Related papers: Nucleosome positioning and energetics: Recent adva…
The volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
The three-dimensional organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state - accessibility and the amount of gene expression - of the chromatin. Recent advances in chromosome…
The genomic DNA of bacteria occupies only a fraction of the cell called the nucleoid, although it is not bounded by any membrane and would occupy a volume hundreds of times larger than the cell in the absence of constraints. The two most…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop…
No systematic method exists to derive intra-chromosomal potentials between nucleosomes along a chromosome consistently across a given genome. Such potentials can yield information on nucleosomal ordering, thermal as well as mechanical…
Quantum Chromodynamics (QCD) is generally assumed to be the fundamental theory underlying nuclear physics. In recent years there is progress towards investigating the nucleon structure from first principles of QCD. Although this structure…
The cell nucleus is increasingly recognized as a mechanosensitive organelle whose mesoscale mechanical heterogeneity (100 nm 10 um) is inseparable from genome regulation yet remains weakly integrated into systems biology and omics…
The helical coil is ubiquitous in biological and natural systems and often it is the basic form that leads to complex structures. This paper considers the question of its dimensionality in biological information as the helical coil goes…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
The epigenome, i.e. the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
Recent experiments have been able to visualise chromosome organization in fast-growing E.coli cells. However, the mechanism underlying the spatio-temporal organization remains poorly understood. We propose that the DNA adopts a specific…
More than 30 years ago, we published a paper entitled as abnormal chromatin configuration and oncogenesis, which proposed the first hypothesis that links oncogenesis to abnormal three-dimensional (3D) genome structure. Recently, many…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
Structural-Maintenance-of-Chromosome (SMC) complexes such as condensins organise the folding of chromosomes. However, their role in modulating the entanglement of DNA and chromatin is not fully understood. To address this question, we…
We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-H\"uckel electrostatics and uses a two-angle zig-zag model for the geometry…
Heterochromatin protein 1 (HP1) participates in establishing and maintaining heterochromatin via its histone modification dependent chromatin interactions. In recent papers HP1 binding to nucleosomal arrays was measured in vitro and…