Chia-Pet Workshop:
Methods for chromatin interaction analysis

4th – 8th April 2011
Genome, Biopolis, Singapore


Welcome address by Workshop Leader

Welcome to the Genome Institute of Singapore. The ChIA-PET workshop will be held from 4th to 8th April 2011. While many parts of the world are still very cold, Singapore welcomes you with its warm weather and sunny skies. On this trip, you will need to prepare some tropical wear such as t-shirts, bermuda shorts and sandals. What you will also need to prepare for is five full days of intensive work, in both wet lab and dry lab. You are encouraged to bring with you your ChIP samples for trial as well as your lap tops for data analysis.

Dr Yijun RUAN
Senior Group Leader
Genome Technology & Biology
Genome Institute of Singapore


Introduction to the technology and the workshop

Genomes are organized into high-order architectures for functions. However little is known at molecular levels how chromosomes are organized and what types of structural platforms are implemented for genome functions. The ChIA-PET method is developed to address these questions. In this approach, long-range chromatin interactions are captured by formaldehyde cross-linking and the fragmented DNA-protein complexes are enriched by chromatin immunoprecipitation (ChIP). Tethered DNA fragments in each of the chromatin complexes are joined to each other via DNA linkers through proximity ligation. Paired-End diTags are extracted from the ligation products, and are analyzed by massive parallel high-throughput sequencing. The ChIA-PET tag reads are then mapped to reference genome sequences to reveal contacting information between remote DNA elements presumably brought together in close spatial proximity by target protein factors.

Since the publication of the ChIA-PET method (Fullwood et al. 2009), we have received overwhelming requests from various scientific organisations to learn the method. In order to respond to this huge volume of requests, we have decided to organize a hands-on workshop.

This workshop will be a five-day intensive training course. During these five days, we will cover the most critical experimental aspects in ChIP sample preparation and ChIA-PET library construction. We will also touch base on the unique features of sequencing the ChIA-PET libraries, and introduce the basic concepts for computational analysis of ChIA-PET data.

For the training to be most effective, our plan is to host a small class of about 20 - 25 participants, from 4th to 8th April 2011, in Singapore.


Dr RUAN Yijun
Ms Winnie Serah LIM


Ms Prudence YEO
Ms CHAN Siok Bin

About the Organizing Institutes

The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to improve public health and public prosperity. Established in 2001 as a centre for genomic discovery, the GIS will pursue the integration of technology, genetics and biology towards the goal of individualized medicine. The key research areas at the GIS include Systems Biology, Stem Cell & Developmental Biology, Cancer Biology & Pharmacology, Human Genetics, Infectious Diseases, Genomic Technologies, and Computational & Mathematical Biology. The genomics infrastructure at the GIS is utilized to train new scientific talent, to function as a bridge for academic and industrial research, and to explore scientific questions of high impact.


A*STAR is the lead agency for fostering world-class scientific research and talent for a vibrant knowledge-based and innovation-driven Singapore. A*STAR oversees 14 biomedical sciences, and physical sciences and engineering research institutes, and nine consortia & centres, which are located in Biopolis and Fusionopolis, as well as their immediate vicinity. A*STAR supports Singapore's key economic clusters by providing intellectual, human and industrial capital to its partners in industry. It also supports extramural research in the universities, hospitals, research centres, and with other local and international partners.