Human SWI/SNF Drives Sequence-Directed Repositioning of Nucleosomes on C-myc Promoter DNA Minicircles

Abstract

The human SWI/SNF (hSWI/SNF) ATP-dependent chromatin remodeling complex is a tumor suppressor and essential transcriptional coregulator. SWI/SNF complexes have been shown to alter nucleosome positions, and this activity is likely to be important for their functions. However, previous studies have largely been unable to determine the extent to which DNA sequence might control nucleosome repositioning by SWI/SNF complexes. Here, we employ a minicircle remodeling approach to provide the first evidence that hSWI/SNF moves nucleosomes in a sequence dependent manner, away from nucleosome positioning sequences favored during nucleosome assembly. This repositioning is unaffected by the presence of DNA nicks, and can occur on closed-circular DNAs in the absence of topoisomerases. We observed directed nucleosome movement on minicircles derived from the human SWI/SNF-regulated c-myc promoter, which may contribute to the previously-observed "disruption" of two promoter nucleosomes during c-myc activation in vivo. Our results suggest a model wherein hSWI/SNF-directed nucleosome movement away from default positioning sequences results in sequence-specific regulatory effects.The precise localization of nucleosomes is one of the most important factors influencing transcription factor binding and gene regulation. ATP-dependent chromatin remodeling complexes are expected to act as transcriptional coregulators at least in part by altering nucleosome positions (1,2). However, very little is known about the influence of DNA sequence on nucleosome repositioning by these complexes. Human SWI/SNF (hSWI/SNF 1 ) is an evolutionarily-conserved multi-protein chromatin remodeling complex containing a core catalytic ATPase domain of either BRG1 or hBRM. It functions as a transcriptional coactivator or corepressor when recruited to promoters by over two dozen different activator and repressor proteins, including p53 and Rb as well as virtually all of the nuclear hormone receptors (3,4).

Divergent human remodeling complexes remove nucleosomes from strong positioning sequences

“…The 5S NPS was also of particular interest here because of recent studies showing that both WICH components (WSTF and SNF2h) are associated with human 5S genes and that shRNA knock down of WSTF decreases 5S transcript levels (19). Here, as was also seen in prior studies by us and others, we found that the 5S NPS is characterized by a cluster of overlapping individual nucleosome positions (Figure 5B, black bars for nucleosomes with centers between 100 and 140 bp) that give rise to a broad peak of nucleosome coverage over the transcription start site located at position 141 [Figure 5A, black lines (27,28,46)]. This is likely to be because the same DNA properties that result in a single high affinity 146 bp sequence (e.g.…”

Chromatin remodelling in mammalian cells by ISWI‐type complexes – where, when and why?

“…DNA sequence and conformation have been shown to be relevant for remodelling activity [50,58–61]. In particular, nucleosome positioning by the ACF complex can be directed by a defined DNA sequence element that displays high intrinsic curvature [50].…”

Control of Nucleosome Positions by DNA Sequence and Remodeling Machines

“…To get around end effects entirely, a second recent study examined human SWI/SNF remodeling on three different circular mononucleosome templates [87]. Strikingly, the results showed that hSWI/SNF moves nucleosomes away from initially favored sequences/NPSes, such that, at effective equilibrium, these sequences become the least well occupied areas of the template.…”