2016 年 91 巻 2 号 p. 49
Life is not a static system composed of constitutive structures, but is regulated by dynamic interactions among its heterogeneous elements. The Grant-in-Aid for Scientific Research on Innovative Areas ‘Correlative Gene System: Establishing Next-Generation Genetics’ from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) was launched to understand such complexity of biological interactions underlying life, at different scales. An ecosystem is shaped by contributions from the interactions between individuals (including interspecies interactions), cells, and even molecules. The project was designed to dissect these different scales by collecting case studies of diverse organisms, and to extract common principles. The research area aimed to study and integrate genomic information across species, as well as establishing new methodologies for future genetic studies.
In this special issue of Genes & Genetic Systems, seven articles from groups affiliated with the project are being published. Three of the articles provide reviews (Buzas; Ishishita and Matsuda; Kitano and Mori), and four provide original data (Furihata et al.; Maeda et al.; Kudo et al.; Sunaga et al.). These articles discuss either the molecular interactions within biological systems (Buzas; Furihata et al.; Maeda et al.; Kudo et al.), the cellular physiological interactions that govern the expression of phenotypes (Ishishita and Matsuda; Sunaga et al.), or adaptation of organisms to their environment (Maeda et al.; Sunaga et al.; Kitano and Mori).
It is clear that molecular interactions regulate development. Diana Buzas reviews recent findings concerning the requirements of iron-sulfur cluster proteins for active DNA methylation in plants. Lack of DNA demethylation causes overproliferation of the endosperm, leading to seed abortion, and loss of epigenetic control perturbs the genetic balance between the parental gametes, which is essential for proper seed development. On the same topic, Akira Kawabe and colleagues investigated the evolution of the Polycomb repressive complex 2 (PRC2) genes in plants. PRC2 has an essential role in genomic imprinting during seed development. They discuss the importance of gene duplication events and neo-functionalization of the PRC2 components in establishing maternal imprinting. To reveal the molecular interactions between microRNAs and their target genes that confer robustness to environmental changes, Masao Watanabe and coauthors performed transcriptomic analysis of cool-temperature-treated rice cultivars. Not only did they find some candidate genes responsible for sensitivity to cool-temperature, but they also found novel microRNAs. Generally speaking, any study of a biological interaction requires a comparative reference that is not influenced by the biological interaction in question. Using large-scale re-analysis of transcriptomic datasets, Kentaro Yano and colleagues establish guidelines for selecting stable reference genes for quantitative mRNA expression analysis.
At the cellular level, cell-to-cell communications and trait-to-trait interactions may be studied using model systems. Satoshi Ishishita and Yoichi Matsuda review model systems for studying interspecies hybrid incompatibilities in vertebrates. Hypotheses on cellular and subcellular defects associated with hybrid sterility and inviability are discussed. In the fruit fly, geographic clines of body pigmentation are observed in populations from different parts of the world. Aya Takahashi and coworkers investigated a panel of genetic strains to study the complex associations between body pigmentation and physiological phenotypes. Possible forces underlying the long-term maintenance of pigmentation variation in this species are discussed. Jun Kitano and Seiichi Mori provide a review and discussion of the importance of sticklebacks as genetic resources to study speciation. These fish species are valuable living examples for studying interspecies incompatibility, but at the same time are often being endangered and even made extinct by anthropogenic perturbations.
As exemplified by these studies, individual organisms and species have highly polymorphic genomes and epigenomes, in which complex correlative gene interactions drive the diversity of phenotypes. Gene duplication and epigenetic regulation are emerging as common basic mechanisms underlying correlative gene systems. Further systematic studies to uncover common principles of correlative gene systems will be important for understanding the diversity of natural organisms and their evolution.