The histone deacetylase domain of almost all members of higher eukaryotic histone deacetylases already identified (HDAC family) is highly homologous to that of yeast RPD3. In this paper we report the cloning of two cDNAs encoding members of a new family of histone deacetylase in mouse that show a better homology to yeast HDA1 histone deacetylase. These cDNAs encode relatively large proteins, presenting an in vitro trichostatin A-sensitive histone deacetylase activity. Interestingly, one, mHDA2, encodes a protein with two putative deacetylase domains, and the other, mHDA1, contains only one deacetylase homology domain, located at the C-terminal half of the protein. Our data showed that these newly identified genes could belong to a network of genes coordinately regulated and involved in the remodeling of chromatin during cell differentiation. Indeed, the expression of mHDA1 and mHDA2 is tightly linked to the state of cell differentiation, behaving therefore like the histone H1°-encoding gene. Moreover, like histone H1°gene, mHDA1 and mHDA2 gene expression is induced upon deacetylase inhibitor treatment. We postulate the existence of a regulatory mechanism, commanding a coordinate expression of a group of genes involved in the remodeling of chromatin not only during cell differentiation but also after abnormal histone acetylation.Enzymes involved in the modification of histones by acetylation, histone acetyltransferases (HAT) 1 and histone deacetylases (HD), are believed to play an important role in the regulation of transcription (1, 2). Moreover, acetylation appears to be a signaling process that involves not only histones but also non-histone proteins, mostly transcriptional regulators (3, 4). The identification of HATs and HDs are therefore crucial for the full understanding of the function of the signaling pathways through acetylation. The first histone deacetylase identified, HDAC1, showed a striking sequence homology with a yeast protein, RPD3 (5). After this discovery, not only histone deacetylases have been identified in many higher eukaryotes, but also variants have been reported (6 -8). Sequence analysis performed on these proteins showed that they all contain a conserved feature; a large domain of homology with the yeast RPD3, covering the 2/3 N-terminal of the protein and a short C-terminal region with the most variable sequence (9). The RPD3 homology domain is also shared by several procaryotic proteins interacting with various acetylated substrates (9 -11). These observations strongly suggested that this homology domain is also the deacetylase domain (9). Recently, mutagenesis of this domain confirmed its involvement in the enzymatic activity (12). Biochemical study in yeast allowed the identification (13) and the cloning of another histone deacetylase, HDA1 (14). Indeed, in yeast, two histone deacetylase complexes have been functionally identified (although, based on sequence homology, other potential members have been identified (14)): one, containing the histone deacetylase RPD3 (HDB complex), an...