 trillion cells with identical genomes can have completely different functions. Of course one of the major contributors to these distinct functions is epigenetic regulation by chromatin-modifying complexes. However, a major deficiency in our understanding is how these complexes are targeted to the genome. Work from our lab shows that a significant number of large non-coding RNAs interact with chromatin-modifying complexes in both human and mouse cells. Furhermore, siRNA knockdown of large non-coding RNAs results in alterations in gene expression similar to those observed when we knockdown chromatin-modifying complexes suggesting that they function in the same pathway. Alterations in non-coding RNAs interactions with chromatin-modifying complexes may represent novel paradigms in human disease such as cancer. Ongoing work should shed more light on these interactions and their role in establishing cell identity.
**EpiGenie would like to thank Dr. Ahmad Khalil from Harvard Medical School for providing us with this conference coverage.