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2016 ; 125
(3
): 497-521
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Homeodomain proteins: an update
#MMPMID26464018
Bürglin TR
; Affolter M
Chromosoma
2016[Jun]; 125
(3
): 497-521
PMID26464018
show ga
Here, we provide an update of our review on homeobox genes that we wrote together
with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes
have become possible due to genome sequencing projects. Using the 103 Drosophila
homeobox genes as example, we present an updated classification. In animals,
there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four
subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the
TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there
are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX,
PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most
of these classes encode additional domains apart from the homeodomain. Numerous
insights have been obtained in the last two decades into how homeodomain proteins
bind to DNA and increase their specificity by interacting with other proteins to
regulate cell- and tissue-specific gene expression. Not only protein-DNA base
pair contacts are important for proper target selection; recent experiments also
reveal that the shape of the DNA plays a role in specificity. Using selected
examples, we highlight different mechanisms of homeodomain protein-DNA
interaction. The PRD class of homeobox genes was of special interest to Walter
Gehring in the last two decades. The PRD class comprises six families in
Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the
Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the
OAR motif. Homologs of the co-repressor protein Groucho are also present in
plants (TOPLESS), where they have been shown to interact with small amphipathic
motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MAT?2.