scholarly journals Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells

2020 ◽  
Author(s):  
Sarah G. Swygert ◽  
Dejun Lin ◽  
Stephanie Portillo-Ledesma ◽  
Po-Yen Lin ◽  
Dakota R. Hunt ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Chromatin Fiber ◽  
Cellular Processes ◽  
Quiescent Cells ◽  
Physiological Relevance ◽  
Local Compaction ◽  
Chromatin Fibers ◽  
In Cells

AbstractDetermining the conformation of chromatin in cells at the nucleosome level and its relationship to cellular processes has been a central challenge in biology. We show that in quiescent yeast, widespread transcriptional repression coincides with the local compaction of chromatin fibers into structures that are less condensed and more heteromorphic than canonical 30-nanometer forms. Acetylation or substitution of H4 tail residues decompacts fibers and leads to global transcriptional de-repression. Fiber decompaction also increases the rate of loop extrusion by condensin. These findings establish a role for H4 tail-dependent local chromatin fiber folding in regulating transcription and loop extrusion in cells. They also demonstrate the physiological relevance of canonical chromatin fiber folding mechanisms even in the absence of regular 30-nanometer structures.

scholarly journals Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Sarah G Swygert ◽  
Dejun Lin ◽  
Stephanie Portillo-Ledesma ◽  
Po-Yen Lin ◽  
Dakota R Hunt ◽  
...  
Keyword(s):  
Chromatin Fiber ◽  
State Transitions ◽  
Chromatin Domain ◽  
Global Changes ◽  
Histone H4 ◽  
Mitotic Chromosomes ◽  
Quiescent Cells ◽  
Genome Wide ◽  
Dividing Cells ◽  
The Relationship

A longstanding hypothesis is that chromatin fiber folding mediated by interactions between nearby nucleosomes represses transcription. However, it has been difficult to determine the relationship between local chromatin fiber compaction and transcription in cells. Further, global changes in fiber diameters have not been observed, even between interphase and mitotic chromosomes. We show that an increase in the range of local inter-nucleosomal contacts in quiescent yeast drives the compaction of chromatin fibers genome-wide. Unlike actively dividing cells, inter-nucleosomal interactions in quiescent cells require a basic patch in the histone H4 tail. This quiescence-specific fiber folding globally represses transcription and inhibits chromatin loop extrusion by condensin. These results reveal that global changes in chromatin fiber compaction can occur during cell state transitions, and establish physiological roles for local chromatin fiber folding in regulating transcription and chromatin domain formation.

scholarly journals Diffusion in the aqueous compartment.

1984 ◽  
Vol 99 (1) ◽  
pp. 180s-187s ◽  
Author(s):  
A M Mastro ◽  
A D Keith
Keyword(s):  
Rotational Motion ◽  
Spin Label ◽  
Mammalian Cells ◽  
Translational Motion ◽  
Diffusion Constant ◽  
Rotational Correlation Time ◽  
Model Systems ◽  
Quiescent Cells ◽  
Spin Resonance ◽  
In Cells

Measurements of diffusion of molecules in cells can provide information about cytoplasmic viscosity and structure. In a series of studies electron-spin resonance was used to measure the diffusion of a small spin label in the aqueous cytoplasm of mammalian cells. Translational and rotational motion were determined from the same spectra. Based on measurements made in model systems, it was hypothesized that calculations of the apparent viscosity of the cytoplasm from both rotational and translational motion would distinguish between the effects of viscosity and structure on diffusion. The diffusion constant measured in several cell lines averaged 3.3 X 10(-6) cm2/s. It was greater in growing cells and in cells treated with cytochalasin B than in quiescent cells. The viscosity of the cytoplasm calculated from the translational diffusion constant or the rotational correlation time was 2.0-3.0 centipoise, about two to three times that of the spin label in water. Therefore, over the dimensions measured by the technique, 50-100 A, solvent viscosity appears to be the major determinant of particle movement in cells under physiologic conditions. However, when cells were subjected to hypertonic conditions, the translational motion of the spin label decreased threefold, whereas the rotational motion changed by less than 20%. These data suggest that the decrease in cell volume under hypertonic conditions is accompanied by an increase in cytoplasmic barriers and a decrease in the space between existing cytoplasmic components without a significant increase in viscosity in the aqueous phase. In addition, a comparison of reported diffusion values of a variety of molecules in water and in cells indicates that cytoplasmic structure plays an important role in the diffusion of proteins such as bovine serum albumin.

scholarly journals Vesicle Size Regulates Nanotube Formation in the Cell

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Qian Peter Su ◽  
Wanqing Du ◽  
Qinghua Ji ◽  
Boxin Xue ◽  
Dong Jiang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Model Systems ◽  
Organelle Biogenesis ◽  
Membrane Deformation ◽  
Vesicle Size ◽  
Cellular Processes ◽  
Vesicle Recycling ◽  
Physiological Relevance

Abstract Intracellular membrane nanotube formation and its dynamics play important roles for cargo transportation and organelle biogenesis. Regarding the regulation mechanisms, while much attention has been paid on the lipid composition and its associated protein molecules, effects of the vesicle size has not been studied in the cell. Giant unilamellar vesicles (GUVs) are often used for in vitro membrane deformation studies, but they are much larger than most intracellular vesicles and the in vitro studies also lack physiological relevance. Here, we use lysosomes and autolysosomes, whose sizes range between 100 nm and 1 μm, as model systems to study the size effects on nanotube formation both in vivo and in vitro. Single molecule observations indicate that driven by kinesin motors, small vesicles (100–200 nm) are mainly transported along the tracks while a remarkable portion of large vesicles (500–1000 nm) form nanotubes. This size effect is further confirmed by in vitro reconstitution assays on liposomes and purified lysosomes and autolysosomes. We also apply Atomic Force Microscopy (AFM) to measure the initiation force for nanotube formation. These results suggest that the size-dependence may be one of the mechanisms for cells to regulate cellular processes involving membrane-deformation, such as the timing of tubulation-mediated vesicle recycling.

scholarly journals An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Amir Momen-Roknabadi ◽  
Panos Oikonomou ◽  
Maxwell Zegans ◽  
Saeed Tavazoie
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptional Repression ◽  
Nucleosome Occupancy ◽  
Design Parameters ◽  
Experimental Conditions ◽  
Crispr Interference ◽  
Cellular Processes ◽  
Genome Wide ◽  
Reliable Assessment ◽  
A Genome

AbstractGenome-scale CRISPR interference (CRISPRi) is widely utilized to study cellular processes in a variety of organisms. Despite the dominance of Saccharomyces cerevisiae as a model eukaryote, an inducible genome-wide CRISPRi library in yeast has not yet been presented. Here, we present a genome-wide, inducible CRISPRi library, based on spacer design rules optimized for S. cerevisiae. We have validated this library for genome-wide interrogation of gene function across a variety of applications, including accurate discovery of haploinsufficient genes and identification of enzymatic and regulatory genes involved in adenine and arginine biosynthesis. The comprehensive nature of the library also revealed refined spacer design parameters for transcriptional repression, including location, nucleosome occupancy and nucleotide features. CRISPRi screens using this library can identify genes and pathways with high precision and a low false discovery rate across a variety of experimental conditions, enabling rapid and reliable assessment of genetic function and interactions in S. cerevisiae.

scholarly journals Cas3 Protein—A Review of a Multi-Tasking Machine

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 208 ◽  
Author(s):  
Liu He ◽  
Michael St. John James ◽  
Marin Radovcic ◽  
Ivana Ivancic-Bace ◽  
Edward L. Bolt
Keyword(s):  
Cell Biology ◽  
Protein A ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Cellular Processes ◽  
Concise Review ◽  
In Cells

Cas3 has essential functions in CRISPR immunity but its other activities and roles, in vitro and in cells, are less widely known. We offer a concise review of the latest understanding and questions arising from studies of Cas3 mechanism during CRISPR immunity, and highlight recent attempts at using Cas3 for genetic editing. We then spotlight involvement of Cas3 in other aspects of cell biology, for which understanding is lacking—these focus on CRISPR systems as regulators of cellular processes in addition to defense against mobile genetic elements.

scholarly journals The PRH/Hex repressor protein causes nuclear retention of Groucho/TLE co-repressors

2008 ◽  
Vol 417 (1) ◽  
pp. 121-132 ◽  
Author(s):  
Cecile Desjobert ◽  
Peter Noy ◽  
Tracey Swingler ◽  
Hannah  Williams ◽  
Kevin Gaston ◽  
...  
Keyword(s):  
Transcriptional Repression ◽  
Dominant Negative ◽  
Vertebrate Development ◽  
Nuclear Retention ◽  
Subnuclear Localization ◽  
Cellular Processes ◽  
Haematopoietic Cells ◽  
Repressor Proteins ◽  
Homeobox Protein ◽  
Important Regulator

The PRH (proline-rich homeodomain) [also known as Hex (haematopoietically expressed homeobox)] protein is a transcription factor that functions as an important regulator of vertebrate development and many other processes in the adult including haematopoiesis. The Groucho/TLE (transducin-like enhancer) family of co-repressor proteins also regulate development and modulate the activity of many DNA-binding transcription factors during a range of diverse cellular processes including haematopoiesis. We have shown previously that PRH is a repressor of transcription in haematopoietic cells and that an Eh-1 (Engrailed homology) motif present within the N-terminal transcription repression domain of PRH mediates binding to Groucho/TLE proteins and enables co-repression. In the present study we demonstrate that PRH regulates the nuclear retention of TLE proteins during cellular fractionation. We show that transcriptional repression and the nuclear retention of TLE proteins requires PRH to bind to both TLE and DNA. In addition, we characterize a trans-dominant-negative PRH protein that inhibits wild-type PRH activity by sequestering TLE proteins to specific subnuclear domains. These results demonstrate that transcriptional repression by PRH is dependent on TLE availability and suggest that subnuclear localization of TLE plays an important role in transcriptional repression by PRH.

SAFB1- and SAFB2-mediated transcriptional repression: relevance to cancer

2012 ◽  
Vol 40 (4) ◽  
pp. 826-830 ◽  
Author(s):  
Elaine A. Hong ◽  
Hannah L. Gautrey ◽  
David J. Elliott ◽  
Alison J. Tyson-Capper
Keyword(s):  
Stress Response ◽  
Cell Growth ◽  
Family Member ◽  
Potential Function ◽  
Transcriptional Repression ◽  
Current Knowledge ◽  
Present Review ◽  
Multifunctional Proteins ◽  
Cellular Processes ◽  
Attachment Factor

SAFB1 (scaffold attachment factor B1) and a second family member SAFB2, are multifunctional proteins implicated in a variety of cellular processes including cell growth, apoptosis and stress response. Their potential function as tumour suppressors has been proposed based on well-described roles in tran-scriptional repression. The present review summarizes the current knowledge of SAFB1 and SAFB2 proteins in transcriptional repression with relevance to cancer.

Dynamics of DNA Supercoils

Science ◽  
2012 ◽  
Vol 338 (6103) ◽  
pp. 94-97 ◽  
Author(s):  
M. T. J. van Loenhout ◽  
M. V. de Grunt ◽  
C. Dekker
Keyword(s):  
Ionic Strength ◽  
Long Range ◽  
Time Scale ◽  
Double Helix ◽  
Long Distance ◽  
Cellular Processes ◽  
Millisecond Time Scale ◽  
In Cells

DNA in cells exhibits a supercoiled state in which the double helix is additionally twisted to form extended intertwined loops called plectonemes. Although supercoiling is vital to many cellular processes, its dynamics remain elusive. In this work, we directly visualize the dynamics of individual plectonemes. We observe that multiple plectonemes can be present and that their number depends on applied stretching force and ionic strength. Plectonemes moved along DNA by diffusion or, unexpectedly, by a fast hopping process that facilitated very rapid (<20 milliseconds) long-range plectoneme displacement by nucleating a new plectoneme at a distant position. These observations directly reveal the dynamics of plectonemes and identify a mode of movement that allows long-distance reorganization of the conformation of the genome on a millisecond time scale.

Dining in with BCL-2: new guests at the autophagy table

2009 ◽  
Vol 118 (3) ◽  
pp. 173-181 ◽  
Author(s):  
Marc Germain ◽  
Ruth S. Slack
Keyword(s):  
Nervous System ◽  
Neuronal Survival ◽  
Cell Loss ◽  
Active Role ◽  
Present Review ◽  
Cellular Processes ◽  
Catabolic Process ◽  
In Cells

BCL-2 homologues are major regulators of apoptosis and, as such, play an active role in the survival of adult neurons following injury. In recent years, these proteins have also been associated with the regulation of autophagy, a catabolic process involved in the recycling of nutrients upon starvation. Basal levels of autophagy are also required to eliminate damaged proteins and organelles. This is illustrated by the accumulation of ubiquitin-positive aggregates in cells deficient in autophagy and, in the nervous system, this is associated with progressive cell loss and signs of neurodegeneration. Given the importance of both apoptosis and autophagy for neuronal survival in adult neurons, understanding how BCL-2 homologues co-ordinately regulate these processes will allow a better understanding of the cellular processes leading to neurodegeneration. In the present review, we will discuss the roles of BCL-2 homologues in the regulation of apoptosis and autophagy, focussing on their impact on adult neurons.

scholarly journals Actin disassembly by cofilin, coronin, and Aip1 occurs in bursts and is inhibited by barbed-end cappers

2008 ◽  
Vol 182 (2) ◽  
pp. 341-353 ◽  
Author(s):  
Hao Yuan Kueh ◽  
Guillaume T. Charras ◽  
Timothy J. Mitchison ◽  
William M. Brieher
Keyword(s):  
Actin Filaments ◽  
Mammalian Cells ◽  
Cytochalasin D ◽  
Reaction Intermediates ◽  
Latrunculin B ◽  
Interacting Protein ◽  
Physiological Relevance ◽  
High Concentrations ◽  
End Capping ◽  
In Cells

Turnover of actin filaments in cells requires rapid actin disassembly in a cytoplasmic environment that thermodynamically favors assembly because of high concentrations of polymerizable monomers. We here image the disassembly of single actin filaments by cofilin, coronin, and actin-interacting protein 1, a purified protein system that reconstitutes rapid, monomer-insensitive disassembly (Brieher, W.M., H.Y. Kueh, B.A. Ballif, and T.J. Mitchison. 2006. J. Cell Biol. 175:315–324). In this three-component system, filaments disassemble in abrupt bursts that initiate preferentially, but not exclusively, from both filament ends. Bursting disassembly generates unstable reaction intermediates with lowered affinity for CapZ at barbed ends. CapZ and cytochalasin D (CytoD), a barbed-end capping drug, strongly inhibit bursting disassembly. CytoD also inhibits actin disassembly in mammalian cells, whereas latrunculin B, a monomer sequestering drug, does not. We propose that bursts of disassembly arise from cooperative separation of the two filament strands near an end. The differential effects of drugs in cells argue for physiological relevance of this new disassembly pathway and potentially explain discordant results previously found with these drugs.

Sign in / Sign up

Export Citation Format

Share Document