Despite the key role of linker histone H1 in chromatin structure and dynamics, its location interactions with nucleosomal DNA have not been elucidated. In this work we used a combination electron cryomicroscopy, hydroxyl radical footprinting, nanoscale modeling to analyze precisely positioned mono-, di-, trinucleosomes containing physiologically assembled full-length or truncated mutants protein. Single-base resolution •OH footprinting shows that globular domain (GH1) interacts minor groove...

DNA supercoiling acts as a global transcriptional regulator in bacteria, that plays an important role adapting their expression programme to environmental changes, but for which no quantitative or even qualitative regulatory model is available. Here, we focus on spatial heterogeneities caused by the transcription process itself, strongly contribute this regulation mode. We propose new mechanistic modeling of transcription-supercoiling dynamical coupling along genome, allows simulating and...

DNA torsional stress is generated by virtually all biomolecular processes involving the double helix, in particular transcription where a significant level of propagates over several kilobases. If another promoter located this range, may strongly modify its opening properties, and hence facilitate or hinder transcription. This mechanism implies that transcribed genes distant few kilobases are not independent, but coupled stress, an effect for which we propose first quantitative systematic...

The interaction of histone H1 with linker DNA results in the formation nucleosomal stem structure, considerable influence on chromatin organization. In a recent paper [Syed,S.H., Goutte-Gattat,D., Becker,N., Meyer,S., Shukla,M.S., Hayes,J.J., Everaers,R., Angelov,D., Bednar,J. and Dimitrov,S. (2010) Single-base resolution mapping H1-nucleosome interactions 3D organization nucleosome. Proc. Natl Acad. Sci. USA, 107, 9620–9625], we published biochemical footprinting cryo-electron-micrographs...

Small non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data, which are efficient for eukaryotic sRNAs but remain inaccurate the longer and highly structured bacterial sRNAs. We present APERO, a new algorithm detect small transcripts paired-end data. In contrast previous that start read coverage distribution, APERO analyzes boundaries individual sequenced fragments infer 5' 3' ends...

DNA supercoiling (SC), the over- and under-winding of DNA, is generated by transcription as described in twin-domain model. Conversely, SC also impacts through torsional stress. therefore regulates independent factor binding, classic protein-based regulatory mechanism, particularly context chromosomal topological domains actions topoisomerases. SC-coupled has inspired several computational models, but a systematic quantitative assessment parameters controlling this complex interplay missing....

Bacterial pathogenic growth requires a swift coordination of pathogenicity function with various kinds environmental stress encountered in the course host infection. Among factors critical for bacterial adaptation are changes DNA topology and binding effects nucleoid-associated proteins transducing signals to chromosome coordinating global transcriptional response stress. In this study, we use model phytopathogen Dickeya dadantii analyse organisation transcription by heterodimeric protein...

In this study, we highlight the role of discriminator as a global sensor supercoiling variations and propose first quantitative regulatory model principle, based on specific step promoter opening during transcription initiation. It defines predictive rule by which SC quantitatively modulates expression rate bacterial promoters, depending G/C content their independently from promoter-specific proteins.

This is the first transcriptomic map of a Dickeya species. It may therefore significantly contribute to further progress in field phytopathogenicity.

Retroviral integrases (INs) catalyse the integration of reverse transcribed viral DNA into host cell genome. This process is selective, and chromatin has been proposed to be a major factor regulating this step in life cycle. However, precise underlying mechanisms are still under investigation. We have developed new vitro assay using physiologically-relevant, reconstituted genomic acceptor high-throughput determination nucleosome positions sites, parallel. A quantitative analysis resulting...

We study water-immersed granular avalanches in a long rectangular cell of small thickness. By video means, both the angle pile and velocity profiles grains across depth are recorded as function time. These measurements give access to instantaneous flux. inclining at initial angles larger than maximum stability, triggered last for time, up several hours grains, during which slope flux relax slowly. show that relaxation is quasi-steady so there no inertia: given time controlled only by This...

The isostatic jamming limit of frictionless spherical particles from Edwards' statistical mechanics [Song \emph{et al.}, Nature (London) {\bf 453}, 629 (2008)] is generalized to arbitrary dimension $d$ using a liquid-state description. asymptotic high-dimensional behavior the self-consistent relation obtained by saddle-point evaluation and checked numerically. resulting random close packing density scaling $\phi\sim d\,2^{-d}$ consistent with that other approaches, such as replica theory...

Abstract DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level mainly regulated by topoisomerase I and gyrase. Inhibiting either these enzymes with antibiotics leads to global modifications subsequent changes in gene expression. In previous studies, genes responding relaxation induced gyrase inhibition were categorised as ‘supercoiling-sensitive’. Here, we studied the opposite variation phytopathogen Dickeya dadantii using non-marketed antibiotic...

Abstract Motivation Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA’s response to mechanical distortion. ThreaDNA estimates this based on high-resolution structures of the protein–DNA complex interest. Implementing an efficient nanoscale modeling DNA deformations involving essentially no adjustable parameters, it returns profile deformation energy along whole genomes, at base-pair resolution, within minutes usual laptop/desktop computers. Our predictions...

Abstract In this work we analyzed protein-protein interactions (PPIs) formed by E. coli replication proteins under three disparate bacterial growth conditions. The chosen conditions corresponded to fast exponential growth, slow and cessation at the stationary phase. We performed affinity purification coupled with mass spectrometry (AP-MS) of chromosomally expressed (DnaA, DnaB, Hda, SeqA, DiaA, DnaG, HolD, NrdB), tagged sequential peptide (SPA) tag. Composition protein complexes was...

DNA supercoiling acts as a global transcriptional regulator in bacteria, but the promoter sequence or structural determinants controlling its effect remain unclear. It was previously proposed to modulate torsional angle between -10 and -35 hexamers, thereby regulate formation of closed-complex depending on length 'spacer' them. Here, we develop thermodynamic model this notion based elasticity, providing quantitative parameter-free predictions relative activation promoters containing short...

Gene expression is an inherently stochastic process, owing to its dynamic molecular nature. Protein amount distributions, which can be acquired by cytometry using a reporter gene, inform about the mechanisms of underlying microscopic system. By different clones chicken erythroid progenitor cells harboring integration sites CMV-driven mCherry protein, we investigated dynamical behavior such distributions. We show that, on short term, clone distributions quickly regenerated from small...

DNA supercoiling, the level of under- or overwinding polymer around itself, is widely recognized as an ancestral regulation mechanism gene expression in bacteria. Higher levels negative supercoiling facilitate opening double helix at promoters and thereby increase transcription rates. Different have been measured bacteria exposed to different environments, leading hypothesis that variations could be a response changes environment. Moreover, has shown generate local and, therefore, impact...