Roman Barth
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View article: Telomeres stall DNA loop extrusion by condensin
Telomeres stall DNA loop extrusion by condensin Open
DNA loop extrusion by SMC proteins is a key process underlying chromosomal organization. It is unknown how loop extruders interact with telomeres where DNA is densely covered with proteins. Using complementary in vivo and in vitro single-m…
View article: Cohesin supercoils DNA during loop extrusion
Cohesin supercoils DNA during loop extrusion Open
Cohesin extrudes genomic DNA into loops that promote chromatin assembly, gene regulation, and gene recombination. Loop extrusion depends on large-scale conformational changes in cohesin, but how these translocate DNA is poorly understood. …
View article: Two CTCF motifs impede cohesin-mediated DNA loop extrusion
Two CTCF motifs impede cohesin-mediated DNA loop extrusion Open
Cohesin extrudes DNA into loops and is positioned along the genome by stalling at CTCF upon encountering its N-terminal region (NTR). The mechanism underlying this stalling, however, is unresolved. Using single-molecule assays that monitor…
View article: SMC motor proteins extrude DNA asymmetrically and can switch directions
SMC motor proteins extrude DNA asymmetrically and can switch directions Open
Structural maintenance of chromosomes (SMC) complexes organize the genome via DNA loop extrusion. Although some SMCs were reported to do so symmetrically, reeling DNA from both sides into the extruded DNA loop simultaneously, others perfor…
View article: All eukaryotic SMC proteins induce a twist of −0.6 at each DNA loop extrusion step
All eukaryotic SMC proteins induce a twist of −0.6 at each DNA loop extrusion step Open
Eukaryotes carry three types of structural maintenance of chromosome (SMC) protein complexes, condensin, cohesin, and SMC5/6, which are ATP-dependent motor proteins that remodel the genome via DNA loop extrusion (LE). SMCs modulate DNA sup…
View article: All eukaryotic SMC proteins induce a twist of -0.6 at each DNA-loop-extrusion step
All eukaryotic SMC proteins induce a twist of -0.6 at each DNA-loop-extrusion step Open
Eukaryotes carry three types of Structural Maintenance of Chromosomes (SMC) protein complexes, condensin, cohesin, and SMC5/6, which are ATP-dependent motor proteins that remodel the genome via DNA loop extrusion. SMCs modulate DNA superco…
View article: Cohesin supercoils DNA during loop extrusion
Cohesin supercoils DNA during loop extrusion Open
Cohesin extrudes genomic DNA into loops that promote chromatin assembly, gene regulation and recombination. Here we show that cohesin introduces negative supercoils into extruded DNA. Supercoiling requires engagement of cohesin’s ATPase he…
View article: SMC motor proteins extrude DNA asymmetrically and contain a direction switch
SMC motor proteins extrude DNA asymmetrically and contain a direction switch Open
Summary Structural Maintenance of Chromosomes (SMC) complexes organize the genome via DNA loop extrusion. While some SMCs were reported to do so symmetrically, reeling DNA from both sides into the extruded DNA loop simultaneously, others p…
View article: Single-molecule visualization of twin-supercoiled domains generated during transcription
Single-molecule visualization of twin-supercoiled domains generated during transcription Open
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 that, during transcription, the DNA-dependent RNA polymerase …
View article: Telomere protein arrays stall DNA loop extrusion by condensin
Telomere protein arrays stall DNA loop extrusion by condensin Open
DNA loop extrusion by SMC proteins is a key process underlying chromosomal organization. It is unknown how loop extruders interact with telomeres where chromosome ends are covered with a dense array of tens of neighboring DNA-binding prote…
View article: Dynamic ParB–DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation
Dynamic ParB–DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation Open
In most bacteria, chromosome segregation is driven by the ParABS system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex …
View article: Single-molecule visualization of twin-supercoiled domains generated during transcription
Single-molecule visualization of twin-supercoiled domains generated during transcription Open
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 that, during transcription, the DNA-dependent RNA polymerase …
View article: Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation
Dynamic ParB-DNA interactions initiate and maintain a partition condensate for bacterial chromosome segregation Open
In most bacteria, chromosome segregation is driven by the ParAB S system where the CTPase protein ParB loads at the parS site to trigger the formation of a large partition complex. Here, we present in vitro studies of the partition complex…
View article: Accompanying code for the publication de Franceschi et al., Nature Nanotechnology, 2023
Accompanying code for the publication de Franceschi et al., Nature Nanotechnology, 2023 Open
# Description The supplied python code is used to quantify the normalized fluorescence recovery ratio used to quantify liposome scission and hemiscission events, as well as events in which no scission occurred based on FRAP data. The code …
View article: Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments
Testing pseudotopological and nontopological models for SMC-driven DNA loop extrusion against roadblock-traversal experiments Open
DNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much debated. The…
View article: Looping the Genome with SMC Complexes
Looping the Genome with SMC Complexes Open
SMC (structural maintenance of chromosomes) protein complexes are an evolutionarily conserved family of motor proteins that hold sister chromatids together and fold genomes throughout the cell cycle by DNA loop extrusion. These complexes p…
View article: CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion
CTCF is a DNA-tension-dependent barrier to cohesin-mediated loop extrusion Open
In eukaryotes, genomic DNA is extruded into loops by cohesin 1 . By restraining this process, the DNA-binding protein CCCTC-binding factor (CTCF) generates topologically associating domains (TADs) 2,3 that have important roles in gene regu…
View article: Dynamin A as a one-component division machinery for synthetic cells
Dynamin A as a one-component division machinery for synthetic cells Open
Membrane abscission, the final cut of the last connection between emerging daughter cells, is an indispensable event in the last stage of cell division, as well as in other cellular processes such as endocytosis, virus release, or bacteria…
View article: Genome-wide analysis of the dynamic and biophysical properties of chromatin and nuclear proteins in living cells with Hi-D
Genome-wide analysis of the dynamic and biophysical properties of chromatin and nuclear proteins in living cells with Hi-D Open
To understand the dynamic nature of the genome in real-time, the localization and rearrangement of DNA and DNA-binding proteins must be analyzed across the entire nucleus of single living cells. Recently, we developed a new computational l…
View article: SMC complexes can traverse physical roadblocks bigger than their ring size
SMC complexes can traverse physical roadblocks bigger than their ring size Open
Ring-shaped structural maintenance of chromosomes (SMC) complexes like condensin and cohesin extrude loops of DNA. It remains, however, unclear how they can extrude DNA loops in chromatin that is bound with proteins. Here, we use in vitro …
View article: CTCF is a DNA-tension-dependent barrier to cohesin-mediated DNA loop extrusion
CTCF is a DNA-tension-dependent barrier to cohesin-mediated DNA loop extrusion Open
In eukaryotes, genomic DNA is extruded into loops by cohesin 1 . By restraining this process, the DNA-binding protein CTCF generates topologically associating domains (TADs) 2-4 that play key roles in gene regulation and recombination duri…
View article: Dataset for the article "Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion" by Roman Barth and Haitham Shaban
Dataset for the article "Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion" by Roman Barth and Haitham Shaban Open
The data set comprises all raw microscopy images and DFCC analyses as presented in Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion by Roman Barth and Haitham Shaban, published …
View article: Dataset for the article "Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion" by Roman Barth and Haitham Shaban
Dataset for the article "Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion" by Roman Barth and Haitham Shaban Open
The data set comprises all raw microscopy images and DFCC analyses as presented in Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion by Roman Barth and Haitham Shaban, published …
View article: Can pseudotopological models for SMC-driven DNA loop extrusion explain the traversal of physical roadblocks bigger than the SMC ring size?
Can pseudotopological models for SMC-driven DNA loop extrusion explain the traversal of physical roadblocks bigger than the SMC ring size? Open
SUMMARY DNA loop extrusion by structural-maintenance-of-chromosome (SMC) complexes has emerged as a primary organizing principle for chromosomes. The mechanism by which SMC motor proteins extrude DNA loops is still unresolved and much deba…
View article: ParB proteins can bypass DNA-bound roadblocks via dimer-dimer recruitment
ParB proteins can bypass DNA-bound roadblocks via dimer-dimer recruitment Open
The ParAB S system is essential for prokaryotic chromosome segregation. After loading at parS on the genome, ParB (partition protein B) proteins rapidly redistribute to distances of ~15 kilobases from the loading site. It has remained puzz…
View article: Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion
Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion Open
Gene transcription by RNA polymerase II (RNAPol II) is a tightly regulated process in the genomic, temporal, and spatial context. Recently, we have shown that chromatin exhibits spatially coherently moving regions over the entire nucleus, …
View article: Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion
Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion Open
Gene transcription by RNA polymerase II (RNAP II) is a tightly regulated process in the genomic, temporal, and spatial context. Transcriptionally active genes often spatially cluster at RNA Pol II foci, called transcription factories, caus…