Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.

DNA double-strand breaks (DSBs) are known to be the most serious lesions in irradiated cells. Several protein pathways exist for repair. The mechanisms by which cells determine a specific pathway for repair remain poorly understood. DSB induction and repair can be spatiotemporally monitored by ionizing radiation-induced foci (IRIFs) and the formation of repair complexes. IRIF analyses revealed that DSB formation, repair and misrepair are strongly dependent on the radiation characteristics and the microarchitecture of the chromatin environment. However, the IRIF nano-architecture remains unknown, as does its impact on the decision-making process and follow-up protein recruitment. New insights into the relationship between the physical properties of radiation, environmental chromatin architecture, IRIF architecture and DSB repair mechanisms are presented using single-molecule localization microscopy. Ripley distance statistics and persistent homology calculations have shifted our ability to analyze chromatin and IRIF architectures from imaging to topology and structure calculations. We discuss these approaches for cancer treatment-relevant irradiation processes on selected cell systems and consider whether this “structuromics” can enhance our knowledge about the radiation response.