Mi2β Shows Chromatin Enzyme Specificity by Erasing a DNase I-hypersensitive Site Established by ACF

Abstract

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 Mi2␤ 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 Mi2␤ 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.

Structure and function of active chromatin and DNase I hypersensitive sites

“…Different classes of remodelling enzymes can have opposing actions on chromatin. In one such example, TFE3 recruits ACF to create a DHS within the IgH intronic enhancer, whereas PU.1 can subsequently recruit Mi2b to erase this DHS [227]. Interestingly, in this example, PU.1 remains bound to the enhancer even after the DHS is erased.…”

ATP-dependent chromatin remodeling in T cells1This article is part of Special Issue entitled Asilomar Chromatin and has undergone the Journal’s usual peer review process.

“…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).…”

“…Biochemical activities include chromatin assembly, nucleosome displacement, nucleosome translocation (sliding), histone replacement, and nucleosome unfolding. The intrinsic biochemical function of remodeling ATPases are similar in very simple assays, resulting in increasing local accessibility, though they appear to differ in more complicated assays (Aalfs et al, 2001; Boyer et al, 2000; Fan et al, 2005; Ishii et al, 2009). Remodeling enzymes are thought to be recruited to specific sites through interactions with transcription factors, histone modifications and non-coding RNAs, and are generally thought to lack DNA-binding specificity (Biddie and Hager, 2009; Clapier and Cairns, 2009; Ho and Crabtree, 2010; Tarakhovsky, 2010; Thompson, 2009; Wysocka et al, 2006).…”

“…Due in part to its direct association with a histone deacetylase, NuRD has largely been viewed as a negative regulator of transcription. Mi2 can alter chromatin structure to increase nuclease accessibility in cell free systems (Boyer et al, 2000; Xue et al, 1998; Zhang et al, 1998) and can also “erase” open chromatin marks created by another remodeling enzyme in a reaction that is not well understood (Ishii et al, 2009). …”

Unveiling the gene regulatory landscape in diseases through the identification of DNase I‑hypersensitive sites (Review)

“…DHSs are dynamic and fine-tuned by different classes of remodeling enzymes. For example, TFE3 combines with ACF to stimulate the occurrence of an active DHS site in the IgH intronic enhancer, whereas PU.1 has been demonstrated to recruit Mi2β and subsequently erase this DHS (16).…”