scholarly journals Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

2019 ◽  
Author(s):  
Felix R. Wagner ◽  
Christian Dienemann ◽  
Haibo Wang ◽  
Alexandra Stützer ◽  
Dimitry Tegunov ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Family Member ◽  
Chromatin Remodelling ◽  
Family Function ◽  
Histone Octamer ◽  
Nucleosomal Dna ◽  
Cancer Mutations ◽  
Key Features ◽  
Protein Modules ◽  
Eukaryote Genome

AbstractChromatin remodelling complexes of the SWI/SNF family function in the formation of nucleosome-depleted regions and transcriptionally active promoters in the eukaryote genome. The structure of the Saccharomyces cerevisiae SWI/SNF family member RSC in complex with a nucleosome substrate reveals five protein modules and suggests key features of the remodelling mechanism. A DNA-interacting module grasps extra-nucleosomal DNA and helps to recruit RSC to promoters. The ATPase and arm modules sandwich the nucleosome disc with their ‘SnAC’ and ‘finger’ elements, respectively. The translocase motor engages with the edge of the nucleosome at superhelical location +2 to pump DNA along the nucleosome, resulting in a sliding of the histone octamer along DNA. The results elucidate how nucleosome-depleted regions are formed and provide a basis for understanding human chromatin remodelling complexes of the SWI/SNF family and the consequences of cancer mutations that frequently occur in these complexes.

Heat shock factor can activate transcription while bound to nucleosomal DNA in Saccharomyces cerevisiae

1994 ◽  
Vol 14 (1) ◽  
pp. 189-199
Author(s):  
D S Pederson ◽  
T Fidrych
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Heat Shock ◽  
Transcription Initiation ◽  
Heat Shock Factor ◽  
Micrococcal Nuclease ◽  
Nucleosome Assembly ◽  
Heat Shock Element ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nucleosomal Dna

After each round of replication, new transcription initiation complexes must assemble on promoter DNA. This process may compete with packaging of the same promoter sequences into nucleosomes. To elucidate interactions between regulatory transcription factors and nucleosomes on newly replicated DNA, we asked whether heat shock factor (HSF) could be made to bind to nucleosomal DNA in vivo. A heat shock element (HSE) was embedded at either of two different sites within a DNA segment that directs the formation of a stable, positioned nucleosome. The resulting DNA segments were coupled to a reporter gene and transfected into the yeast Saccharomyces cerevisiae. Transcription from these two plasmid constructions after induction by heat shock was similar in amount to that from a control plasmid in which HSF binds to nucleosome-free DNA. High-resolution genomic footprint mapping of DNase I and micrococcal nuclease cleavage sites indicated that the HSE in these two plasmids was, nevertheless, packaged in a nucleosome. The inclusion of HSE sequences within (but relatively close to the edge of) the nucleosome did not alter the position of the nucleosome which formed with the parental DNA fragment. Genomic footprint analyses also suggested that the HSE-containing nucleosome was unchanged by the induction of transcription. Quantitative comparisons with control plasmids ruled out the possibility that HSF was bound only to a small fraction of molecules that might have escaped nucleosome assembly. Analysis of the helical orientation of HSE DNA in the nucleosome indicated that HSF contacted DNA residues that faced outward from the histone octamer. We discuss the significance of these results with regard to the role of nucleosomes in inhibiting transcription and the normal occurrence of nucleosome-free regions in promoters.

scholarly journals Capped mRNA Degradation Intermediates Accumulate in the Yeast spb8-2 Mutant

1998 ◽  
Vol 18 (9) ◽  
pp. 5062-5072 ◽  
Author(s):  
Ronald Boeck ◽  
Bruno Lapeyre ◽  
Christine E. Brown ◽  
Alan B. Sachs
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Family Member ◽  
Gene Deletion ◽  
Binding Protein ◽  
Mrna Degradation ◽  
Protein Family ◽  
Suppressor Mutation ◽  
Mrna Decapping ◽  
Mrna Species ◽  
Degradation Intermediates

ABSTRACT mRNA in the yeast Saccharomyces cerevisiae is primarily degraded through a pathway that is stimulated by removal of the mRNA cap structure. Here we report that a mutation in the SPB8(YJL124c) gene, initially identified as a suppressor mutation of a poly(A)-binding protein (PAB1) gene deletion, stabilizes the mRNA cap structure. Specifically, we find that thespb8-2 mutation results in the accumulation of capped, poly(A)-deficient mRNAs. The presence of this mutation also allows for the detection of mRNA species trimmed from the 3′ end. These data show that this Sm-like protein family member is involved in the process of mRNA decapping, and they provide an example of 3′-5′ mRNA degradation intermediates in yeast.

scholarly journals The AMPK Family Member Snf1 Protects Saccharomyces cerevisiae Cells upon Glutathione Oxidation

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e58283 ◽  
Author(s):  
Maria Pérez-Sampietro ◽  
Celia Casas ◽  
Enrique Herrero
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Family Member ◽  
Glutathione Oxidation

scholarly journals Nucleosome Remodeling by the Human SWI/SNF Complex Requires Transient Global Disruption of Histone-DNA Interactions

2002 ◽  
Vol 22 (11) ◽  
pp. 3653-3662 ◽  
Author(s):  
Sayura Aoyagi ◽  
Geeta Narlikar ◽  
Chunyang Zheng ◽  
Saïd Sif ◽  
Robert E. Kingston ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Atp Hydrolysis ◽  
Dnase I ◽  
Cross Linking ◽  
Dna Interactions ◽  
Nucleosome Remodeling ◽  
Histone Octamer ◽  
Nucleosomal Dna ◽  
Single Cross ◽  
A Site

ABSTRACT We utilized a site-specific cross-linking technique to investigate the mechanism of nucleosome remodeling by hSWI/SNF. We found that a single cross-link between H2B and DNA virtually eliminates the accumulation of stably remodeled species as measured by restriction enzyme accessibility assays. However, cross-linking the histone octamer to nucleosomal DNA does not inhibit remodeling as monitored by DNase I digestion assays. Importantly, we found that the restriction enzyme-accessible species can be efficiently cross-linked after remodeling and that the accessible state does not require continued ATP hydrolysis. These results imply that the generation of stable remodeled states requires at least transient disruption of histone-DNA interactions throughout the nucleosome, while hSWI/SNF-catalyzed disruption of just local histone-DNA interactions yields less-stable remodeled states that still display an altered DNase I cleavage pattern. The implications of these results for models of the mechanism of SWI/SNF-catalyzed nucleosome remodeling are discussed.

scholarly journals Molecular mechanisms of microtubule-dependent kinetochore transport toward spindle poles

2007 ◽  
Vol 178 (2) ◽  
pp. 269-281 ◽  
Author(s):  
Kozo Tanaka ◽  
Etsushi Kitamura ◽  
Yoko Kitamura ◽  
Tomoyuki U. Tanaka
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Family Member ◽  
Lateral Surface ◽  
Molecular Mechanisms ◽  
Microtubule Depolymerization ◽  
Spindle Poles ◽  
Dam1 Complex ◽  
Pulling Force

In mitosis, kinetochores are initially captured by the lateral sides of single microtubules and are subsequently transported toward spindle poles. Mechanisms for kinetochore transport are not yet known. We present two mechanisms involved in microtubule-dependent poleward kinetochore transport in Saccharomyces cerevisiae. First, kinetochores slide along the microtubule lateral surface, which is mainly and probably exclusively driven by Kar3, a kinesin-14 family member that localizes at kinetochores. Second, kinetochores are tethered at the microtubule distal ends and pulled poleward as microtubules shrink (end-on pulling). Kinetochore sliding is often converted to end-on pulling, enabling more processive transport, but the opposite conversion is rare. The establishment of end-on pulling is partly hindered by Kar3, and its progression requires the Dam1 complex. We suggest that the Dam1 complexes, which probably encircle a single microtubule, can convert microtubule depolymerization into the poleward kinetochore-pulling force. Thus, microtubule-dependent poleward kinetochore transport is ensured by at least two distinct mechanisms.

scholarly journals A Novel Cas Family Member, HEPL, Regulates FAK and Cell Spreading

2008 ◽  
Vol 19 (4) ◽  
pp. 1627-1636 ◽  
Author(s):  
Mahendra K. Singh ◽  
Disha Dadke ◽  
Emmanuelle Nicolas ◽  
Ilya G. Serebriiskii ◽  
Sinoula Apostolou ◽  
...  
Keyword(s):  
Family Member ◽  
Cell Invasion ◽  
Focal Adhesions ◽  
Cell Spreading ◽  
Protein Family ◽  
Scaffolding Protein ◽  
Family Function ◽  
Evolutionarily Conserved ◽  
Complete Protein ◽  
Cas Proteins

For over a decade, p130Cas/BCAR1, HEF1/NEDD9/Cas-L, and Efs/Sin have defined the Cas (Crk-associated substrate) scaffolding protein family. Cas proteins mediate integrin-dependent signals at focal adhesions, regulating cell invasion and survival; at least one family member, HEF1, regulates mitosis. We here report a previously undescribed novel branch of the Cas protein family, designated HEPL (for HEF1-Efs-p130Cas-like). The HEPL branch is evolutionarily conserved through jawed vertebrates, and HEPL is found in some species lacking other members of the Cas family. The human HEPL mRNA and protein are selectively expressed in specific primary tissues and cancer cell lines, and HEPL maintains Cas family function in localization to focal adhesions, as well as regulation of FAK activity, focal adhesion integrity, and cell spreading. It has recently been demonstrated that upregulation of HEF1 expression marks and induces metastasis, whereas high endogenous levels of p130Cas are associated with poor prognosis in breast cancer, emphasizing the clinical relevance of Cas proteins. Better understanding of the complete protein family should help inform prediction of cancer incidence and prognosis.

scholarly journals Remosomes: RSC generated non-mobilized particles with approximately 180 bp DNA loosely associated with the histone octamer

2010 ◽  
Vol 107 (5) ◽  
pp. 1936-1941 ◽  
Author(s):  
Manu Shubhdarshan Shukla ◽  
Sajad Hussain Syed ◽  
Fabien Montel ◽  
Cendrine Faivre-Moskalenko ◽  
Jan Bednar ◽  
...  
Keyword(s):  
Restriction Enzymes ◽  
Dna Interactions ◽  
One Pot ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Force Microscopy ◽  
Histone Octamer ◽  
Distinct Variable ◽  
Nucleosomal Dna ◽  
Dnase I Footprinting

Chromatin remodelers are sophisticated nano-machines that are able to alter histone-DNA interactions and to mobilize nucleosomes. Neither the mechanism of their action nor the conformation of the remodeled nucleosomes are, however, yet well understood. We have studied the mechanism of Remodels Structure of Chromatin (RSC)-nucleosome mobilization by using high-resolution microscopy and biochemical techniques. Atomic force microscopy and electron cryomicroscopy (EC-M) analyses show that two types of products are generated during the RSC remodeling: (i) stable non-mobilized particles, termed remosomes that contain about 180 bp of DNA associated with the histone octamer and, (ii) mobilized particles located at the end of DNA. EC-M reveals that individual remosomes exhibit a distinct, variable, highly-irregular DNA trajectory. The use of the unique “one pot assays” for studying the accessibility of nucleosomal DNA towards restriction enzymes, DNase I footprinting and ExoIII mapping demonstrate that the histone-DNA interactions within the remosomes are strongly perturbed, particularly in the vicinity of the nucleosome dyad. The data suggest a two-step mechanism of RSC-nucleosome remodeling consisting of an initial formation of a remosome followed by mobilization. In agreement with this model, we show experimentally that the remosomes are intermediate products generated during the first step of the remodeling reaction that are further efficiently mobilized by RSC.

scholarly journals Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

2018 ◽  
Author(s):  
Ramasubramanian Sundaramoorthy ◽  
Amanda L. Hughes ◽  
Hassane El-Mkami ◽  
David Norman ◽  
Tom Owen-Hughes
Keyword(s):  
Histone H3 ◽  
Bound State ◽  
Chromatin Remodelling ◽  
Dna Interactions ◽  
Histone Octamer ◽  
Nucleosome Structure ◽  
Protein Dna Interactions ◽  
Dna Strands ◽  
Regulate Protein ◽  
Related Proteins

AbstractATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here we present structures of the yeast Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.

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