Related papers: Resolving the degree of order in the bacterial chr…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
A prominent organizational feature of bacterial chromosomes was revealed by Hi-C experiments, indicating anomalously high contacts between the left and right chromosomal arms. These long-range contacts have been attributed to various…
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…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
We present a framework based on conditional entropy and the Dirichlet distribution for classifying chromosomes based on the degree to which they use synonymous codons uniformly or preferentially, that is, whether or not codons that code for…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…
The principles that govern the organization of genomes, which are needed for a deeper understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three-dimensional (3D) structures are known.…
In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring…
Using a bead-spring model of bacterial DNA polymers of {\em C. crescentus} and {\em E. coli} we show that just $33$ and $38$ effective cross-links at special positions along the chain contour of the DNA can lead to the large-scale…
Pathogenic chromosome abnormalities are very common among the general population. While numerical chromosome abnormalities can be quickly and precisely detected, structural chromosome abnormalities are far more complex and typically require…
Bacteria are able to maintain a narrow distribution of cell sizes by regulating the timing of cell divisions. In rich nutrient conditions, cells divide much faster than their chromosomes replicate. This implies that cells maintain multiple…
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
We investigate the large-scale geometry of the DNA-protein complex of chromatin using a generalized optimality principle, which requires that not only should all sub-parts of a natural process be optimal but also the unfolding of higher…
One-dimensional arrays of nucleosomes (DNA-bound histone octamers separated by stretches of linker DNA) fold into higher-order chromatin structures which ultimately make up eukaryotic chromosomes. Chromatin structure formation leads to…