InterPro domain: IPR003107

The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing [ 1 ]. The HAT motif has striking structural similarities to HEAT repeats ( IPR000357 ), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats. Some studies have suggested that the HAT repeats may be involved in protein-protein interactions [ 2 , 3 ]. However, the HAT repeats of Arabidopsis HCF107 protein have been shown to bind RNA [ 4 ].

Proteins containing this domain includes:

• Crooked neck (Crn) from Drosophila. It associates with the RNA-binding protein HOW to control glial cell maturation [ 5 ].
• Clf1, Prp6 and Prp39 from S. cerevisiae. Clf1 is part of the of the NineTeen Complex (NTC) that stabilises U6 snRNA in catalytic forms of the spliceosome containing U2, U5, and U6 snRNAs [ 6 , 7 ]. Prp6 and Prp39 are involved in pre-mRNA splicing.
• Cleavage stimulation factor subunit 3 (CSTF3 or CstF-77) and crooked neck-like protein 1 (CRNKL1) from mammals. CSTF3 is required for polyadenylation and 3'-end cleavage of mammalian pre-mRNAs [ 8 ].
• Protein high chlorophyll fluorescent 107 (HCF107) from Arabidopsis. HCF107 exhibits sequence-specific RNA binding and RNA remodeling activities, probably leading to the activation of translation of the target gene cluster psbB-psbT-psbH-petB-petD [ 9 ]. It blocks 5'-3' and 3'-5' exoribonucleases (e.g. polynucleotide phosphorylase (PNPase), RNase R) in vitro [ 9 ]. It is necessary for intercistronic RNA processing of the psbH 5' untranslated region or the stabilization of 5' processed psbH RNAs and is also required for the synthesis of psbB [ 9 , 10 , 11 ].

1. The HAT helix, a repetitive motif implicated in RNA processing. Trends Biochem. Sci. 23, 15-6
2. A structural model for the HAT domain of Utp6 incorporating bioinformatics and genetics. Protein Eng. Des. Sel. 22, 431-9
3. A direct interaction between the Utp6 half-a-tetratricopeptide repeat domain and a specific peptide in Utp21 is essential for efficient pre-rRNA processing. Mol. Cell. Biol. 28, 6547-56
4. RNA binding and RNA remodeling activities of the half-a-tetratricopeptide (HAT) protein HCF107 underlie its effects on gene expression. Proc. Natl. Acad. Sci. U.S.A. 109, 5651-6
5. The splicing factor crooked neck associates with the RNA-binding protein HOW to control glial cell maturation in Drosophila. Neuron 52, 969-80
6. The Clf1p splicing factor promotes spliceosome assembly through N-terminal tetratricopeptide repeat contacts. J. Biol. Chem. 278, 7875-83
7. The Prp19-associated complex is required for specifying interactions of U5 and U6 with pre-mRNA during spliceosome activation. J. Biol. Chem. 280, 31190-9
8. The conserved intronic cleavage and polyadenylation site of CstF-77 gene imparts control of 3' end processing activity through feedback autoregulation and by U1 snRNP. PLoS Genet. 9, e1003613
9. The nucleus-encoded HCF107 gene of Arabidopsis provides a link between intercistronic RNA processing and the accumulation of translation-competent psbH transcripts in chloroplasts. Plant Cell 13, 2127-41
10. The nuclear gene HCF107 encodes a membrane-associated R-TPR (RNA tetratricopeptide repeat)-containing protein involved in expression of the plastidial psbH gene in Arabidopsis. Plant J. 42, 720-30