Characterization of a human SWI2/SNF2 like protein hINO80: Demonstration of catalytic and DNA binding activity Rachit Bakshi a , Abhishek Kumar Mehta a , Ritu Sharma a , Souvik Maiti b , Santosh Pasha b , Vani Brahmachari a, * a Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India b Institute of Genomics and Integrative Biology (CSIR) Delhi-110007, India Received 22 October 2005 Available online 15 November 2005 Abstract The proteins belonging to SWI2/SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling com- plexes that are implicated in epigenetic control of gene expression. We have identified a human gene with a putative DNA binding domain, which belongs to the INO80 subfamily of SWI2/SNF2 proteins. Here we report the cloning, expression, and functional activity of the domains from hINO80 gene both in terms of the DNA dependent ATPase as well as DNA binding activity. A differential expres- sion of the various domains within this gene is detected in human tissues while a ubiquitous expression is detected in mice. The intra- nuclear localization is demonstrated using antibodies directed against the DBINO domain of hINO80. Ó 2005 Elsevier Inc. All rights reserved. Keywords: Ino80; SWI2/SNF2; Chromatin remodeling; DNA binding domain; DNA dependent ATPase The compaction of eukaryotic genome into chromatin structure has profound implications on nuclear processes such as replication [1,2], transcription [3,4], DNA repair [5], and recombination [6,7]. Dynamic changes in chro- matin structure underlie much of the transcriptional con- trol in the eukaryotic nucleus. These structural changes are largely mediated by covalent modifications of the flexible N-terminal amino acids of the core histones by enzymes. Potential modifications include histone acetyla- tion, methylation, phosphorylation, ubiquitylation, and ADP-ribosylation [8–10]. A second line of chromatin alterations is brought about in more subtle and transient ways. These so-called chromatin remodeling factors alter histone–DNA interactions such that nucleosomal DNA becomes much more accessible to interacting proteins. These perturbations of the nucleosome may lead to the relocation of histone octamers from a particular DNA fragment to the available acceptor DNA in cis or trans, establishing a ‘‘fluid’’ state of chromatin in which the overall packaging of DNA is maintained, but individual sequences are transiently exposed to interacting factors [11–15]. A distinguishing hallmark of this latter type of nucleo- some remodeling is a dedicated ATPase subunit of the SWI2/SNF2 family of ATPases. The enzymes in this family can be grouped into several subfamilies according to sequence features outside of their ATPase domains [16,17]. Some of the well-characterized subfamilies of SWI2/SNF2 family of ATPases include the SNF2 subfam- ily (Snf2, Sth1, hBRM, and BRG1), ISWI subfamily (Iswi1, Iswi2, SNF2l, and SNF2h), CHD1 subfamily (CHD1, Mi-2 a/CHD3, and Mi2 b/CHD4), and the RAD54 subfamily (Rad54, ATRX, and ARIP4) [17]. SWI2/SNF2-like proteins participate in various nuclear activities including transcriptional control [18,19], DNA repair, chromosome segregation [20], and chromosome folding [21]. The members of two SWI2/SNF2-type sub- families, ATRX and DDM1, are involved in the control of DNA methylation [22,23]. 0006-291X/$ - see front matter Ó 2005 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2005.10.206 * Corresponding author. Fax: +91 11 27666248. E-mail address: vbrahmachari@acbr.du.ac.in (V. Brahmachari). www.elsevier.com/locate/ybbrc Biochemical and Biophysical Research Communications 339 (2006) 313–320 BBRC