ATP-dependent chromatin remodelling complexes contribute to precise spatiotemporal transcription through distinct combinations of regulatory DNA sequences, DNA-binding transcription regulators, and chromatin-modifying enzymes. ATP-dependent chromatin remodeling complexes hydrolyze ATP and use the energy to exchange dimers of canonical histones in nucleosomes for dimers of histone variants (Qin, Zhao et al. 2014). The ATP-dependent SWR1 chromatin remodelling complex (SWR1-C) catalyzes the replacement of H2A-H2B dimers with H2A.Z-H2B dimers in nucleosome structures, thus producing variant nucleosomes with dynamic properties (Mizuguchi, Shen et al. 2004, Choi and Kim 2016). In eukaryotes, the organization of genomic DNA into chromatin and the ordered regulation of its accessibility to the transcription machinery are central to gene regulation.
Mechanisms for regulation of chromatin structure include ATP-dependent chromatin remodeling as well as post-translational histone modifications. ATP-dependent chromatin remodeling complexes alter nucleosome composition and positioning, and thus can regulate DNA accessibility via chromatin compactness. Through its distinct physicochemical properties, H2A.
Z influences nucleosome stability, and therefore chromatin structure, to modulate gene expression. These properties along with its incorporation into the chromatin out of mitosis have made H2A.Z central to transcriptional regulation underlying development and environmental responses. The components and function of SWR1c have been shown to be conserved in Arabidopsis. Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation (Berriri, Gangappa et al. 2016).
H2A.Z is incorporated into chromatin via processes specifically catalyzed by multisubunit chromatin-remodeling complexes—SWR1 in yeast and the related SRCAP and Tip60 complexes in mammals (Liang, Shan et al. 2016). The yeast SWR1 enzyme contains fourteen subunits: the Swr1 ATPase, Swc2, Bdf1, Swc3, Arp6, Swc5, Yaf9, Swc6, and Swc7 subunits are encoded by genes not essential for cell viability; Rvb1, Rvb2, Arp4, Swc4 (also known as Eaf2), and Act1 are encoded by essential genes. Some subunits are not unique to the SWR1 complex and thus have functions apart from SWR1. For example, Rvb1, Rvb2, Act1, and Arp4 are shared components with another ATP-dependent chromatin remodeling complex INO80. Act1 and Arp4, along with Swc4 and Yaf9, are also shared with the histone acetyltransferase complex NuA4, Bdf1 interacts with TFIID at TATA-less promoters during RNA polymerase II transcription initiation. Deletion analysis of a number of nonessential SWR1 subunits has revealed that chromatin deposition of H2A.
Z in vivo is dependent on Swc2, Arp6, Swc6, and Yaf9 as well as the Swr1 ATPase (Wu, Wu et al. 2009).Three putative Arabidopsis SWR1 (At-SWR1) subunits have been identified and studied: PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), ACTIN-RELATED PROTEIN6 (ARP6), and SWR1 COMPLEX6 (SWC6) (Rosa, Von Harder et al. 2013), One of the mechanisms involved in chromatin remodelling is so-called ‘histone replacement’. An example of such a mechanism is the substitution of canonical H2A histone by the histone variant H2A.Z.(March-Diaz, Garcia-Dominguez et al.
2008). The SWR1 and SRCAP complexes facilitate ATP-dependent histone replacement of canonical H2A with the H2AZ variant in the nucleosome; this H2AZ histone exchange mechanism is a multistep process that uses the function of the SWR1 complex2 (Swc2), Swc6 and Arp6 subunits of the complex (Morrison and Shen 2009).Gene functions are regulated by the modulation of chromatin structure as well as by the spatial association of genes with nuclear regions, including the nuclear lamina and the nucleolus. Chromatin remodeling complexes play central roles in the change of chromatin structure through their enzymatic activity and their regulatory subunits (Kitamura, Matsumori et al. 2015).PIE1 is homologous to the yeast Swr1 and human SRCAP proteins.
ARP6 and SEF are homologues of Arp6 and Swc6, two conserved subunits of the yeast SWR1 complex. Mutations in these three genes provoke early flowering due to down-regulation of FLOWERING LOCUS C (FLC), a MADS-box transcription factor that represses floral transition, Deal et al. (2007) have shown that PIE1 and ARP6 are required for deposition of H2A.Z at the FLC, MADS-AFFECTING FLOWERING 4 (MAF4) and MADS-AFFECTING FLOWERING 5 (MAF5) loci, suggesting that the PIE1/ARP6/SEF complex is functionally related to the yeast SWR1 complex (March-Diaz, Garcia-Dominguez et al. 2008).The orthologue of Swr1 in Arabidopsis is PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1) (Xu, Leichty et al. 2018), Three components of SWR1-C are essential for its function in yeast.
The ATPase, Swr1, provides the catalytic activity for the complex, and works in association with accessory proteins, Arp6 and Swc6 (Xu, Leichty et al. 2018) In the yeast SWR1 complex, ARP6 facilitates binding between other subunits, such as Swc2, and the ATPase domain of SWR1 (Qin, Zhao et al. 2014) Swc2 binds directly to and is essential for transfer of H2AZ. Swc6 and Arp6 are necessary for the association of Swc2 and for nucleosome binding, other subunits, Swc5 and Yaf9, are required for H2AZ transfer but neither H2AZ nor nucleosome binding (Wu, Alami et al. 2005). In budding yeast, ARP6 and SWC6 have been shown to be essential subunits in SWR1c for H2A.
Z deposition. Along with SWC2, another component of the SWR1c in yeast, they act as a sub-complex that requires all three proteins for their association with the complex and for histone exchange (Mizuguchi, Shen et al. 2004, Wu, Alami et al.
2005, Berriri, Gangappa et al. 2016).