The DDT has been named after the better characterised DNA-binding homeobox-containing proteins and the Different Transcription and chromatin remodellingfactors in which it is found. It is a domain of about 60 amino acids which isexclusively associated with nuclear domains like AT-Hook,PHD finger, methyl-CpG-binding domain, bromodomain and DNA-binding homeodomain.The DDT domain is characterised by a number of conserved aromatic and chargedresidues and is predicted to consist of three alpha helices. A DNA-bindingfunction for the DDT domain has been proposed [].
WHIM1 is a conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins [].Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins [, ]. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes []. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA [].
The ISWI chromatin remodeling complexes are widely present in eukaryotic species. This entry represents the plant ISWI binding proteins, the DDT domain proteins, including RLT1 and RLT2 from Arabidopsis []. AtISWI physically interacts with RLTs, and this prevents plants from activating the vegetative-to-reproductive transition early by regulating several key genes that contribute to flower timing []. RLT2 may also be involved in the transcriptional regulation of endogenous seed genes [].
This entry represents the WHIM2 domain found in diverse eukaryotic chromatin proteins, such as animal BAZ/WAL and BPTF proteins, plant RLT, and yeast Itc1. This domain contains the D-TOX E motif (also known as the Williams-Beuren syndrome DDT (WSD) motif) that is conserved from yeasts to animals [, , ].WHIM2 domain is a conserved alpha helical motif that along with the WHIM1 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins []. Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins [, ]. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes []. The acidic residue from the GxD signature of WHIM2 is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion of the WHIM2 motif also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA [].
ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms.It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
