In preparation of a proposal to the International Human Epigenome Consortium, the delegates from Korea, Japan, China and Singapore had agreed to have an annual meeting for close regional interactions in Asia. Following the preceding meetings held in Seoul, Tokyo and Shanghai, the 4th Asian Epigenomics Meeting, organized by Huck Hui Ng and Edwin Cheung of the Genome Institute of Singapore (GIS; Singapore), took place on August 24–25 under the title of ‘Epigenetics in Development and Diseases‘. A total of 28 renowned speakers were invited from Asia, Europe and the USA, with more than 300 delegates participating.
A wide range of epigenetic mechanisms was addressed, including histone modifications, nucleosome remodeling, DNA methylation, chromatin interactions of transcription factors, long-range chromosomal interactions and genome–nuclear lamina interactions. Technical advances in the combination of chromatin immunoprecipitation and sequencing (ChIP-Seq); the combination of chromatin immunoprecipitation and paired-end tag sequencing (ChIP-PET); the combination of chromatin interaction analysis and paired-end tag sequencing (ChIA-PET) and chromatin conformation capture (3C); chromatin conformation capture-on-chip (4C); DNA adenine methyltransferase identification (DamID); and single-cell analysis methods seem to have helped answer novel biological questions pertaining to these mechanisms.
Edison Liu and Edwin Cheung (GIS)combined various current technologies such as ChIP-Seq, ChIP-PET, ChIA-PET and 3C to map DNA-binding sites of estrogen receptors (ERs) alongside histone modification marks and long-range chromatin interactions. In combination with a motif-finding algorithm, they suggest that histone modification plays a greater role in binding sites with less optimal motifs. In particular, histone H3 monomethylation of lysin 4 (H3K4me1) is suggested to play a role in condition-specific binding, as revealed in a comparison of binding sites between MCF-7 and T47D cell lines. In addition, ER-binding sites are preferentially located far away from the transcription start site, suggesting extensive regulation by long-range chromatin interactions, hundreds of which have been identified in breast cancer cells.
Marian Walhout (University of Massachusetts Medical School, MA, USA) used Caenorhabditis elegans to map the dynamic changes of transcription factor-binding profiles under different physiological conditions. Taken together, these studies illustrate that transcription-factor binding is a complex process involving the interplay of DNA recognition, local chromatin configurations and long-range chromatin interactions.
Another technological expansion, chromatin conformation capture–carbon copy (5C), combines 3C with deep sequencing for high-throughput mapping of interactions between genomic elements. Job Dekker (University of Massachusetts Medical School), who originally developed the 3C technology, presented a comprehensive interaction map for 30 Mb of the human genome. Analysis of the interaction data identified large domains that preferentially interacted with each other. Actively transcribed genes engaged more frequently with distant elements, probably reflecting transcription factor-mediated chromatin interactions.
The developer of the DamID technology, Bas van Steensel (Netherlands Cancer Institute, Amsterdam, The Netherlands), used this approach to construct a full-genome map of the interactions of chromosomes with nuclear lamina components. Genes contained in lamina-associated domains (LADs) show a low expression level. Based on the proposed role of the nuclear lamina in channeling of signals to the genome, reshaping of LADs during development may dictate genomic responses to developmental signals in a cell-type-specific manner, as revealed by comparative LAD patterns in different stages of development. Chia-Lin Wei (GIS) associated these patterns with CCCTC-binding factor (CTCF) demarcation and p300 binding.
In another technology-driven novel study, Paul Robson (GIS) set out to examine blastocyst formation in the context of single-cell gene expression by utilizing nanofluidic devices (fluidigm dynamic array). The molecular signatures of three distinct cell types of the blastocyst were defined by means of the expression of 48 prescreened genes in single cells of the 32-celled mouse blastocyst. Whereas this approach seems to provide insights into the network and hierarchical expression of genes regulating lineage fate, commitment and segregation during early embryonic development, the role of epigenetics remains unknown.
The work by Antoine Peters and colleagues (Friedrich Miescher Institute, Basel, Switzerland) shows that promoter regions in human and mouse sperm are marked by H3K4me2 and/or H3K27me3 in a gene-specific manner. Their extensive bioinformatic analyses suggest that these modifications may indeed serve conserved roles in transgenerational regulation of embryonic gene expression in the subsequent generation.
Cell-fate determination by epigenetic mechanisms has been widely studied for single-celled organisms. For example, in our own presentation, whole-genome single-cell expression data for yeast were related to nucleosome positioning patterns in the promoter. Exceptional positioning of a single nucleosome at the typical nucleosome-free region increases cell–cell variation or stochastic noise in gene expression. These genes also show high responsiveness to environmental stimuli as seen in stress response or cell differentiation. Investigation into the role of nucleosome positioning in cell-fate determination in yeast and in mammalian stem cells will be an exciting extension of these studies.
Another finding from our study was that H3K4me1 and H3K4me2 were enriched on the specifically responding promoters, reminiscent of the role of H3K4me1 in cell-line-specific ER binding and H3K4me2 in sperm development. Sam El-Osta (Baker IDI Institute, Victoria, Australia) showed that transient hyperglycemia promotes p65 transcription via the recruitment of the histone methyltransferase Set7. Intriguingly, only H3K4me1, and not H3K4me3, showed a significant association. These studies together hint at a possible role for H3K4me1 and H3K4me2 in marking genes poised for gene activation in response to specific conditions.
This illustrates that there are numerous different histone modifications and, except for a couple of popular ones, many of them have been off everybody‘s radar and are awaiting our attention. For another example, Ernesto Guccione (Institute of Molecular and Cell Biology, Singapore)studied the dimethylation of arginine 2 of histone 3 (H3R2me2) by means of peptide arrays based on a library of protein domains.
As another form of biological expansion, the interactions of DNA methylation with other epigenetic mechanisms have just started to be revealed. Guo-Liang Xu (Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China) studies the interaction of DNA methyltransferases with histone tails by means of knockout experiments, and Peter Jones (University of Southern California, CA, USA) shows DNA methylation-induced nucleosome remodeling in the context of cancer epigenetic therapy.
Further new discoveries are in store for us as researchers, including Alex Meissner (Broad Institute, MA, USA), Bing Ren (University of California, CA, USA) and Jingde Zhu (Shanghai Cancer Institute, Shnaghai, China) endeavoring to improve epigenome mapping technologies and collate different epigenomes, such as various histone modifications, DNA methylation and noncoding RNAs.
In the midst of these technological and biological expansions, many epigeneticists have shown much progress by focusing their efforts on well-known epigenetic mechanisms. Rho Hyun Seong (Seoul National University, Seoul, Korea) demonstrated the requirement of a nucleosome remodeling complex in the development of a pre B-cell population using extensive cell-sorting analysis of hematopoietic cells from a Srg3 mutant mouse, and Jae-Bum Kim (Seoul National University) presented the coordinated histone modification of promoters specifically required for the alternative differentiation pathways leading to osteoblast and osteoclast generation. Based on the analysis of brain tumor-propagating cell differentiation, Yutaka Kondo (Aichi Cancer Center, Aichi, Japan) proposed epigenetic plasticity regulated by Polycomb-mediated H3K27 trimethylation as a key mechanism of adaptation of tumors to their environment, supporting the effort of epigenetic therapy targeting EZH2 histone methyltransferase. Hiroyuki Aburatani (University of Tokyo, Tokyo, Japan) presented aberrant methylation patterns found in liver cancer using Illumina epigenotyping bead arrays (CA, USA), and Kazu Ushijima (National Cancer Center Research Institute, Tokyo, Japan) demonstrated a tight link between Helicobacter pylori infection and a methylation pattern in gastric mucosae, and its underlying mechanisms.
The application of epigenetic regulation for therapeutic purpose is another area explored with high expectation. Jonathan Sedgwick (Lilly Singapore, Singapore) reviewed the potential of epigenetic drugs from the perspective of a conventional drug development process, and suggested possible solutions for the development of new drugs based on epigenetic mechanisms. Qiang Yu (GIS) and Ricky Johnstone (Peter MacCallum Cancer Center, Victoria, Australia) presented an effective approach to inhibit cancer growth using a drug combination approach that targets EZH2 and histone deacetylase, respectively. Erwei Song (Sun-Yat-Sen University, Guangdong, China) managed to effectively suppress the stemness of breast tumor-initiating cells by introducing let-7 microRNA, nicely demonstrating the potential value of small RNA in cancer therapy.
In parallel with these ongoing efforts by conventional molecular biology techniques, pioneering studies assisted by rapid technological developments are pushing the boundaries by exploring uncharted areas of the epigenetics field. In summary, the audience of the 4th Asian Epigenomics Meeting has witnessed the rapid expansion of epigenetics research, and been shown that this field still has a lot of room for technological and biological expansion. We anticipate also seeing an organizational expansion, thanks to the participation of more Asian countries at the next meeting, which is scheduled for next year in Korea. There are great expectations for the growing Asian community of epigenetics researchers.
Acknowledgements
We thank all the speakers for their contribution to the meeting and comments on our meeting report.
Financial & competing interests disclosure
This work was supported by the Korea Foundation for International Cooperation of Science and Technology (KICOS) through a grant provided by the Korean Ministry of Education, Science and Technology (MEST) (K20704000006–08A0500–00610). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.
No writing assistance was utilized in the production of this manuscript.