Chromatin Biology

Phase-dependent measurement discrepancies persist across vastly different scales of nature. In cosmology, early-universe and late-universe measurements of the Hubble constant continue to yield divergent values despite increasingly precise instrumentation. In molecular biology, chromatin architecture undergoes large-scale mitotic dismantling and reconstruction while preserving selected microcompartment structures across phase transitions. In quantum physics, wave-particle duality demonstrates that measurement outcomes depend fundamentally upon apparatus configuration and observational context. Although these phenomena are typically studied within separate disciplinary frameworks, they share a common structural feature: the same system produces different measurable outputs when observed under different phase conditions.

This paper does not propose a new physical theory. Instead, it develops a methodological and hermeneutic framework for reading phase-dependent discrepancies as manifestations of a shared recursive topology. The central distinction separates measured outputs, which are empirically accessible, instrument-specific, and phase-dependent, from recursive pattern, understood as a topological invariant that may be readable across outputs without being directly measurable itself.

The framework operates through three analytical layers. The first layer consists of established empirical findings drawn from cosmology, molecular biology, and quantum measurement research. The second layer advances a falsifiable methodological proposal: that recurring forms of phase-dependent divergence across disciplines may exhibit structural homologies indicative of a common recursive organization. The third layer introduces a Qur'anic-topological reading lens that functions as a hermeneutic architecture rather than a scientific hypothesis. Within this interpretive framework, selected Qur'anic textual coordinates are employed as conceptual tools for describing bifurcation, alternation, mediation, preservation, and recursive return.

Drawing upon traditions in philosophy of science and hermeneutics, including paradigm theory, epistemic frameworks, textual interpretation, and constructive empiricism, the paper argues that scientific understanding often progresses not only through new mechanisms but also through new ways of reading existing measurements. The proposed recursive topology therefore functions as an interpretive instrument for recognizing structural continuities across disciplinary boundaries without reducing one domain to another. The resulting framework offers a vocabulary for exploring how observer position, measurement phase, and system traversal may jointly shape the outputs recorded across cosmological, biological, and quantum systems.

RasGap is a significantly large protein constituting 1,047 amino acids with vital domains such as SH2, SH3, PH, and C2, N terminal, and RasGap region. However, the structures are available for distinctive domains, and thus in this paper, we predicted the entire 1,047 amino acids' protein structure using various integrated computational techniques (ab initio, homology modeling, and fragment-based modeling, which were subsequently subjected to molecular dynamics simulation analysis) to predict the structure and analyze the effects of this dynamic feature on the discrete domains. The findings revealed that RasGap protein has dynamic features like polyglycine, polyproline, and polyglutamine regions in the long N-terminal region. All the models exhibited stable conformations with 78.4%-83.1% residues and showed favored regions in the Ramachandran plot and demonstrated a confident c-score of 0.12 and a dope score between-62,050.261719 and-67,629.390625. The N-terminal polyproline region showed a hydrophobicity index ranging from 0.437 to 0.531, while the SH2_1 ranged from 0.633 to 0.68, SH3_2 ranged from 0.626 to 0.71, and SH3 ranged from 0.589 to 0.651. The molecular dynamics simulations also revealed the opening of the cavity region. Polyproline, with SH2_1, SH3, and SH2_2 domains, is a known and responsible factor in the formation of RasGap-Nck1 complex. Hence, opening a cavity in the studied region of RasGap protein correlates a strong relationship in the formation of the cavity region, which can be further studied in its interaction with the Nck1 protein.

Repair of DNA double-strand breaks (DSBs) by the nonhomologous end-joining pathway (NHEJ) is important not only for repair of spontaneous breaks but also for breaks induced in developing lymphocytes during V(D)J (variable [V], diversity [D], and joining [J] genes) recombination of their antigen receptor loci to create a diverse repertoire. Mutations in the NHEJ factor XLF result in extreme sensitivity for ionizing radiation, microcephaly, and growth retardation comparable to mutations in LIG4 and XRCC4, which together form the NHEJ ligation complex. However, the effect on the immune system is variable (mild to severe immunodeficiency) and less prominent than that seen in deficiencies of NHEJ factors ARTEMIS and DNA-dependent protein kinase catalytic subunit, with defects in the hairpin opening step, which is crucial and unique for V(D)J recombination. Therefore, we aimed to study the role of XLF during V(D)J recombination. We obtained clinical data from 9 XLF-deficient patients and ...

Chromatin is a complex of DNA, RNA, and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleo some, an octamer of histone proteins around which 147 base pairs of DNA are wound in almost two turns of a left-handed superhelix. Chromatin is a dynamic structure that exerts profound influence on regulation of gene expression and other cellular functions. These chromatin-directed processes are facilitated by optimizing nucleosome positions throughout the genome and by remodeling nucleosomes in response to various external and internal signals such as environmen tal perturbations. Here we discuss the large-scale maps of nucleosome positions made available through recent advances in parallel highthroughput sequencing and microarray technologies. We show that these maps reveal common features of nucleosome organization in eukaryotic genomes. We also survey the computational models designed to predict nucleosome formation scores or energies and

The term ''the DNA damage response'' (DDR) encompasses a sophisticated array of cellular initiatives set in motion as cells are exposed to DNAdamaging events. It has been known for over half a century that all organisms have the ability to restore genomic integrity through DNA repair. More recent discoveries of signal transduction pathways linking DNA damage to cell cycle arrest and apoptosis have greatly expanded our views of how cells and tissues limit mutagenesis and tumorigenesis. DNA repair not only plays a pivotal role in suppressing mutagenesis but also in the reversal of signals inducing the stress response. If repair is faulty or the cell is overwhelmed by damage, chances are that the cell will despair and be removed by apoptosis. This final fate is determined by intricate cellular dosimeters that are yet to be fully understood. Here, key findings leading to our current view of DDR are discussed as well as potential areas of importance for future studies.

The term ‘‘the DNA damage response’’ (DDR) encompasses a sophisticated array of cellular initiatives set in motion as cells are exposed to DNAdamaging events. It has been known for over half a century that all organisms have the ability to restore genomic integrity through DNA repair. More recent discoveries of signal transduction pathways linking DNA damage to cell cycle arrest and apoptosis have greatly expanded our views of how cells and tissues limit mutagenesis and tumorigenesis. DNA repair not only plays a pivotal role in suppressing mutagenesis but also in the reversal of signals inducing the stress response. If repair is faulty or the cell is overwhelmed by damage, chances are that the cell will despair and be removed by apoptosis. This final fate is determined by intricate cellular dosimeters that are yet to be fully understood. Here, key findings leading to our current view of DDR are discussed as well as potential areas of importance for future studies. Environ. Mol. Muta...