Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI

Sala, Anna; Toto, M; Pinello, Luca; Gabriele, Alessandra; Benedetto, Valeria Di; Ingrassia, Antonia Maria Rita; Bosco, Giosuè Lo; Gesù, Vito Di; Giancarlo, Raffaele; Corona, Davide

doi:10.1038/emboj.2011.98

Cited by 57 publications

(63 citation statements)

References 35 publications

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“…Similar approaches performed on ISWI family members in flies and Saccharomyces cerevisiae have documented subtle changes at the TSS or TTS (41)(42)(43) or more dramatic and dispersed effects across the genome (44). From our experiments, we observed that most changes in nucleosome occupancy occurred at an NFR located Ͼ1 kb away from a TSS or TTS.…”

Section: Discussionmentioning

confidence: 51%

Functional Interactions between NURF and Ctcf Regulate Gene Expression

Qiu

Song

Malakouti

et al. 2015

Molecular and Cellular Biology

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Gene expression frequently requires chromatin-remodeling complexes, and it is assumed that these complexes have common gene targets across cell types. Contrary to this belief, we show by genome-wide expression profiling that Bptf, an essential and unique subunit of the nucleosome-remodeling factor (NURF), predominantly regulates the expression of a unique set of genes between diverse cell types. Coincident with its functions in gene expression, we observed that Bptf is also important for regulating nucleosome occupancy at nucleosome-free regions (NFRs), many of which are located at sites occupied by the multivalent factors Ctcf and cohesin. NURF function at Ctcf binding sites could be direct, because Bptf occupies Ctcf binding sites in vivo and has physical interactions with CTCF and the cohesin subunit SA2. Assays of several Ctcf binding sites using reporter assays showed that their regulatory activity requires Bptf in two different cell types. Focused studies at H2-K1 showed that Bptf regulates the ability of Klf4 to bind near an upstream Ctcf site, possibly influencing gene expression. In combination, these studies demonstrate that gene expression as regulated by NURF occurs partly through physical and functional interactions with the ubiquitous and multivalent factors Ctcf and cohesin. C ell differentiation requires the establishment and maintenance of specific gene expression profiles. Central to this process are transcription factors and their associated coregulatory complexes. The functions of these complexes are diverse and include ATP-dependent chromatin remodeling. ATP-dependent chromatin-remodeling complexes are frequently multiprotein enzymes which alter the position, composition, or presence of nucleosomes as a means to regulate chromatin structure. Changes in chromatin structure regulate the ability of trans-acting factors to access the underlying DNA, which in turn affects DNA-dependent processes like gene expression (1). Because of their importance for DNA-dependent processes, many subunits of chromatin-remodeling complexes are essential for mammalian development (2).One chromatin-remodeling complex essential for mammalian development is the nucleosome-remodeling factor (NURF). In mammals, NURF is a three-subunit complex containing bromodomain PHD finger-containing transcription factor (BPTF), the ATPase SNF2L, and the Trp-Asp (WD) repeat protein pRBAP46/48 (3, 4). NURF slides nucleosomes in cis without eviction or the exchange of histones from the nucleosome. NURF is proposed to remodel chromatin through physical interactions with both cell-type-restricted (PR and Smad) and ubiquitous (AP-1, Srf, and USF1) transcription factors and ubiquitously utilized histone modifications (H3K4me2/3) (5). These observations are not exclusive to NURF; several studies have documented both cell-type-specific and ubiquitous functions for many chromatinremodeling complexes through interactions with ubiquitous factors like the centrosome, RNA polymerases, nuclear lamins, and a variety of cell-type-specific transcri...

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Section: Discussionmentioning

confidence: 51%

Functional Interactions between NURF and Ctcf Regulate Gene Expression

Qiu

Song

Malakouti

et al. 2015

Molecular and Cellular Biology

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“…In vivo, ACF and CHRAC behave as assembly factors, promoting the formation of chromatin, particularly repressive chromatin states. Nevertheless, high-resolution mapping of nucleosomes in Iswi mutant males and females indicates that the chromosome condensation defects that they show, especially of the X chromosome in males, are not correlated with global ISWI-dependent nucleosome spacing changes (Sala et al 2011). A more convincing explanation is provided by the observation that ISWI facilitates the association of linker histone H1 and that a reduction of the H1 leads to a chromosomal phenotype similar to the one described above for ISWI loss of function (Siriaco et al 2009).…”

Section: Influence Of Global Chromatin Factorsmentioning

confidence: 85%

Dosage Compensation inDrosophila

Lucchesi

Kuroda

2015

Cold Spring Harb Perspect Biol

192

173

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SUMMARYDosage compensation in Drosophila increases the transcription of genes on the single X chromosome in males to equal that of both X chromosomes in females. Site-specific histone acetylation by the malespecific lethal (MSL) complex is thought to play a fundamental role in the increased transcriptional output of the male X. Nucleation and sequence-independent spreading of the complex to active genes serves as a model for understanding the targeting and function of epigenetic chromatin-modifying complexes. Interestingly, two noncoding RNAs are key for MSL assembly and spreading to active genes along the length of the X chromosome.

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“…For example, Isw2, an ISWI homolog in yeast, was found to bind transiently on chromatin and to scan the genome for its targets (Gelbart et al, 2005). Also, Drosophila ISWI appears to bind genes near their promoters, causing specific alterations in nucleosome positioning at the transcription start site (Sala et al, 2011). This premise may be transposed to insulator function as well, i.e.…”

Section: Research Articlementioning

confidence: 99%

ISWI contributes to ArsI insulator function in development of the sea urchin

2012

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SUMMARYInsulators are genomic elements that regulate transcriptional activity by forming chromatin boundaries. Various DNA insulators have been identified or are postulated in many organisms, and the paradigmatic CTCF-dependent insulators are perhaps the best understood and most widespread in function. The diversity of DNA insulators is, however, understudied, especially in the context of embryonic development, when many new gene territories undergo transitions in functionality. Here we report the functional analysis of the arylsulfatase insulator (ArsI) derived from the sea urchin, which has conserved insulator activity throughout the many metazoans tested, but for which the molecular mechanism of function is unknown. Using a rapid in vivo assay system and a highthroughput mega-shift assay, we identified a minimal region in ArsI that is responsible for its insulator function. We discovered a small set of proteins specifically bound to the minimal ArsI region, including ISWI, a known chromatin-remodeling protein. During embryogenesis, ISWI was found to interact with select ArsI sites throughout the genome, and when inactivated led to misregulation of select gene expression, loss of insulator activity and aberrant morphogenesis. These studies reveal a mechanistic basis for ArsI function in the gene regulatory network of early development. KEY WORDS: Sea urchin, Insulator, ISWI, Embryogenesis, Gene regulation, Strongylocentrotus purpuratus ISWI contributes to ArsI insulator function in development of the sea urchinMamiko Yajima*, William G. Fairbrother and Gary M. Wessel* DEVELOPMENT 3614 Watanabe et al., 2006;Tajima et al., 2006). It is not known how this DNA element functions as an insulator, nor what proteins are associated with its activity. We sought to expand our understanding of diverse insulators and their functions and report here that the ArsI sequence is found throughout the genome and interacts with a small cohort of nuclear proteins responsible for its insulator activity. One of the ArsI-associated proteins discovered here, an ortholog of the chromatin-remodeling protein ISWI, was found to function in ArsI activities in vivo and to associate with ArsI sites differentially during the course of embryonic development. These results demonstrate in vivo important regulation of early embryonic development by a DNA insulator and document another essential element in our understanding of GRNs during embryonic development. MATERIALS AND METHODS Mega-shift assay, cloning and sequencingA high-throughput binding assay called mega-shift (microarray evaluation of genomic aptamers by shift) was used to narrow down the exact location(s) of the ArsI sequence-protein complexes. For detailed methods, see Tantin et al. (Tantin et al., 2008). Briefly, a previously identified 573 bp region of ArsI sequence and its adjacent 1.4 kb sequence from the genomic loci of the Strongylocentrotus purpuratus arylsulfatase ortholog (Sp-Ars; accession number NW_001468620) were synthesized as a pool of tiled 30-mers with a common flankin...

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Genome-wide characterization of chromatin binding and nucleosome spacing activity of the nucleosome remodelling ATPase ISWI

Cited by 57 publications

References 35 publications

Functional Interactions between NURF and Ctcf Regulate Gene Expression

Functional Interactions between NURF and Ctcf Regulate Gene Expression

Dosage Compensation inDrosophila

ISWI contributes to ArsI insulator function in development of the sea urchin

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