ATP-dependent chromatin-remodeling enzymes are linked to changes in gene expression; however, it is not clear how the multiple
remodeling enzymes found in eukaryotes differ in function and work together. In this report, we demonstrate that the ATP-dependent
remodeling enzymes ACF and Mi2β can direct consecutive, opposing chromatin-remodeling events, when recruited to chromatin
by different transcription factors. In a cell-free system based on the immunoglobulin heavy chain gene enhancer, we show that
TFE3 induces a DNase I-hypersensitive site in an ATP-dependent reaction that requires ACF following transcription factor binding
to chromatin. In a second step, PU.1 directs Mi2β to erase an established DNase I-hypersensitive site, in an ATP-dependent
reaction subsequent to PU.1 binding to chromatin, whereas ACF will not support erasure. Erasure occurred without displacing
the transcription factor that initiated the site. Other tested enzymes were unable to erase the DNase I-hypersensitive site.
Establishing and erasing the DNase I-hypersensitive site required transcriptional activation domains from TFE3 and PU.1, respectively.
Together, these results provide important new mechanistic insight into the combinatorial control of chromatin structure.
"CD4 silencer), the simplest explanation is they are doing different things. Some examples where different remodeling enzymes are recruited to the same locus in cell-free (Ishii et al., 2009) and cell based systems (Gao et al., 2009; Precht et al., 2010; Ramirez-Carrozzi et al., 2006) illustrate this point. ATP-dependent remodeling has been found to alter histone modifications, a simple illustration of remodeling enzymes having different roles at the same locus (DiRenzo et al., 2000; Letimier et al., 2007; Ramirez-Carrozzi et al., 2006; Wurster and Pazin, 2008). "
[Show abstract][Hide abstract] ABSTRACT: One of the best studied systems for mammalian chromatin remodeling is transcriptional regulation during T cell development. The variety of these studies have led to important findings in T cell gene regulation and cell fate determination. Importantly, these findings have also advanced our knowledge of the function of remodeling enzymes in mammalian gene regulation. First we briefly present biochemical and cell-free analysis of 3 types of ATP dependent remodeling enzymes (SWI/SNF, Mi2, and ISWI) to construct an intellectual framework to understand how these enzymes might be working. Second, we compare and contrast the function of these enzymes during early (thymic) and late (peripheral) T cell development. Finally, we examine some of the gaps in our present understanding.
[Show abstract][Hide abstract] ABSTRACT: T helper cell differentiation and activation require specific transcriptional programs accompanied by changes in chromatin structure. However, little is known about the chromatin remodeling enzymes responsible. We performed genome-wide analysis to determine the general principles of BRG1 binding, followed by analysis of specific genes to determine whether these general rules were typical of key T cell genes. We found that binding of the remodeling protein BRG1 was programmed by both lineage and activation signals. BRG1 binding positively correlated with gene activity at protein-coding and microRNA (miRNA) genes. BRG1 binding was found at promoters and distal regions, including both novel and previously validated distal regulatory elements. Distal BRG1 binding correlated with expression, and novel distal sites in the Gata3 locus possessed enhancer-like activity, suggesting a general role for BRG1 in long-distance gene regulation. BRG1 recruitment to distal sites in Gata3 was impaired in cells lacking STAT6, a transcription factor that regulates lineage-specific genes. Together, these findings suggest that BRG1 interprets both differentiation and activation signals and plays a causal role in gene regulation, chromatin structure, and cell fate. Our findings suggest that BRG1 binding is a useful marker for identifying active cis-regulatory regions in protein-coding and miRNA genes.
[Show abstract][Hide abstract] ABSTRACT: Chromatin is by its very nature a repressive environment which restricts the recruitment of transcription factors and acts as a barrier to polymerases. Therefore the complex process of gene activation must operate at two levels. In the first instance, localized chromatin decondensation and nucleosome displacement is required to make DNA accessible. Second, sequence-specific transcription factors need to recruit chromatin modifiers and remodellers to create a chromatin environment that permits the passage of polymerases. In this review I will discuss the chromatin structural changes that occur at active gene loci and at regulatory elements that exist as DNase I hypersensitive sites.
Sandra Schick, David Fournier, Sudhir Thakurela, Sanjeeb Kumar Sahu, Angela Garding, Vijay K Tiwari
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