Isolation of human NURF: a regulator of Engrailed gene expression

Barak, Orr; Lazzaro, Maribeth A.; Lane, William S.; Speicher, David W.; Picketts, David J.; Shiekhattar, Ramin

doi:10.1093/emboj/cdg582

Cited by 160 publications

(167 citation statements)

References 81 publications

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“…Similar results were obtained with transiently transfected HEK 293T cells (Fig. S6), which, in contrast to U2OS cells, express active Snf2L endogenously (31). Here, values of 2 ± 1% and 2.0 ± 0.4 μm 2 ·s −1 (Snf2L) in comparison with 1 ± 1% and 2.7 ± 0.4 μm 2 ·s −1 (Snf2L+13) for the effective diffusion coefficient and the immobile fraction were measured.…”

Section: Lack Of Atpase Activity Leads To a Small Increase In Snf2h Asupporting

confidence: 87%

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

Erdel

Schubert

Marth

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

109

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Chromatin remodeling complexes can translocate nucleosomes along the DNA in an ATP-dependent manner. Here, we studied autofluorescent protein constructs of the human ISWI family members Snf2H, Snf2L, the catalytically inactive Snf2L+13 splice variant, and the accessory Acf1 subunit in living human and mouse cells by fluorescence microscopy/spectroscopy. Except for Snf2L, which was not detected in the U2OS cell line, the endogenous ISWI proteins were abundant at nuclear concentrations between 0.14 and 0.83 μM. A protein interaction analysis showed the association of multimeric Snf2H and Acf1 into a heterotetramer or higher-order ACF complex. During the G1/2 cell cycle phase, Snf2H and Snf2L displayed average residence times <150 ms in the chromatin-bound state. The comparison of active and inactive Snf2H/Snf2L indicated that an immobilized fraction potentially involved in active chromatin remodeling comprised only 1-3%. This fraction was largely increased at replication foci in S phase or at DNA repair sites. To rationalize these findings we propose that ISWI remodelers operate via a "continuous sampling" mechanism: The propensity of nucleosomes to be translocated is continuously tested in transient binding reactions. Most of these encounters are unproductive and efficient remodeling requires an increased binding affinity to chromatin. Due to the relatively high intranuclear remodeler concentrations cellular response times for repositioning a given nucleosome were calculated to be in the range of tens of seconds to minutes.nucleosome translocation | fluorescence recovery after photobleaching | fluorescence correlation spectroscopy

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Section: Lack Of Atpase Activity Leads To a Small Increase In Snf2h Asupporting

confidence: 87%

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

Erdel

Schubert

Marth

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

109

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“…Falz contains a bromodomain, which are known to bind acetylated lysines in histones and nonhistone proteins (for review, see Yang 2004), suggesting that Falz might recruit mSin3A/HDAC complexes to such targets to deacetylate specific promoter regions or modify the transcriptional activity of nonhistone proteins. A human NURF complex was shown to contain, beside FALZ, also RbAp46 and RbAp48, two proteins that are often found in complex with mSin3A (Barak et al 2003). Notably, Nurf301 can act as a negative regulator of the JAK/STAT signaling pathway, downstream of the STAT proteins, suggesting that mSin3A may regulate gene transcription through both DNA-binding transcription factors (Badenhorst et al 2002).…”

Section: Discussionmentioning

confidence: 99%

mSin3A corepressor regulates diverse transcriptional networks governing normal and neoplastic growth and survival

Dannenberg

Gourichon²,

Zhong³

et al. 2005

Genes Dev.

215

255

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mSin3A is a core component of a large multiprotein corepressor complex with associated histone deacetylase (HDAC) enzymatic activity. Physical interactions of mSin3A with many sequence-specific transcription factors has linked the mSin3A corepressor complex to the regulation of diverse signaling pathways and associated biological processes. To dissect the complex nature of mSin3A's actions, we monitored the impact of conditional mSin3A deletion on the developmental, cell biological, and transcriptional levels. mSin3A was shown to play an essential role in early embryonic development and in the proliferation and survival of primary, immortalized, and transformed cells. Genetic and biochemical analyses established a role for mSin3A/HDAC in p53 deacetylation and activation, although genetic deletion of p53 was not sufficient to attenuate the mSin3A null cell lethal phenotype. Consistent with mSin3A's broad biological activities beyond regulation of the p53 pathway, time-course gene expression profiling following mSin3A deletion revealed deregulation of genes involved in cell cycle regulation, DNA replication, DNA repair, apoptosis, chromatin modifications, and mitochondrial metabolism. Computational analysis of the mSin3A transcriptome using a knowledge-based database revealed several nodal points through which mSin3A influences gene expression, including the Myc-Mad, E2F, and p53 transcriptional networks. Further validation of these nodes derived from in silico promoter analysis showing enrichment for Myc-Mad, E2F, and p53 cis-regulatory elements in regulatory regions of up-regulated genes following mSin3A depletion. Significantly, in silico promoter analyses also revealed specific cis-regulatory elements binding the transcriptional activator Stat and the ISWI ATP-dependent nucleosome remodeling factor Falz, thereby expanding further the mSin3A network of regulatory factors. Together, these integrated genetic, biochemical, and computational studies demonstrate the involvement of mSin3A in the regulation of diverse pathways governing many aspects of normal and neoplastic growth and survival and provide an experimental framework for the analysis of essential genes with diverse biological functions.[Keywords: Histone modifications; knock-out; mSin3 complex; mSin3A; transcriptional regulation; tumorigenesis] Supplemental material is available at http://www.genesdev.org.

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“…It should be noted that there are likely to be two copies of BPTF within the NURF complex 103 ; in addition, there are further putative effector modules within the BPTF polypeptide and in other subunits of the complex (FIG. 2b).…”

Section: Harnessing the Nucleosome Unitmentioning

confidence: 99%

“…c | Chromatin metabolism complexes, exemplified by the MLL1 (ref. 122), NURF 103,123 and CtBP 11 core complexes, have multiple putative effector domains. The predicted domain structure of subunits of the complex members are shown as a linear arrangement from N to C terminus.…”

Section: In Vivo Approachesmentioning

confidence: 99%

Multivalent engagement of chromatin modifications by linked binding modules

Ruthenburg

Patel

et al. 2007

Nat Rev Mol Cell Biol

956

893

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Various chemical modifications on histones and regions of associated DNA play crucial roles in genome management by binding specific factors that, in turn, serve to alter the structural properties of chromatin. These so-called effector proteins have typically been studied with the biochemist's paring knife -the capacity to recognize specific chromatin modifications has been mapped to an increasing number of domains that frequently appear in the nuclear subset of the proteome, often present in large, multisubunit complexes that bristle with modification-dependent binding potential. We propose that multivalent interactions on a single histone tail and beyond may have a significant, if not dominant, role in chromatin transactions.The eukaryotic genome is assembled into chromatin, and the nucleosome serves as its fundamental organizational unit. This unit is composed of an octamer of core histone proteins (two copies of H2A, H2B, H3 and H4) encircled by ∼146 bp of DNA. Histones project unstructured N-terminal 'tails' from the α-helical protein core of the nucleosome through the superhelical turns of DNA that enshroud the radial surface of the histone octamer. The majority of known histone post-translational modifications (PTMs) localize to residues in the unstructured tails, particularly at the N termini, yet a burgeoning number of modifications also appear to reside within the helical secondary structure and loops of folded histones 1 . Further diversifying the nucleosome core particle is a set of histone isoforms known as histone variants, some of which appear to have essential roles in various stages of DNA management [2][3][4][5] .The lowest order of chromatin structure is the nucleosomal unit iterated in extended conformation to resemble 'beads on a string', which can be consolidated into higher-order structures through the intermediacy of attendant proteins, RNA and cations. Physiological chromatin structure is a vital arbiter of DNA function, in that structural variation appears to regulate the accessibility of underlying DNA, ranging from condensed heterochromatin to more 'open' euchromatin 6,7 . Rather than mere static packaging of the genome, the spatial arrangement of chromatin serves as an information carrier that may help to preserve cell Correspondence to C.D.A., D.J.P and A.J.R. alliscd@rockefeller.edu, pateld@mskcc.org, aruthenbur@rockefeller.edu. HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript identity through mitotic division 8 , and yet the local structure is sufficiently dynamic that it may be rapidly modulated by signalling cascades in response to external stimuli 9-11 .Phenotypic traits that are not encoded in the Watson-Crick base pairing of the genome are collectively referred to as epigenetic phenomena and appear to manifest physically as the faithful heritability of chromatin states by daughter cells [12][13][14] . The precise mechanisms of epigenetic phenomena are poorly understood, but causal connections between chemical modifications to DN...

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Isolation of human NURF: a regulator of Engrailed gene expression

Cited by 160 publications

References 81 publications

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites

mSin3A corepressor regulates diverse transcriptional networks governing normal and neoplastic growth and survival

Multivalent engagement of chromatin modifications by linked binding modules

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