Epigenetics 2012


With all of the cutting edge epigenetics research coming out of Australian labs over the last few years, the Australian EpiAlliance Epigenetics 2012 conference promised to be an really exciting one. We were also extremely pleased to have the Peter MacCallum Cancer Centre’s Alexander Dobrovic agree to cover the whole thing and share his experience with EpiGenie readers. Take a look at what went on:

Australian EpiAlliance Epigenetics 2012 Conference Overview

Australia holds a major conference covering most areas of epigenetics every two years. This time it was the turn of Adelaide. Adelaide is the capital of South Australia and enjoys a Mediterranean climate i.e. hot in Summer and cold in Winter. The timing of the conference in early May gave us a warm and sunny “Indian Summer” prior to the onset of Southern hemisphere winter. The glorious radiant weather outside the conference venue was a real lure but the very strong program kept the delegates indoors.

The conference was convened by Hamish Scott, and featured a line-up of international and Australian speakers that although generally not considered the usual “big names”, maintained an impressive standard of excellence throughout the conference. There was a stronger focus this time on human and mammalian epigenetics although there were several excellent talks presented on epigenetic studies in plant model organisms like Arabidopsis.

Epigenetics Tackles All Disease

It would be outside the scope of this short report to briefly, let alone comprehensively, cover every single talk, many of which were given by early career researchers and often reached the standard, if not the virtuosity, of their more senior colleagues. This bodes well for the future of epigenetic research in Australia. One theme of the conference might have been “Epigenetics takes on all disease.” Thus, while epigenetic studies into cancer were well represented, there were presentations on diabetes (Sam El-Osta, Baker Medical Research Institute), schizophrenia (Ruth Pidsley, King’s College London), and Friedreich’s ataxia (Marguerite Evans-Galea, University of Melbourne).

Genome Wide Mapping of DNAse Hypersensitive Sites

John Stamatoyannopoulos, University of Washington
The Conference reached its peak early with a virtuoso presentation by Dr. Stamatoyannopoulos who used the power of next generation sequencing to comprehensively map DNAse hypersensitive sites genome wide in multiple cell types. This presentation kept me on the edge of my seat. Keep watching Nature for this work to appear in press. It will change the way that you think about the genome and help you understand the apparently weird hits in genome wide association studies.

Non-Coding RNA, Epigenetic Modifiers, and Cancer Biomarkers

John Mattick, Garvan Institute of Medical Research
Emma Whitelaw, Queensland Institute of Medical Research
Peter Molloy, CSIRO
There were excellent presentations by some of the internationally known Australian stars of epigenetics. John Mattick continued making us revise our concepts of how the genome is organised by emphasising the critical role of non-coding RNA. Emma Whitelaw reviewed her lab’s excellent work on identifying epigenetic modifiers. Several more innovative methodologies as well as new colorectal cancer biomarkers came from Peter Molloy’s lab.

Nucleosome Occuapancy at Enhancers and Relationship of DNA and H3K27 Methylation

Susan Clark, Garvan Institute of Medical Research
Sue Clark unfortunately could not attend, but Philippa Taberlay and Clare Stirzaker represented her lab. Philippa presented her recently published work with Peter Jones (University of Southern California) showing that the repressed and silenced states of MYOD1 are distinguished by H2A.Z enrichment and altered nucleosome occupancy at the enhancer. Clare used methylation analysis of DNA from methylated H3K27 precipitated chromatin to show the complex relationship between DNA and H3K27 methylation

Epigenetic Differences in Twins

Jeff Craig, Murdoch Childrens Research Institute
Dr. Craig presented new data on the perennially interesting topic of why there are differences between genetically identical twins. Apparently, this is due to a combination of stochastic epigenetic effects and different intrauterine environments, which in the wrong combination could cause low birth weight and pre-programming for diabetes and heart disease. This has just appeared in a Genome Research, July 2012 article with co-senior author Richard Saffery.

SWAN Analysis of Infinium Chip Data

Jovana Maksimovic, Murdoch Childrens Research Institute
One presentation that stood out for me was by Jovana Maksimovic from Alicia Oshlack’s Bioinformatics group from the MCRI in Melbourne. We learned that the widely used Illumina Infinium HumanMethylation450 BeadChip uses two separate probe designs to assay the methylation at 485,577 CpG sites. They developed a new analysis method, Subset-quantile Within Array Normalization (SWAN), to improve the results from this platform by reducing technical variation within and between arrays. This has just been published in Genome Biology, June 2012.

DNA Methylation After Fertilization

Chris O’Neill, University of Sydney
Dr O’Neill’s presentation “Persistence of Cytosine Methylation of DNA following Fertilization in the Mouse” was a real game changer. It seems that the apparent global loss of methylation following fertilization in the mouse zygote, which I have seen in dozens of seminars, is an artifact. Read more about this in PLoS One, January 2012.

Epigenetic Researchers Making a Mark

Other rising stars such as Catherine Suter (Victor Chang Cardiac Research Institute), Jose Polo (Monash University) and Marnie Blewitt (Walter and Eliza Hall Institute) also presented. Ryan Lister, who has just been appointed as professor of computational biology at the University of Western Australia, ended the meeting with a keynote presentation based on his studies of methylomes.

Other outstanding presentations came from colleagues in Asian countries. Qiani Yu from Singapore talked on a topic, close to my heart “Cancer Epignetics and Therapeutic targeting”. Waychamp Mah, also from Singapore, spoke on methylation profiling of hepatocellular carcinoma. Yoshinori Watanabe (Japan) highlighted the connection between epigenetics and chromosome stability. Jason Lee (Korea) talked on  the epigenetic regulation of hypoxia genes in breast cancer. Guoliang Xu (China) discussed the role of TET3 in the early embryo and Xiafeng Cao (China) talked on the dynamic regulation of histone methylation in Arabidopsis

Prizes for the best poster, sponsored by Adelaide University and Life Technologies, went to Rhiannon Walters (Queensland Institute of Medical Research) and Karen Humphreys (Flinders Centre for Innovation in Cancer). The title of Rhiannon’s talk was “Peripheral Blood DNA Methylation of Repetitive DNA Elements is Associated with Early-‐Onset Colorectal Cancer but not with a Family History of Colorectal Cancer “ and Karen’s talk was “Histone deacetylase inhibition in colorectal cancer cells reveals competing roles for members of the oncogenic miR-17-92 cluster “ Prizes for the best Oral Presentation, sponsored by the South Australian Health and Medical Research Institute, went to David Martino (Murdoch Childrens Research Institute) and Cheryl Li (Victor Chang Cardiac Research Institute) for their respective talks “Genome-‐scale profiling reveals a subset of genes regulated by DNA methylation that program somatic T-‐cell phenotypes in humans” and “Microparticle-‐derived small RNAs and transcription state in recipient cells.”

Those who want a more detailed look at the program and a complete list of presenters and titles, the website is still active: http://epi12.asnevents.com.au/program-5/. We eagerly await the next meeting to be held in Sydney in 2014.

**EpiGenie would like to extend a huge “Thank You” to Alexander Dobrovic who is a Principal Research Fellow and the Head of Molecular Pathology R&D at Peter MacCallum Cancer Centre.