Domino: A chromatin remodeler ATPase

dom (CG9696) has been isolated in a screen for regulators of hematopoiesis. Lymph glands of larvae homozygous for a dom mutation are melanized and turn black, making the white larvae look like Domino tokens. Thus the authors named the identified gene domino (Braun et al., 1997; Braun et al., 1998). Like its homologs, dom is a vital gene that binds to DNA and can be recruited via interaction with H3K4me3 (Fazzio et al., 2008b;

Kusch et al., 2014; Ueda et al., 2007). dom null mutation is early larval lethal and cell

clones induced with null mutant alleles were not recovered (Ruhf et al., 2001). dom contains 18 exons and is encoded on chromosome 2R (Figure 5 A). Alternative splicing produces four different isoforms dom-RA, RE, RD and RG, which all share the first four exons (Figure 5 B). The resulting proteins encode ATPases from the Swi2/Snf2-type, which contain a DExx-domain for ATP-binding (in this case the DEXDx-subtype), and a HELICc-helicase domain. Dom proteins contain a long insertion between these domains, which specifies them as members of the INO80-family, also termed split-ATPases. As other INO80 family members, Dom proteins contain a helicase SANT domain (HSA), which is believed to interact with Actin-related protein subunits in the chromatin remodeler complex. Additionally, several coiled-coil motifs can be identified (Figure 5 C).

The larger isoforms Dom-PA, PD and PG contain a C-terminal myb/SANT-like DNA binding domain, found in the c-Myb family of transcriptional activators and poly-glutamine (poly-Q) stretches (Clapier and Cairns, 2009).

The smaller isoform Dom-PE (previously annotated as Dom-PB) has a unique C-terminus, which is conserved only in three closely related Drosophila species D. simulans, D. willis and D. buskii. This C-terminal domain was identified as a potential Baz-interacting domain in a Yeast two-hybrid screen previously conducted in our lab (Egger-Adam, 2005).

Figure 5: The domino gene locus and encoded transcripts and protein isoforms.

dom (CG9696) encodes four transcripts and proteins. (A): Exon and introns of dom. The startcodon is located in exon 2 and is removed by the null mutation dom¹⁴. The GFP open reading frame (ORF) in the GFP-Dom trap line (BA00164) is inserted before the start codon and might be translated from an alternative start codon (CTG) two codons beforethe GFP insertion. The antibody detecting Dom is directed against the protein sequence resulting from exons 2 – 4, which are shared by all isoforms A, D, E, G (B): All isoforms are targeted by dom-RNAi lines used. (C): Dom proteins encode chromatin remodelers of the split-ATPase family, characterized by an ATPase domain (DEXDc) and a helicase domain (HELICc) separated by a long insertion. Dom also contains a helicase/SANT-domain (HSA) and four coiled coil motifs. A myb/SANT-like DNA-binding domain and several poly-Q stretches are found in the larger isoforms A,D and G. Isoform E (previously DomB) has a unique C-terminus found in our yeast two-hybrid screen as a potential Baz-binding site (Egger-Adam, 2005).

The human homologs of Dom are p400 and SRCAP. p400 and SRCAP function as ATPase subunits of the Tip60 complex and the SRCAP-complex, respectively (Fuchs et al., 2001;

Johnston et al., 1999a). While p400 misregulation is connected to tumorigenesis, SRCAP mutation is found to cause a rare disease, the Floating-Harbor syndrome, which leads to dysmorphia and mental retardation (Kehrer et al., 2014; Mattera et al., 2009; Nagasaki et al., 2014). In Drosophila both ATPase subunits are encoded by dom. It has been proposed that the DomA isoform functions as p400-homolog in the Tip60 complex and the isoform DomE functions as SRCAP-homolog (Börner and Becker, 2016; Eissenberg et al., 2005;

Kusch et al., 2004). As SRCAP-homolog, Dom functions as an activator of the Notch signaling pathway (Eissenberg et al., 2005). Mutations in dom, like mutations in the Tip60-subunit Nipped-A or in mammalian TRRAP, have been shown to modulate Notch signaling phenotypes upon mutation of Notch or mastermind (mam) (Gause et al., 2006; Hall et al., 2004; Kwon et al., 2013). The intracellular domain of Notch interacts with Mastermind to activate the expression of responsive genes. Dom is a co-activator of Notch-responsive gene expression and further modifies the Notch pathway by negatively regulating Notch mRNA expression levels. It has been proposed that Dom recruits the HAT CBP (expressed by nejire) to regulate Notch targets. This mechanism was supposed to be independent of Tip60 and therefore might be a function of the SRCAP-complex (Eissenberg et al., 2005). Also the Tip60 subunit Nipped-A modulates Notch singaling in Drosophila (Eissenberg et al., 2005; Gause et al., 2006). However, in mouse Nipped-A can positively regulate Notch signaling independent of Tip60 and Dom within a distinct complex, SAGA, which contains the Gcn5 HAT (Kurooka and Honjo, 2000). In mammals the Tip60 HAT negatively regulates Notch signaling upon UV-irradiation, by acetylation of Notch (Kim et al., 2007). Although the functions of Dom, Nipped-A and also Tip60 in Notch signaling are well established, it is unclear whether the SRCAP complex, the Tip60 complex or a sub-complex acts in Notch regulation.

The function of Dom in Notch signaling and the ambiguity of participating complexes underline how important it is to study chromatin remodeling complexes as a whole instead of having only a restricted view on single subunits. Recent studies have connected Dom to the regulation of alternative splicing and the microRNA pathway (Pressman et al., 2012). However, the lack of data about Dom interacting proteins makes it speculative

which complexes are involved. Likewise, the importance of Dom or the homolog p400 in the Tip60 complex is well established in various processes. The specific function is thereby dependent on the cellular context, the cellular state and different interacting proteins.