Chromatin and development: a special issue

It is now approximately 40 years since chromatin studies changed drastically with the first visualization of ‘nu bodies’, that we now know as nucleosomes. The ‘beads on a string’ that appeared in electron micrographs (Olins and Olins, 1974) showed the structural units of chromatin and provided the foundation for a field that has been expanding ever since then. One of the major advances in chromatin studies has been the identification of numerous connections between nucleosome organization, including the plethora of histone post-translational modifications, and gene function. Studies in an apparently different field, development of multicellular organisms, have also revealed that developmental transitions and organogenesis are strictly dependent on the establishment, maintenance and modification of highly regulated gene expression patterns. Therefore, efforts to learn about chromatin organization and function, gene expression and developmental transitions converge, contributing to provide a complete picture. In this Special Issue on ‘Chromatin and epigenetics at the nexus between cell division, differentiation and development’ we have gathered articles from leading scientists in their fields discussing a broad spectrum of topics relating chromatin structure and function with developmental transitions: the special organization and functional properties of centromeres and telomeres, genome maintenance and integrity, nucleosome remodeling and modification complexes, histone dynamics, epigenetic memory and chromatin during gametophyte development. Centromeres, unique structural chromosomal entities important for genetic stability, have a complex biology both in somatic and reproductive stages (Lermontova et al., 2015). One key aspect is identifying what elements contribute to define a centromere. Large arrays of satellite repeats are often found at centromeric regions of dicotyledonous species whereas retro-elements are found in many monocotyledonous species, in both cases with rapid evolutionary divergence even between close relatives. In contrast to the difficulties in defining centromeres at the sequence level, the presence of kinetochore complex, containing >100 proteins, is a general mark of a centromere. Linked to kinetochore assembly is the incorporation of the specific centromeric histone H3 (CENH3), which has gained wide attention in plant biology since the expression of certain artificial CENH3 fusion proteins can lead to genome haploidization. Plant telomeres and ribosomal genes are not only exceptional from their DNA composition and the repetitive sequence organization, but also from their chromatin status of both elements. This together with the surprising similarities between them is discussed in the corresponding review article (Dvo r a ckov a et al., 2015), including epigenetic modifications and the role of long non-coding RNAs. Maintenance of genetic material and the necessary intermixing of the parental genotypes during propagation to the next generation are topics at the core of genome stability. Progression through the cell cycle depends on the occurrence of a series of events, several of which rely on drastic changes in chromatin organization. The intimate relationship between genome replication and chromatin landscapes is discussed by Sequeira-Mendes and Gutierrez (Sequeira-Mendes and Gutierrez, 2015). Although genome replication occurs during the S-phase, certain steps (access of replication initiation proteins to chromatin and specification of replication origins) take place soon after mitosis and during the G1 phase and are highly dependent on the chromatin status. Interestingly, they are multiple chromatin signatures associated with the origin location, some of which are remarkably similar to those identified in animal cells. Other aspects relevant for genome integrity and development such as prevention of duplicating genomic regions more than once per cell cycle (re-replication) and the transition from the cell cycle to the endocycle, which is a necessary step for many plants cells before they can fully differentiate, are also discussed. The exchange of genetic information between parental chromosomes, known as ‘cross-overs’ (COs), occur during meiotic recombination and are events required in plant breeding to unlink adverse from beneficial traits that are coded in close proximity on the same chromosome. This question of basic and applied relevance is discussed by Choi and Henderson (Choi and Henderson, 2015) by focusing on the study of CO hotspots. Interestingly chromatin structure plays a very important, but still not completely understood role in this process. Most often hotspots are found in association with genes and particularly within promoter regions of genes that have an open chromatin structure. One of the major factors contributing to chromatin organization is nucleosome positioning and histone composition. The ATPase-containing chromatin remodeling complexes during plant development are discussed by D. Wagner and colleagues (Han et al., 2015) with emphasis on SWI/SNF and CHD3. These factors function as enhancers with a role in pluripotency, differentiation and developmental phase transitions, and their defects lead to pleiotropic consequences. At the gene level, it is becoming clear that certain genes depend more on chromatin remodeling than others, in particular if they function as master