scholarly journals Evidence for DNA Translocation by the ISWI Chromatin-Remodeling Enzyme

2003 ◽  
Vol 23 (6) ◽  
pp. 1935-1945 ◽  
Author(s):  
Iestyn Whitehouse ◽  
Chris Stockdale ◽  
Andrew Flaus ◽  
Mark D. Szczelkun ◽  
Tom Owen-Hughes
Keyword(s):  
Nucleic Acids ◽  
Atpase Activity ◽  
Chromatin Remodeling ◽  
Dna Translocation ◽  
Catalytic Core ◽  
Dna Translocase

ABSTRACT The ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin-remodeling activities. Here, we studied the interaction of the ISWI protein with nucleosomal substrates. We found that the ability of nucleic acids to bind and stimulate the ATPase activity of ISWI depends on length. We also found that ISWI is able to displace triplex-forming oligonucleotides efficiently when they are introduced at sites close to a nucleosome but successively less efficiently 30 to 60 bp from its edge. The ability of ISWI to direct triplex displacement was specifically impeded by the introduction of 5- or 10-bp gaps in the 3′-5′ strand between the triplex and the nucleosome. In combination, these observations suggest that ISWI is a 3′-5′-strand-specific, ATP-dependent DNA translocase that may be capable of forcing DNA over the surface of nucleosomes.

scholarly journals DNA Translocation and Loop Formation Mechanism of Chromatin Remodeling by SWI/SNF and RSC

2006 ◽  
Vol 24 (4) ◽  
pp. 559-568 ◽  
Author(s):  
Yongli Zhang ◽  
Corey L. Smith ◽  
Anjanabha Saha ◽  
Stephan W. Grill ◽  
Shirley Mihardja ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Formation Mechanism ◽  
Loop Formation ◽  
Dna Translocation

Functional diversity of ISWI complexes

2004 ◽  
Vol 82 (4) ◽  
pp. 482-489 ◽  
Author(s):  
Sara S Dirscherl ◽  
Jocelyn E Krebs
Keyword(s):  
Chromatin Remodeling ◽  
Catalytic Core ◽  
Chromatin Remodelers ◽  
Form And Function ◽  
Curr Opin Cell Biol ◽  
Chromatid Cohesion ◽  
Chromatin Remodeling Complexes ◽  
And Function ◽  
Diverse Groups ◽  
Nuclear Processes

The yeast SWI/SNF ATP-dependent chromatin remodeling complex was first identified and characterized over 10 years ago (F. Winston and M. Carlson. 1992. Trends Genet. 8: 387–391.) Since then, the number of distinct ATP-dependent chromatin remodeling complexes and the variety of roles they play in nuclear processes have become dizzying (J.A. Martens and F. Winston. 2003. Curr. Opin. Genet. Dev. 13: 136–142; A. Vacquero et al. 2003. Sci. Aging Knowledge Environ. 2003: RE4) — and that does not even include the companion suite of histone modifying enzymes, which exhibit a comparable diversity in both number of complexes and variety of functions (M.J. Carrozza et al. 2003. Trends Genet. 19: 321–329; W. Fischle et al. 2003. Curr. Opin. Cell Biol. 15: 172–183; M. Iizuka and M.M. Smith. 2003. Curr. Opin. Genet. Dev. 13: 1529–1539). This vast complexity is hardly surprising, given that all nuclear processes that involve DNA — transcription, replication, repair, recombination, sister chromatid cohesion, etc. — must all occur in the context of chromatin. The SWI/SNF-related ATP-dependent remodelers are divided into a number of subfamilies, all related by the SWI2/SNF2 ATPase at their catalytic core. In nearly every species where researchers have looked for them, one or more members of each subfamily have been identified. Even the budding yeast, with its comparatively small genome, contains eight different chromatin remodelers in five different subfamilies. This review will focus on just one subfamily, the Imitation Switch (ISWI) family, which is proving to be one of the most diverse groups of chromatin remodelers in both form and function.

scholarly journals Tension-dependent nucleosome remodeling at the pericentromere in yeast

2012 ◽  
Vol 23 (13) ◽  
pp. 2560-2570 ◽  
Author(s):  
Jolien S. Verdaasdonk ◽  
Ryan Gardner ◽  
Andrew D. Stephens ◽  
Elaine Yeh ◽  
Kerry Bloom
Keyword(s):  
Chromatin Remodeling ◽  
Mitotic Spindle ◽  
Structural Integrity ◽  
Physical Force ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nucleosome Remodeling ◽  
Nucleosome Dynamics ◽  
Chromosome Arm ◽  
Dna Translocase ◽  
Kinetochore Function

Nucleosome positioning is important for the structural integrity of chromosomes. During metaphase the mitotic spindle exerts physical force on pericentromeric chromatin. The cell must adjust the pericentromeric chromatin to accommodate the changing tension resulting from microtubule dynamics to maintain a stable metaphase spindle. Here we examine the effects of spindle-based tension on nucleosome dynamics by measuring the histone turnover of the chromosome arm and the pericentromere during metaphase in the budding yeast Saccharomyces cerevisiae. We find that both histones H2B and H4 exhibit greater turnover in the pericentromere during metaphase. Loss of spindle-based tension by treatment with the microtubule-depolymerizing drug nocodazole or compromising kinetochore function results in reduced histone turnover in the pericentromere. Pericentromeric histone dynamics are influenced by the chromatin-remodeling activities of STH1/NPS1 and ISW2. Sth1p is the ATPase component of the Remodels the Structure of Chromatin (RSC) complex, and Isw2p is an ATP-dependent DNA translocase member of the Imitation Switch (ISWI) subfamily of chromatin-remodeling factors. The balance between displacement and insertion of pericentromeric histones provides a mechanism to accommodate spindle-based tension while maintaining proper chromatin packaging during mitosis.

scholarly journals Transcriptional Suppression by Transient Recruitment of ARIP4 to Sumoylated Nuclear Receptor Ad4BP/SF-1

2009 ◽  
Vol 20 (19) ◽  
pp. 4235-4245 ◽  
Author(s):  
Hidesato Ogawa ◽  
Tomoko Komatsu ◽  
Yasushi Hiraoka ◽  
Ken-ichirou Morohashi
Keyword(s):  
Transcription Factors ◽  
Atpase Activity ◽  
Nuclear Receptors ◽  
Chromatin Remodeling ◽  
Target Genes ◽  
Fine Tuning ◽  
Binding Region ◽  
Interacting Protein ◽  
Double Stranded Dna ◽  
Transcriptional Suppression

The small ubiquitin-like modifier SUMO conjugates transcription factors and suppresses their respective activation of target genes. Although various SUMO-modified transcription factors have been isolated, mechanisms whereby sumoylated-substrates modulate transcription remain unknown. Here, we purified ARIP4 (AR interacting protein 4, a Rad54 family member and a SNF2 chromatin remodeling factor), which interacts with sumoylated Ad4BP/SF-1 through two SUMO-interacting motifs and one Ad4BP/SF-1–binding region. Remarkably, ARIP4 also interacts selectively with other sumoylated nuclear receptors including LRH-1, AR, and GR. Interestingly, the ATPase activity of ARIP4 was stimulated in the presence of sumoylated Ad4BP/SF-1 and the Ad4BP/SF-1–binding site containing double-stranded DNA. ChIP assays and siRNA studies strongly suggested that ARIP4 temporally suppresses Ad4BP/SF-1–mediated transcription through its transient recruitment to target genes. These findings suggest that ARIP4 may be a cofactor that modulates SUMO-mediated fine-tuning of transcriptional suppression.

Chromatin remodeling through directional DNA translocation from an internal nucleosomal site

2005 ◽  
Vol 12 (9) ◽  
pp. 747-755 ◽  
Author(s):  
Anjanabha Saha ◽  
Jacqueline Wittmeyer ◽  
Bradley R Cairns
Keyword(s):  
Chromatin Remodeling ◽  
Dna Translocation

scholarly journals Structural insights into the molecular mechanisms of the Mycobacterium evolvability factor Mfd

2019 ◽  
Author(s):  
Sivasankar Putta ◽  
Swayam Prabha ◽  
Vinayak Bhat ◽  
Gavin C. Fox ◽  
Martin A. Walsh ◽  
...  
Keyword(s):  
Bound States ◽  
Molecular Mechanisms ◽  
Nucleotide Binding ◽  
Dna Translocation ◽  
Flip Flop ◽  
Functional Studies ◽  
Negative Stain ◽  
Structural Insights ◽  
Dna Translocase

ABSTRACTMfd is a highly conserved ATP dependent DNA translocase that mediates the role of Transcription-Coupled-DNA-Repair(TCR) in bacteria. The molecular mechanisms and conformational remodelling that occurs in Mfd upon ATP binding, hydrolysis, and DNA translocation are poorly defined. Here we report a series of crystal and electron microscopy(EM) structures of Mfd from Mycobacterium tuberculosis (MtbMfd) and Mycobacterium smegmatis Mfd, solved in both the apo and nucleotide-bound states. The structures reveal the mechanism of nucleotide-binding, which lead to the remodeling of the Walker A motif at the catalytic pocket, inducing a flip-flop action of the hinge and flexible linker regions. Specifically, nucleotide binding unlocks the Translocation in RecG motif of the D6-domain to induce a ratchet-like motion. Functional studies of MtbMfd-RNAP complexes show that MtbMfd rescues stalled Transcription Elongation Complexes. We also report negative-stain and cryo-EM single particle reconstructions of MtbMfd higher order oligomer, that reveal an unexpected dodecameric assembly state. Given that Mfd accelerates the evolution of antimicrobial resistance(AMR), our results establish a framework for the design of new “anti-evolution” therapeutics to counter AMR.

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.

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