scholarly journals Dependency of ISW1a Chromatin Remodeling on Extranucleosomal DNA

2007 ◽  
Vol 27 (8) ◽  
pp. 3217-3225 ◽  
Author(s):  
Vamsi K. Gangaraju ◽  
Blaine Bartholomew
Keyword(s):  
Atpase Activity ◽  
Chromatin Remodeling ◽  
Molecular Basis ◽  
The Other ◽  
Entry And Exit ◽  
Exit Site ◽  
Optimal Length ◽  
Nucleosome Remodeling ◽  
Dna Footprinting ◽  
Nucleosomal Dna

ABSTRACT The nucleosome remodeling activity of ISW1a was dependent on whether ISW1a was bound to one or both extranucleosomal DNAs. ISW1a preferentially bound nucleosomes with an optimal length of ∼33 to 35 bp of extranucleosomal DNA at both the entry and exit sites over nucleosomes with extranucleosomal DNA at only one entry or exit site. Nucleosomes with extranucleosomal DNA at one of the entry/exit sites were readily remodeled by ISW1a and stimulated the ATPase activity of ISW1a, while conversely, nucleosomes with extranucleosomal DNA at both entry/exit sites were unable either to stimulate the ATPase activity of ISW1a or to be mobilized. DNA footprinting revealed that a major conformational difference between the nucleosomes was the lack of ISW1a binding to nucleosomal DNA two helical turns from the dyad axis in nucleosomes with extranucleosomal DNA at both entry/exit sites. The Ioc3 subunit of ISW1a was found to be the predominant subunit associated with extranucleosomal DNA when ISW1a is bound either to one or to both extranucleosomal DNAs. These two conformations of the ISW1a-nucleosome complex are suggested to be the molecular basis for the nucleosome spacing activity of ISW1a on nucleosomal arrays. ISW1b, the other isoform of ISW1, does not have the same dependency for extranucleosomal DNA as ISW1a and, likewise, is not able to space nucleosomes.

scholarly journals Regulation of ISW2 by Concerted Action of Histone H4 Tail and Extranucleosomal DNA

2006 ◽  
Vol 26 (20) ◽  
pp. 7388-7396 ◽  
Author(s):  
Weiwei Dang ◽  
Mohamedi N. Kagalwala ◽  
Blaine Bartholomew
Keyword(s):  
Incubation Time ◽  
Photoaffinity Labeling ◽  
Histone H4 ◽  
Concerted Action ◽  
Optimal Length ◽  
Nucleosome Remodeling ◽  
Dna Footprinting ◽  
Nucleosomal Dna ◽  
Histone Octamers

ABSTRACT The stable contact of ISW2 with nucleosomal DNA ∼20 bp from the dyad was shown by DNA footprinting and photoaffinity labeling using recombinant histone octamers to require the histone H4 N-terminal tail. Efficient ISW2 remodeling also required the H4 N-terminal tail, although the lack of the H4 tail can be mostly compensated for by increasing the incubation time or concentration of ISW2. Similarly, the length of extranucleosomal DNA affected the stable contact of ISW2 with this same internal nucleosomal site, with the optimal length being 70 to 85 bp. These data indicate the histone H4 tail, in concert with a favorable length of extranucleosomal DNA, recruits and properly orients ISW2 onto the nucleosome for efficient nucleosome remodeling. One consequence of this property of ISW2 is likely its previously observed nucleosome spacing activity.

Models for chromatin remodeling: a critical comparison

2003 ◽  
Vol 81 (3) ◽  
pp. 169-172 ◽  
Author(s):  
K van Holde ◽  
T Yager
Keyword(s):  
Diffusion Model ◽  
Chromatin Remodeling ◽  
Experimental Studies ◽  
Nucleosome Remodeling ◽  
Defect Generation ◽  
Critical Comparison ◽  
Nucleosomal Dna ◽  
Reptation Model ◽  
Cast Doubt ◽  
Random Diffusion

Nucleosome remodeling has been shown, in many cases, to involve cis displacement of nucleosomes on the DNA. This process seems similar to the long-recognized random diffusion of nucleosomes along DNA, but the remodeling process is unidirectional and ATP dependent. Several years ago, we developed a model for nucleosome migration, based on the diffusion of "twist-defects" within the nucleosomal DNA. This has been modified into a model that incorporates ATP-dependent defect generation, and can account for many observations concerning remodeling. However, certain experimental studies in recent years have cast doubt on the applicability of the twist-diffusion model for remodeling, and seem to favor instead a "reptation" model. We discuss herein these problems and propose a resolution.Key words: nucleosome, remodeling, chromatin.

scholarly journals Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling

2021 ◽  
Vol 118 (36) ◽  
pp. e2107277118
Author(s):  
Soon-Keat Ooi ◽  
Shigeo Sato ◽  
Chieri Tomomori-Sato ◽  
Ying Zhang ◽  
Zhihui Wen ◽  
...  
Keyword(s):  
Liver Cancer ◽  
Atpase Activity ◽  
Chromatin Remodeling ◽  
Multiple Roles ◽  
Nucleosome Remodeling ◽  
Multiple Functions

The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+. A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.

scholarly journals Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome

2019 ◽  
Vol 47 (17) ◽  
pp. 9400-9409 ◽  
Author(s):  
Sagar Chittori ◽  
Jingjun Hong ◽  
Yawen Bai ◽  
Sriram Subramaniam
Keyword(s):  
Electron Microscopy ◽  
Chromatin Remodeling ◽  
Initial Step ◽  
Atpase Domain ◽  
Nucleosome Remodeling ◽  
Cryo Electron Microscopy ◽  
Nucleosomal Dna ◽  
Primed State ◽  
Histone Core

Abstract ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the nucleosome bound to an ISWI fragment with deletion of the AutoN and HSS regions in nucleotide-free conditions and the free nucleosome at ∼ 4 Å resolution. In the bound conformation, the ATPase domain interacts with the super helical location 2 (SHL 2) of the nucleosomal DNA, with the N-terminal tail of H4 and with the α1 helix of H3. Density for other regions of ISWI is not observed, presumably due to disorder. Comparison with the structure of the free nucleosome reveals that although the histone core remains largely unchanged, remodeler binding causes perturbations in the nucleosomal DNA resulting in a bulge near the SHL2 site. Overall, the structure of the nucleotide-free ISWI-nucleosome complex is similar to the corresponding regions of the recently reported ADP bound ISWI-nucleosome structures, which are significantly different from that observed for the ADP-BeFx bound structure. Our findings are relevant to the initial step of ISWI binding to the nucleosome and provide additional insights into the nucleosome remodeling process driven by ISWI.

scholarly journals Novel Interactions of ESCRT-III with LIP5 and VPS4 and their Implications for ESCRT-III Disassembly

2008 ◽  
Vol 19 (6) ◽  
pp. 2661-2672 ◽  
Author(s):  
Soomin Shim ◽  
Samuel A. Merrill ◽  
Phyllis I. Hanson
Keyword(s):  
Atpase Activity ◽  
Binding Site ◽  
Binding Sites ◽  
Essential Role ◽  
Multivesicular Body ◽  
The Other ◽  
Aaa Atpase ◽  
Direct Binding ◽  
Novel Interactions

The AAA+ ATPase VPS4 plays an essential role in multivesicular body biogenesis and is thought to act by disassembling ESCRT-III complexes. VPS4 oligomerization and ATPase activity are promoted by binding to LIP5. LIP5 also binds to the ESCRT-III like protein CHMP5/hVps60, but how this affects its function remains unclear. Here we confirm that LIP5 binds tightly to CHMP5, but also find that it binds well to additional ESCRT-III proteins including CHMP1B, CHMP2A/hVps2–1, and CHMP3/hVps24 but not CHMP4A/hSnf7–1 or CHMP6/hVps20. LIP5 binds to a different region within CHMP5 than within the other ESCRT-III proteins. In CHMP1B and CHMP2A, its binding site encompasses sequences at the proteins' extreme C-termini that overlap with “MIT interacting motifs” (MIMs) known to bind to VPS4. We find unexpected evidence of a second conserved binding site for VPS4 in CHMP2A and CHMP1B, suggesting that LIP5 and VPS4 may bind simultaneously to these proteins despite the overlap in their primary binding sites. Finally, LIP5 binds preferentially to soluble CHMP5 but instead to polymerized CHMP2A, suggesting that the newly defined interactions between LIP5 and ESCRT-III proteins may be regulated by ESCRT-III conformation. These studies point to a role for direct binding between LIP5 and ESCRT-III proteins that is likely to complement LIP5's previously described ability to regulate VPS4 activity.

scholarly journals The SWI/SNF Complex Creates Loop Domains in DNA and Polynucleosome Arrays and Can Disrupt DNA-Histone Contacts within These Domains

1999 ◽  
Vol 19 (2) ◽  
pp. 1470-1478 ◽  
Author(s):  
David P. Bazett-Jones ◽  
Jacques Côté ◽  
Carolyn C. Landel ◽  
Craig L. Peterson ◽  
Jerry L. Workman
Keyword(s):  
Chromatin Remodeling ◽  
Dna Content ◽  
Naked Dna ◽  
Nucleosome Organization ◽  
Nucleosomal Dna ◽  
Close Proximity ◽  
Loop Domains

ABSTRACT To understand the mechanisms by which the chromatin-remodeling SWI/SNF complex interacts with DNA and alters nucleosome organization, we have imaged the SWI/SNF complex with both naked DNA and nucleosomal arrays by using energy-filtered microscopy. By making ATP-independent contacts with DNA at multiple sites on its surface, SWI/SNF creates loops, bringing otherwise-distant sites into close proximity. In the presence of ATP, SWI/SNF action leads to the disruption of nucleosomes within domains that appear to be topologically constrained by the complex. The data indicate that the action of one SWI/SNF complex on an array of nucleosomes can lead to the formation of a region where multiple nucleosomes are disrupted. Importantly, nucleosome disruption by SWI/SNF results in a loss of DNA content from the nucleosomes. This indicates a mechanism by which SWI/SNF unwraps part of the nucleosomal DNA.

scholarly journals Contribution to the research of the chemical intensity erosion in the western Serbia

2003 ◽  
Vol 83 (1) ◽  
pp. 7-14 ◽  
Author(s):  
Slavoljub Dragicevic ◽  
Predrag Manojlovic ◽  
Sanja Mustafic
Keyword(s):  
Analytical Method ◽  
River Basins ◽  
Meteorological Conditions ◽  
The Other ◽  
Entry And Exit ◽  
Chemical Erosion ◽  
Time Period ◽  
Erosion Intensity

Based on the research of the chemical erosion intensity in the upper course of Tamnava, the appearance of its negative value has been found. Further researches, that enclose the lower course, confirmed this fact. This research opened the important question about the causes of this phenomena. Analytical method eliminated all expected causes and led to conclusion that the reason for this should be found by using the more precise research of the mineralisation of the precipitations. It was necessary to continue the measurings of the precipitation mineralisation in the greater number of locations and in the wider time period, as well as in the different meteorological conditions, and after that to establish the subordination between the amount of precipitations and the entered TDS. Only after these additive researches we could be able to find out the relation between ''entry'' and ''exit'' and to find out the intensity of the chemical erosion in this, and in the other river basins. For now, we are able only to find out the carrying of TDS, as well as the reduction of the chemical evacuation for the non - carbonated part of the basin (corrected value).

scholarly journals The molecular mechanism of the inherited phosphofructokinase deficiency associated with hemolysis and myopathy

Blood ◽  
1980 ◽  
Vol 55 (4) ◽  
pp. 629-635
Author(s):  
S Vora ◽  
L Corash ◽  
WK Engel ◽  
S Durham ◽  
C Seaman ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Direct Evidence ◽  
The Other ◽  
Heterogeneous Mixture ◽  
Muscle Type ◽  
Crossover Point ◽  
Normal Human ◽  
Phosphofructokinase Deficiency ◽  
2,3 Dpg ◽  
Chromatographic Profiles

Normal human erythrocyte phosphofructokinase (ATP:c D-fructose-6, P-1- phosphotransferase, EC 2.7.1.11; PFK) has recently been shown to consist of a heterogeneous mixture of five tetrameric isozymes: M4, M3L, M2L2, ML3, and L4 (M, muscle type; L, liver type). In the light of these findings, we have investigated the molecular basis of the inherited erythrocyte PFK deficiency associated with myopathy and hemolysis (Tarui disease). The propositus, a 31-yr-old male, suffered from muscle weakness and myoglobinuria on exertion. He showed mild erythrocytosis despite laboratory evidence of hemolysis. In his erythrocytes a metabolic crossover point was found at the level of PFK; 2,3-diphosphoglycerate (2,3-DPG) was also significantly reduced. The PFK from the patient's erythrocytes consisted exclusively of the L4 isozyme, and there was a complete absence of the other four. The leukocyte and platelet PFKs from the patient showed normal activities, chromatographic profiles, and precipitation with anti-M4 antibody. These studies provide direct evidence that in Tarui disease the M-type subunits are absent; but the liver- and platelet-type subunits of PFK are unaffected. The paradox of mild erythrocytosis despite hemolysis reflects the decreased production of 2,3-DPG.

Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting

2021 ◽  
Author(s):  
Ineke Brouwer ◽  
Emma Kerklingh ◽  
Fred van Leeuwen ◽  
Tineke L Lenstra
Keyword(s):  
Transcription Factor ◽  
Chromatin Remodeling ◽  
Single Molecule ◽  
Binding Sites ◽  
Live Cell Imaging ◽  
Cell Imaging ◽  
Nucleosome Remodeling ◽  
Epistasis Analysis ◽  
Transcriptional Bursting ◽  
Kinetics Of

Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in budding yeast to measure how transcriptional bursting changes upon single and double perturbations of chromatin remodeling factors, the transcription factor Gal4 and preinitiation complex (PIC) components. Using dynamic epistasis analysis, we reveal how remodeling of different nucleosomes regulates individual transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC acts synergistically with Gal4 binding to facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. In the absence of remodelers, nucleosomes at canonical TATA boxes are displaced by TBP binding to allow for transcription activation. Overall, our results reveal how promoter nucleosome remodeling, together with transcription factor and PIC binding regulates the kinetics of transcriptional bursting.

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