The AT-rich interaction domain (ARID) is an ~100-amino acid DNA-binding module found in a large number of eukaryotic transcription factors that regulate cell proliferation, differentiation and development [1,2]. The ARID domain appears as a single-copy motif and can be found in association with other domains, such as JmjC, JmjN, Tudor (see <PDOC50304>) and PHD-type zinc finger (see <PDOC50016>) [3].

The basic structure of the ARID domain domain appears to be a series of six α-helices separated by β-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes:

• Minimal ARID proteins that consist of a core domain formed by six α- helices;
• ARID proteins that supplement the core domain with an N-terminal α- helix;
• Extended-ARID proteins, which contain the core domain and additional α- helices at their N- and C-termini.

Minimal ARIDs are distributed in all eukaryotes, while extended ARIDs are restricted to metazoans. The ARID domain binds DNA as a monomer, recognizing the duplex through insertion of a loop and an α-helix into the major groove, and by extensive non-specific anchoring contacts to the adjacent sugar-phosphate backbone [1,2,4].

Some proteins known to contain a ARID domain are listed below:

• Eukaryotic transcription factors of the jumonji family.
• Mammalian Bright, a B-cell-specific trans-activator of IgH transcription.
• Mammalian PLU-1, a protein that is upregulated in breast cancer cells.
• Mammalian RBP1 and RBP2, retinoblastoma binding factors.
• Mammalian Mrf-1 and Mrf-2, transcriptional modulators of the cytomegalovirus major intermediate-early promoter.
• Drosophila melanogaster Dead ringer protein, a transcriptional regulatory protein required for early embryonic development.
• Yeast SWI1 protein, from the SWI/SNF complex involved in chromatin remodeling and broad aspects of transcription regulation.
• Drosophila melanogaster Osa. It is structurally related to SWI1 and associates with the brahma complex, which is the Drosophila equivalent of the SWI/SNF complex.

The profile we developed covers the ARID core domain.