Fission yeast condensin contributes to interphase chromatin organization and prevents transcription-coupled DNA damage.

BACKGROUND: Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chromatin interactions in mitosis. These compact chromatin and create mechanically stable chromosomes. How condensin contributes to chromatin organization in interphase is less well understood. RESULTS: Here, we use efficient conditional depletion of fission yeast condensin to determine its contribution to interphase chromatin organization. We deplete condensin in G2-arrested cells to preempt confounding effects from cell cycle progression without condensin. Genome-wide chromatin interaction mapping, using Hi-C, reveals condensin-mediated chromatin interactions in interphase that are qualitatively similar to those observed in mitosis, but quantitatively far less prevalent. Despite their low abundance, chromatin mobility tracking shows that condensin markedly confines interphase chromatin movements. Without condensin, chromatin behaves as an unconstrained Rouse polymer with excluded volume, while condensin constrains its mobility. Unexpectedly, we find that condensin is required during interphase to prevent ongoing transcription from eliciting a DNA damage response. CONCLUSIONS: In addition to establishing mitotic chromosome architecture, condensin-mediated long-range chromatin interactions contribute to shaping chromatin organization in interphase. The resulting structure confines chromatin mobility and protects the genome from transcription-induced DNA damage. This adds to the important roles of condensin in maintaining chromosome stability.

Bridging the dynamics and organization of chromatin domains by mathematical modeling.

The genome is 3-dimensionally organized in the cell, and the mammalian genome DNA is partitioned into submegabase-sized chromatin domains. Genome functions are regulated within and across the domains according to their organization, whereas the chromatin itself is highly dynamic. However, the details of such dynamic organization of chromatin domains in living cells remain unclear. To unify chromatin dynamics and organization, we recently demonstrated that structural information of chromatin domains in living human cells can be extracted from analyses of the subdiffusive nucleosome movement using mathematical modeling. Our mathematical analysis suggested that as the chromatin domain becomes smaller and more compact, nucleosome movement becomes increasingly restricted. Here, we show the implication of these results for bridging the gap between chromatin dynamics and organization, and provide physical insight into chromatin domains as efficient units to conduct genome functions in the thermal noisy environment of the cell.

Dissection of open chromatin domain formation by site-specific recombination in Drosophila.

Drosophila polytene interphase chromosomes provide an ideal test system to study the rules that define the structure of chromatin domains. We established a transgenic condensed chromatin domain cassette for the insertion of large pieces of DNA by site-specific recombination. Insertion of this cassette into open chromatin generated a condensed domain, visible as an extra band on polytene chromosomes. Site-specific recombination of DNA sequence variants into this ectopic band allowed us to compare their capacity for open chromatin formation by cytogenetic methods. We demonstrate that the 61C7-8 interband DNA maintains its open chromatin conformation and epigenetic state at an ectopic position. By deletion analysis, we mapped the sequences essential for open chromatin formation to a 490-bp fragment in the proximal part of the 17-kb interband sequence. This fragment overlaps binding sites for the chromatin protein Chriz (also known as Chro), the histone kinase Jil-1 and the boundary element protein CP190. It also overlaps a promoter region that locates between the Rev1 and Med30 transcription units.

Flexible and dynamic nucleosome fiber in living mammalian cells.

Genomic DNA is organized three dimensionally within cells as chromatin and is searched and read by various proteins by an unknown mechanism; this mediates diverse cell functions. Recently, several pieces of evidence, including our cryomicroscopy and synchrotron X-ray scattering analyses, have demonstrated that chromatin consists of irregularly folded nucleosome fibers without a 30-nm chromatin fiber (i.e., a polymer melt-like structure). This melt-like structure implies a less physically constrained and locally more dynamic state, which may be crucial for protein factors to scan genomic DNA. Using a combined approach of fluorescence correlation spectroscopy, Monte Carlo computer simulations, and single nucleosome imaging, we demonstrated the flexible and dynamic nature of the nucleosome fiber in living mammalian cells. We observed local nucleosome fluctuation (~50 nm movement/30 ms) caused by Brownian motion. Our in vivo/in silico results suggest that local nucleosome dynamics facilitate chromatin accessibility and play a critical role in the scanning of genome information.

Characterization of interphase nuclei from triploid hybrids between Pennisetum purpureum Schumach and Pennisetum glaucum (L.) R. Br. / Caracterização de núcleos interfásicos de híbridos tríploides entre Pennisetum purpureum Schumach e Pennisetum glaucum (L.) R. Br.

This study evaluated the structure and the volume of interphase nuclei from root meristems of the genotypes of napier grass (Pennisetum purpureum), pearl millet (Pennisetum glaucum) and hybrids resultant of such breeding. In napier grass, nuclei were areticulate. Both pearl millet and the triploid hybrid had semi-reticulate nuclei; also, the hybrid presented a small proportion (6 percent) of areticulate nuclei. Pearl millet had the highest averages of nuclear dimensions, such as volume, diameter and radius, followed by the interspecific hybrid and napier grass. There was no intraspecific variation for the type of nuclear structure, which indicates this feature is important for cytotaxonomic studies involving the genus Pennisetum. Results demonstrated that chromatin organization in these nuclei was influenced by the number and size of chromosomes, affecting the nucleus volume in the analyzed taxa.

Avaliou-se, neste estudo, a estrutura e o volume de núcleos interfásicos de meristemas radiculares de genótipos do capim-elefante (Pennisetum purpureum), milheto (Pennisetum glaucum) e do híbrido resultante deste cruzamento. O capim-elefante apresentou núcleos do tipo arreticulado. Tanto no milheto como no híbrido triplóide os núcleos apresentaram-se semi-reticulados, sendo que, no híbrido, foi observada uma pequena proporção (6 por cento) de núcleos arreticulados. As maiores médias para as dimensões nucleares como volume nuclear, diâmetro e raio foram obtidas para o milheto, seguidas do híbrido interespecífico e capim-elefante. Não houve variação intraespecífica para tipo de estrutura nuclear indicando que essa característica tem relevância para estudos citotaxonômicos no gênero Pennisetum. Os resultados demonstraram que a organização da cromatina nesses núcleos foi influenciada pelo número e tamanho dos cromossomos e essa afetou o volume nuclear dos táxons analisados.