Histone variant replacement or exchange, was originally only observed with yeast S�R1 complexes of the INO80 family (Kobor et al., 200�; Morillo-�uesca et al., 2010). It ��as sho��n that SWR1 efficiently replaces the canonical histone H2A with histone H2AZ in an ATP-dependent manner in S.cerevisiae
(Mizuguchi et al., 2004; �u et al., 2005). Moreover, INO80 type complexes contribute to a wide variety of chromatin-dependent nuclear transactions, including transcription, DNA repair and DNA replication (Conaway and Conaway, 2008; Bao and Shen, 2011). The INO80 ATPase is a member of the S�I�SNF family but is characterized by a large insertion between the split ATPase domains. INO80 complexes are conserved from yeast to man and share a set of core subunits, which include the INO80 ATPase, two AAA+ ATPases (ATPases associated with variety of cellular activities) referred to as Rvb1 and Rvb2, actin and three actin-related proteins Arp4, Arp5 and Arp8 (Figure 1.8) (Bakshi et al., 2004; van et al., 2004; vanet al., 2004; van Attikum and Gasser, 2005; Clapier and Cairns, 200�). Many INO80 type complexes are complicated remodeling machines as they often contain more than 10 subunits (Bao and Shen, 200�; Clapier and Cairns, 2009; Bao and Shen, 2011; �argreaves and Crabtree, 2011). Recent findings have revealed that fly and human INO80 complexes have evolved from the yeast INO80 complex. Although they share a common core of conserved subunits, the complexes have diverged substantially during evolution and have acquired ne�� subunits ��ith apparently species-specific functions (Cona��ay and Conaway, 2008).
This transition from yeast to vertebrate chromatin-remodeling complexes involved the expansion of several genes encoding the subunits of remodeling complexes and the use of a combinatorial diversity, as proposed for the large TIP60 or the human SCRAP remodeling complex. remodeling complex.remodeling complex. TIP60 and SCRAP are examples, ��hich have lost, gained and shuffled subunits during evolution from yeast to vertebrates. In particular, TIP60, ��hich exists in man and flies, and the human SCRAP complex are putative hybrids of at least two and possibly all three S. cerevisiae complexes INO80, S�R1 and NuA4, since all of them share many subunits (van Attikum and Gasser, 2005; Auger et al., 2008). Accordingly, remodelers of higher organisms like humans and flies (SCRAP and TIP60 ��ith p400�Domino) may be composite HAT remodeler complexes, whereas yeast separate these activities, since the yeast NuA4 complex lacks a remodeler ATPase (Clapier and Cairns, 200�).
Figure 1.8: Major chromatin remodeling complexes of the INO80 family and their homologous subunits
Composition of the S.cerevisiae S�R1, INO80, NuA4 complexes, the human SCRAP and the D. melanogaster
TIP60 complex. Conserved subunits are color coded (see also Table 1.1). The catalytic subunit (purple) of all complexes, except NuA4, is related to the S�I2�SNF2 type ATPase but contains a large insertion between the split ATPase domains. The catalytic subunit of NuA4 is the histone acetyltransferase Esa1, which has its counterpart in TIP60 of the TIP60 complex. The NuA4 subunit Eaf1 has homology with the S�R1 and Domino� p400 ATPase subunits. Because the yeast NuA4, S�R1 and INO80 complexes share many subunits with TIP60
and SCRAP complexes of flies and humans, it is proposed that TIP60 and SCRAP are hybrids of at least t��o and
possibly all three S. cerevisiae complexes (adapted from van Attikum and Gasser, 2005).
The large TIP60 complex exists in a stable nuclear multiprotein complex of approximately 18 subunits. However, depending on the cellular process in which TIP60 participates, it can also form distinct transient complexes with appropriate binding partners (Sapountzi et al., 2006). In humans, the TIP60 complex performs most transcriptional and DNA damage-related functions. The acetyltransferase TIP60 of the TIP60 complex has divergent functions and plays a role in many processes such as cellular signaling, DNA damage repair, cell cycle and checkpoint control or apoptosis (Sapountzi et al., 2006). Another essential component of the human TIP60 complex is the subunit p400�Domino, an ATPase that has chromatin remodeling and histone exchange activity (Ikura et al., 2000; Sapountzi et al., 2006). In flies, the homologue catalytic subunit of the human p�00/Domino protein is termed Domino, which is the homologous subunit to the yeast S�R1 and the human SCRAP.
In summary, many of the INO80 remodeling complexes are involved in histone replacement and exchange (see also Chapter 1.1.3). Surprisingly, even though the TIP60 complex and its emergence is ��ell characterized in human and flies, little is kno��n about its motor protein Domino except for its exchange function as TIP60 subunit. Therefore, one aspect of this study was the analysis of the ATP- dependent chromatin remodeling enzyme Domino with focus on the isoform Domino B, since distinct biological functions and putative interaction partners of Domino remain to be elucidated. More details about Domino will be given in the following chapter.
H2B
TIP60 (Fly) NuA4 (Yeast)
Arp4 Act1 Tra1 TRA1 Domino Ino80 Ies3 Nhp10 Act1 Arp5 Other subunits Rvb2 Rvb1 Arp4 Arp8 Other subunits Eaf2 Yaf9 BAP55 Act87E dDMAP1 dGAS41 Eaf1 Epl1 Esa1 Yng2 E(Pc) TIP60 ING3 Bdf6 dBrd8 Eaf3 Eaf7 Eaf5 MRG15 MRGBP dEaf6 Reptin Pontin
INO80 (Yeast) SWR1 (Yeast)
Swr1 Arp4 Other subunits Act1 Eaf2 Yaf9 Rvb2 Rvb1 H2B H2AZ SCRAP (Human) SCRAP BAF53a Other subunits Arp6 DMAP1 GAS41 Tip49a H2B H2AZ Tip49b Other subunits