A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases [1]. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC [1]. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors [1]. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein [2,3].

1: Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis. Lopez de Saro FJ, Yoshikawa N, Helmann JD; J Biol Chem 1999;274:15953-15958. PMID:10336502

2: Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase. Lopez de Saro FJ, Woody AY, Helmann JD; J Mol Biol 1995;252:189-202. PMID:7545758

3: The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. Aravind L, Iyer LM; Cell Cycle. 2012;11:119-131. PMID:22186017