Meeting report: The biology of genomes and proteomes

Abstract

A mini-symposium of the Genetics Society of Korea was held at Dankook University, Korea on April 24, 2015. The theme of the mini-symposium was ‘The biology of genomes and proteomes.’ This was the first mini-symposium of 2015. There were two sessions that were chaired by Dr. Kyu-Dong Han (Dankook University, Korea) and Dr. Heui-Soo Kim (Pusan National University, Korea). In the first session, three speakers gave talks on genomics and epigenomics. The first speaker, Dr. Keunsoo Kang (Department of Microbiology, Dankook University, Korea), introduced ‘‘An automated analysis pipeline for a large set of ChIP-seq data: AutoChIP (Kim et al. 2014a, b).’’ Recent advances in genomic DNA sequencing have revolutionized the ways to examine molecular events inside cells in several aspects. Next-generation sequencing approaches, which enable the rapid and accurate sequencing of short DNA fragments, have changed the ways researchers approach biological problems. For example, researchers can identify the genome-wide binding sites of proteins by using chromatin immune precipitation coupled with parallel sequencing (ChIP-seq) without any prior knowledge (Johnson et al. 2007; Robertson et al. 2007). Although there are many applications available for the analysis of ChIP-seq data (Henry et al. 2014), users need to know some details about the installation, alignment, and peak-calling procedures in most cases. Dr. Kang summarized his recent advances with the AutoChip assay, which is an easy-to-use application for ChIP-seq analysis. Using the AutoChip, the user automatically downloads and installs programs on his or her computer before launching the actual data analysis. In addition, all procedures for ChIP-seq analyses, such as the alignment of unmapped reads to a reference genome and the identification of genome-wide binding sites for a given protein, can be done by two simple steps coupled with AutoChIP. An evaluation of the cocktail algorithm implemented in AutoChIP showed that the algorithm outperformed a single ChIP-seq tool in terms of the ratio of motif occurrences and the average height of the normalized read density over the identified peaks. In addition, the annotation of the identified peaks with information about known genes and repeat elements provides a comprehensive picture of the genome-wide binding sites of selected proteins. Overall, AutoChIP provides a comprehensive platform to analyze a large set of ChIPseq data in one step. The second speaker, Dr. Kyunghwan Kim (Department of Biology, Chungbuk National University, Korea), gave a presentation entitled ‘Epigenetics and cancer development.’ The regulation of gene expression and the maintenance of chromosome stability in eukaryotes are critically associated with the formation of silent chromatin. Inactive chromatin structures are frequently related to distinctive histone modifications (Suganuma and Workman 2011). Although recent studies have implicated histone modification as a key regulator of chromatin fluidity, the molecular mechanisms underlying such effects remain & Nam-Soo Kim kimnamsu@kangwon.ac.kr