Single-molecule visualization of twin-supercoiled domains generated during transcription

R Janissen, R Barth, M Polinder… - Nucleic Acids …, 2024 - academic.oup.com
Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and
the regulation of genetic processes in all domains of life. It has become common knowledge …

[HTML][HTML] CENP-B-mediated DNA loops regulate activity and stability of human centromeres

F Chardon, A Japaridze, H Witt, L Velikovsky… - Molecular cell, 2022 - cell.com
Chromosome inheritance depends on centromeres, epigenetically specified regions of
chromosomes. While conventional human centromeres are known to be built of long tandem …

Relationship between the Chromosome Structural Dynamics and Gene Expression—A Chicken and Egg Dilemma?

D Le Berre, S Reverchon, G Muskhelishvili, W Nasser - Microorganisms, 2022 - mdpi.com
Prokaryotic transcription was extensively studied over the last half-century. A great deal of
data has been accumulated regarding the control of gene expression by transcription factors …

FIB-milled plasmonic nanoapertures allow for long trap** times of individual proteins

W Yang, M van Dijk, C Primavera, C Dekker - Iscience, 2021 - cell.com
We have developed a fabrication methodology for label-free optical trap** of individual
nanobeads and proteins in inverted-bowtie-shaped plasmonic gold nanopores. Arrays of …

Chromosomal position of ribosomal protein genes affects long-term evolution of Vibrio cholerae

L Larotonda, D Mornico, V Khanna, J Bernal-Bayard… - Mbio, 2023 - journals.asm.org
It is unclear how gene order within the chromosome influences genome evolution. Bacteria
cluster transcription and translation genes close to the replication origin (oriC). In Vibrio …

Xenogeneic nucleoid-associated EnrR thwarts H-NS silencing of bacterial virulence with unique DNA binding

R Ma, Y Liu, J Gan, H Qiao, J Ma, Y Zhang… - Nucleic Acids …, 2022 - academic.oup.com
Type III and type VI secretion systems (T3/T6SS) are encoded in horizontally acquired
genomic islands (GIs) that play crucial roles in evolution and virulence in bacterial …

[HTML][HTML] DNA as a Double-Coding Device for Information Conversion and Organization of a Self-Referential Unity

G Muskhelishvili, W Nasser, S Reverchon, A Travers - DNA, 2024 - mdpi.com
Living systems are capable on the one hand of eliciting a coordinated response to changing
environments (also known as adaptation), and on the other hand, they are capable of …

[HTML][HTML] Extracting and characterizing protein-free megabase-pair DNA for in vitro experiments

M Holub, A Birnie, A Japaridze, J van der Torre… - Cell Reports …, 2022 - cell.com
Chromosome structure and function is studied using various cell-based methods as well as
with a range of in vitro single-molecule techniques on short DNA substrates. Here, we …

Fluidification of entanglements by a DNA bending protein

YAG Fosado, J Howard, S Weir, A Noy, MC Leake… - Physical Review Letters, 2023 - APS
In spite of the nanoscale and single-molecule insights into nucleoid associated proteins
(NAPs), their role in modulating the mesoscale viscoelasticity of entangled DNA has been …

[HTML][HTML] Towards a Better Control of Engineered Circuit Transcription in Bacterial Genomes

N Sarica, L Janniere, BC Jester - Applied Microbiology, 2025 - mdpi.com
The transcription of genes and engineered circuits can deeply vary when inserted into
different genomic loci. This unpredictable performance, termed context sensitivity …