Shanghai (Epigenomics) Surprise

With genetics and genomics being complicated enough, epigenomics adds even more layers of control and regulation of gene expression, and high-throughput global analyses of epigenetic changes further add to the reams of biological information many people are already referring to as the "data-deluge".  As the field is a key part of our “big-data” scope, the GigaScience team was on the road last week for the Shanghai International Conference of Epigenetics in Development and Disease (SICEDD). As the third time this meeting has been held in Shanghai, this year it also merged with 7th Asian Epigenome Alliance meeting, giving it a very interesting flavor of the field over the Asian region and beyond. On top of speakers from the Asia-Pacific, with the Cold Spring Harbor Asia Epigenetics, Chromatin and Transcription meeting held just after in nearby Suzhou, a very international and broad audience and group of speakers was assembled for the 46 talks and 6 themed sessions.

BMC SICEDD boothOur sister BioMed Central journal Genome Medicine organized a particularly strong workshop on the epigenetics/epigenomics of disease, with an initial session on the epigenetics of cancer expertly co-chaired by Genome Medicine’s Becky Furlong, followed by a session on other diseases such as immune disorders, schizophrenia and cardiovascular disease. With the conference put together by BGI-collaborator Jingde Zhu (see here for his recent nice write-up of our talk at BGI’s ICG conference), this coupled with the BMC involvement were further reasons for us to attend, and BMC even had a booth to help promote us and their other journals.

As large-scale "big-data" producing projects are our focus, there was plenty on display, with a number of speakers being involved in the International Human Epigenome Consortium to produce reference maps of human epigenomes for key cellular states relevant to health and diseases. Since the NIH Roadmap Epigenomics Program was announced in 2008, many other global funders and centers have joined and internationalized the effort. Bing Ren plugged the NIH program and resources such as the UCSC epigenome browser, and Henk Stunnenberg flew the flag for European IHEC efforts and the Blueprint project focusing on hematopoetic epigenomes. Large collaborative projects such as IHEC require very standardised operating procedures, data-pipelines and techniques, and steering committee member Susan Clark presented some of her contributions. On top of the more established MeDIP-Seq data presented by many of the speakers, Susan presented new data using a novel bisulphite-treated chromatin immunoprecipitated DNA sequencing technique (BisChiP-seq), and Henk presenting on his related sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) technique. Despite the similarities in application and name, both techniques have just been published back-to-back in Genome Research.

On top of DNA-methylation, there were many talks on other epigenetic changes, with Bin-Tean Teh covering chromatin remodeling in cancer, Craig Peterson presenting on chromatin dynamics in genome integrity, and many talks covering histone modification. Probably the most surprising area covered was trans-generational responses and epigenetic inheritance of complex behaviors, with fascinating, if unexplained phenomena seeming to pass in a Lamarkian manner.  Marcus Pembrey presented fascinating population based data coming from the ALSPAC study, showing that fathers taking up smoking before the age of 11 seem to have effected the BMI of their subsequent children. Unable to explain the mechanisms behind this seemingly epigenetic inheritance, Marcus appealed to experimentalists in the audience to try to explain the basis for these findings. Attempting to tackle this issue using animal models, Isabelle Mansuy presented work on depressive phenotypes passed on transgenerationally due to maternal stress in mice, and has MeDIP data that is currently being analyzed to try to see if alterations DNA-methylation could be responsible. Moshe Szyf presented related studies looking if early life experience alters adult DNA methylation in animal and humans brains, and took a more network modelling approach.

You can follow coverage of the meeting on the @gigascience twitter feed, and (the slightly noisy) #SICEDD hashtag. As Epigenomics is a key area in our scope, we currently have some example epigenomic data is hosted in our GigaDB database, and are already reviewing and handling related papers that will hopefully come out closely timed with our upcoming launch issue. If you have related work on epigenomics (or other areas covered by our broad big-data scope) you are interested in submitting to GigaScience, please contact us at editorial@gigasciencejournal.com or use our online submission system.

References

1. Statham AL, Robinson MD, Song JZ, Coolen MW, Stirzaker C, Clark SJ. Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res. 2012 Mar 30.

2. Brinkman AB, Gu H, Bartels SJ, Zhang Y, Matarese F, Simmer F, Marks H, Bock C, Gnirke A, Meissner A, Stunnenberg HG. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 2012 Mar 30.

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