Last month, we hosted AEpiA’s sixth flagship conference, Epigenetics 2015, in beautiful Hobart, Tasmania.
What an exciting and inspiring three days! Thank you Hobart for welcoming us and well done to Adele Holloway, Jo Dickinson and all the organising committee for their hard work over the past many months. AEpiA was delighted with the attendance at all the sessions and AEpiA president Sue Clark was thrilled to hear all the lively epigenetics discussion that ensued.
On the Friday evening we were welcomed to Government house by Her Excellency Professor the Honourable Kate Warner, AM, Governor of Tasmania, for a memorable evening of music, canapes and socialising.
AEpiA congratulates Joshua Ho from Victor Chang Cardiac Research Institute, who was awarded the Illumina Early Career Research Award for his wonderful work on chromatin organisation.
Some of you have sent us photos and written highlights of the meeting – please scroll down to enjoy them all. Please email us if you would like to share any more stories or pictures.
Thanks to all attendees and we hope to see you all at Epigenetics 2017 in Queensland!
Ksenia Skvortsova (PhD student) from the Garvan Institute writes about her highlights:
Highly conserved epigenome remodelling during the vertebrate phylotypic period
Prof Ryan Lister (University of Western Australia) described a comprehensive vision on the role of epigenetic processes during early organism development in a very beautiful non-trivial model system.
Low dose DNA-demethylating agents target colorectal cancer-initiating cells by activation of MDA5/MAVS/IRF7 pathway
Daniel de Carvalho (University of Toronto) presented an impressive non-traditional view on the mechanism of DNA demethylating agents’ (5-aza) action on tumour cells.
Dr Ruth Pidsley (post-doc) from the Garvan Institute writes:
Intergenerational Risk for Spontaneous Preterm Birth: Insight from Epigenetic Studies
The second day was opened with a talk by Dr Alicia Smith from Emory University, USA. She gave us an overview of her recent study investigating the epigenetic contribution to spontaneous preterm birth in African American mothers.
Roll over Weismann: extracellular vesicles in the transgenerational transmission of environmental effects
Dr Jane Loke (post-doc) and A/Prof Jeff Craig (group leader) from Murdoch Childrens Research Institute write:
Comprehensive analysis of chromatin landscape
Joshua Ho (Victor Chang Cardiac Research Institute), winner of the ‘Early Career Research Award” at Epigenetics 2015, gave an elegant talk on understanding the epigenetic landscape.
He compared histone modification and other patterns of chromatin state across difference species. Bringing together a large number of datasets from the ENCODE and modENCODE consortia, and using a novel non-parametric machine learning method (hiHMM) developed by his team, Joshua concluded that patterns in promoters, gene bodies, and enhancers tend to be largely conserved across humans, flies and worms.
Notable differences across these three species were identified in repressive chromatin regions. These regions were noted as ‘repressive chromatin’ for their enrichment of H3K9me3. Details of this results can be read in this publication. Joshua even started an epigenome project in the filamentous fungus Aspergillus nidulans.
Epigenomics – from mapping to functional interpretation
Jörn Walter leads the German epigenome program called DEEP, which links various epigenomic mapping and functional analysis groups in Germany. DEEP is part of the International Human Epigenome Consortium (IHEC).
Jörn’s group uses a method, NOMe-seq, that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. In his talk Jörn compared methods of genome-wide chromatin accessibility; he saw many similarities in the results, but some method-specific differences. He also found massive regional loss of DNA methylation accompanying differentiation, that topology-associated chromatin domains (TADs) can change over time and that, counterintuitively, loss of methylation was associated with an increase in heterochromatic state. He concluded that local differences in the topology of chromatin are like ‘codes’ in each tissue. Focusing on cells from the brain, he showed that neurons and non-neuronal cells (glia) showed distinct methylomes and that non-CpG DNA methylation was greatly enhanced in neurons but not glia. He also found that different brain cells ‘age’ differently for DNA methylation. Finally, Prof Walter showed that cell heterogeneity made a huge difference to data interpretation, with proportions of neutrophils in being the largest confounder in whole blood samples.
Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana
Donna Bond (University of Cambridge, United Kingdom) gave an overview of her research into the role of epigenetic transitions in RNA-mediated de novo silencing in Arabidopsis thaliana.
Regulation of intron retention by DNA methylation
Justin Wong (University of Sydney, Australia) presented his team’s progress into determining the mechanisms regulating intron retention (IR) that is frequently observed in normal cells.
Intergenerational Risk for Spontaneous Preterm Birth: Insight from Epigenetic Studies
Alicia Smith was an invited speaker from Emory University, USA. She is an Assistant Professor in the department of Psychiatry and Behavioral Science within the School of Medicine. Alicia spoke about her research on the relationship between DNA methylation and preterm birth. Preterm birth was defined as a gestational period less than 37 weeks and is already known to be associated with increased risk for chronic disease.
Qian Du (PhD student) from the Garvan discusses Pilar Blancafort’s talk:
Combinatorial epigenetic approaches for genome engineering: form zinc fingers to novel epigenetic editing tools
Re-engineering the genome via gene therapy to treat disease/cancer has been difficult and dangerous thus far with limited success. But what if we can precisely alter genome function without altering the DNA?
Reprogramming the epigenome in aging and cancer
Professor Jean-Pierre Issa (Temple University School of Medicine, Philadelphia) gave an inspiring talk on the process of epigenetic drift (ED), where the methylation profile of an individual changes over time, and in particular affects the stability of the gene expression profile of the tissue in question.
Intron retention is an epigenetically regulated mechanism of gene expression control
Dr Phuc Loi Luu (post-doc) from the Garvan Institute discusses two of his highlights:
Multiplex bisufite-PCR resequencing of prognostic and predictive biomarkers in breast cancer using clinical FFPE DNA
Breast cancer subtypes as defined by methylome-wide analysis
Eric Joo spoke about exciting work ongoing at Melissa Southey’s lab at the University of Melbourne. They and their team are investigating DNA methylation patterns in subtypes of breast cancer.
This weekend I participated in HealthHack, a national product-building event that ran in Sydney, Perth, Melbourne and Brisbane from Friday evening through to Sunday.
On Friday night I pitched my ‘problem’ to a crowd of developers, user interface designers and software engineers in an attempt to build interest and a team that could work with me over the weekend.
With a focus on communicating science visually and engaging a broad audience in genomics and epigenomics research, I defined my problem as: create a prototype 3D game environment depicting the inside of the nucleus of a cell that can be adapted for virtual reality using the Oculus Rift.
What followed was an intense, team building and successful weekend, which ultimately culminated in us winning equal first prize for our solutions.
There were a few defining moments over the weekend that paved the way for a successful prototype. The first was deciding on two approaches and game engines in order to both to maximize the team’s skill sets and also to reach more audiences. We chose Unity for its rendering and animation capabilities, and Minecraft for its popularity and community aspect strengths. Once we worked out how to efficiently export an appropriate molecular model from Maya (the 3D environment I usually work with) to each of the game engines, the team worked on getting the controllers and functionality working smoothly.
By Sunday lunch time we had achieved three main things: 1) DNA and protein models imported into the two game engines, 2) Each of the games driven by appropriate controllers and 3) VR enabled. This was an exciting moment and the rest of Sunday afternoon was spent refining the games and preparing our final presentation.
HealthHack demonstrates how engaged development teams can work together to achieve great outcomes. In 48 hours we created two different prototypes that can now act as the catalyst for ongoing projects. I would definitely recommend researchers get involved in HealthHack 2016.
Photos courtesy of Kate Patterson, David Ma and ThoughtWorks
In March 2015, the BROAD Institute hosted the 6th VIZBI conference to a large number of attendees. Contrasting to other scientific conferences based on submissions, VIZBI’s speakers are invited and are hand picked based on their relevant research contribution and communication skills. This ensures a fascinating three days of presentations bringing experts in visualization together with the leaders in biology and bioinformatics tools, where the talks happen to be ordered by the physical scale of the topic: starting small with genomics and epigenetics, then transcriptomics, proteins, systems, then finally ending on the last day with tissues, metagenomics and populations.
John Stasko (Georgia Institute of Tech.) gave a great keynote on data visualisation principles, giving examples of how visualizing even existing public data can have a big impact (in this case, it was a student project that visualized the salaries of staff at his institute). Susan Clark (Garvan Institute of Medical Research) discussed the current challenges in understanding epigenomic data.
Jer Thorp’s (New York Times) keynote was a highlight, showcasing numerous projects he had worked on from diverse fields. He demonstrated that the current conventional assumptions on how to visualise a particular dataset, e.g. multidimensional features of shark genetics, may not be the most appropriate. Importantly, he showed examples of the value of interaction to reduce complexity for the user.
Dan Evanko (Nature Publishing Group), who is a familiar face at VIZBI, gave the final keynote about visualisation for scientific publication. Overall, VIZBI 2015 was another success with engaging speakers and relevant tutorials, while also giving the opportunity for attendees to present at the multiple lightning talks and poster sessions.