This book also
contains a chapter on the classification of homeobox
genes written by myself that should give novices a good entry point
understanding all the different types of homeobox genes. (A
Classification of Homeobox Genes, Bürglin, T.R. (1994) in
to the Homeobox Genes. Duboule, D. (ed.) Oxford University Press,
pp 25-71). At present it is out of print.
Although a lot of
information is out of date at this point, it still
has some useful information not found in later papers.
Here on this page some errors and changes are pointed out.
In association with Amazon.com you can look up if a second hand copy is available as paperback version through this link.
Classification of homeobox genes into the following classes:
Hlx, NK-2, TCL, NEC, ems, Dll, msh, NK-1, en, Abd-b, Antp, lab, cad, eve, prd, prd-like, cut, POU, LIM, ZF.
Families within the Antp class are: Dfd, Scr, Antp, Xlox, pd.
These are all typical homeobox genes, i.e., their homeodomains are
amino acid long. In addition to the typical homeodomains, a series of
homeodomains exists, which have more or fewer than 60 amino acids.
Note about the classification: names of families and classes can
have been slightly changed and adapted later, e.g. TCL is no Tlx, and
as class or family may have been altered based on newer sequence analyses.
page 66: NvHbox2.8 has been assigned as HoxA2 by Swissprot. With blast searches it does come out closer to HoxA2 genes. But it should be linked to NvHbox2.7. What is it really? page 48: Fig 10: h HOXB3 is mislabelled; should be h HOXD3 page 17: Pax/Prd family: Pax-6 is small-eyes, and Pax-3 is splotch (was switched) page 89: Athb-1 is HAT5 (page 134), reference is Ruberti, not Roberti as listed in references. page 122: EST01828 is human OTX2 page 43: m HoxD3 sequence is SKRV... instead of SKSV... page 48: the human HB9 sequence was apparently incorrect, the latest database entry does not have the gap of 2 amino acids (X56537), thus Figure 10 can be ignored.
Note: one large subgroup of atypical homeodomains is the TALE group that was defined later.
The Evolution of Homeobox genes. Bürglin, T.R. (1995) in 'Biodiversity and Evolution', Arai, R., Kato, M., Doi, Y. (eds.), The National Science Museum Foundation, Tokyo, pp. 291-336, ISBN 4-9900433-0-8, The National Science Museum Foundation, 7-20 Ueno Park, Taito-ku, Tokyo 110, Japan.
Note about the classification: Subsequently names and classification were revised for TALE homeobox genes (e.g., HAC-ATYP split into BEL and MEIS).
Comparative tree of classes figure.
Columns on the right mark in what groups of animals classes have been found: d: Drosophila, v: vertebrates, c: C. elegans, o: others, i.e. leech, sea urchin, molluscs, planaria etc.
Classes with conserved sequence domains/motifs figure. New classes: ro (rough), so (sine oculis), Mox, Lb (lady-bird). TCL class renamed into Tlx class. New atypical class: pros (prospero); with conserved domain carboxy-terminal to the homeodomain. New domain/motif: so class has a long conserved domain, the Six/so domain, upstream of the homeodomain. All atypical homeobox genes that have 3 extra amino acids between helix 1 and helix 2 have been grouped together (This group is now known as the TALE superclass of homeobox genes). They have been classified into 4 groups: the established PBC class, the new M-ATYP class for the fungal mating type genes, the Kn (Knotted) class for this group of plant genes, and the HAC-ATYP class, a novel class that is conserved between animals and plants. A figure of these sequences shows the conservation between helix 1 and helix 2.
In Figure 1B, in the first column the 'K' is missing in the light grey area. The Kn class is now called the KNOX class (see below). HAC-ATYP is abandoned due to a revised nomenclature (see TALE paper below).