Related papers: Gene clusters reflecting macrodomain structure res…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…
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…
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
Nanoscale chromatin domains, variously termed nucleosome clutches, nanodomains, or packing domains, have emerged as fundamental architectural units of the mammalian genome during interphase and mitosis. Unlike cohesin-dependent loops or…
Different numerical mappings of the DNA sequences have been studied using a new cluster-scaling method and the well known spectral methods. It is shown, in particular, that the nucleotide sequences in DNA molecules have robust…
Deciphering how genes interpret information from the concentration of transcription factors (TFs) within the cell nucleus remains a fundamental question in gene regulation. Recent advancements have unveiled the heterogeneous distribution of…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
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 nucleosome, an octamer of histone proteins around…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
Our understanding of how chromosomes structurally organize and dynamically interact has been revolutionized through the lens of long-chain polymer physics. Major protein contributors to chromosome structure and dynamics are condensin and…
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…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
The connection between chromatin nuclear organization and gene activity is vividly illustrated by the observation that transcriptional coregulation of certain genes appears to be directly influenced by their spatial proximity. This fact…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal…
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites…
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein, which is involved in both gene regulation and DNA compaction. Although it is a key player in genome organization by forming bridges between DNA duplexes,…