References
Aires R, Jurberg AD, Leal F, et al. (2016) Oct4 is a key regulator of vertebrate trunk length diversity. Developmental Cell 38 (3): 262–274.
Andrey G, Montavon T, Mascrez B, et al. (2013) A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 340 (6137): 1234167.
Berlivet S, Paquette D, Dumouchel A, et al. (2013) Clustering of tissue‐specific sub‐TADs accompanies the regulation of HoxA genes in developing limbs. PLoS Genetics 9 (12): e1004018.
Boulet AM and Capecchi MR (2004) Multiple roles of Hoxa11 and Hoxd11 in the formation of the mammalian forelimb zeugopod. Development 131 (2): 299–309.
Burke AC, Nelson CE, Morgan BA and Tabin C (1995) Hox genes and the evolution of vertebrate axial morphology. Development 121: 333–346.
Cobb J and Duboule D (2005) Comparative analysis of genes downstream of the Hoxd cluster in developing digits and external genitalia. Development 132 (13): 3055–3067.
Cohn MJ and Tickle C (1999) Developmental basis of limblessness and axial patterning in snakes. Nature 399 (6735): 474–479.
Dasen JS, Tice BC, Brenner‐Morton S and Jessell TM (2005) A Hox regulatory network establishes motor neuron pool identity and target‐muscle connectivity. Cell 123: 477–491.
De Kumar B, Parrish ME, Slaughter BD, et al. (2015) Analysis of dynamic changes in retinoid‐induced transcription and epigenetic profiles of murine Hox clusters in ES cells. Genome Research 25 (8): 1229–1243.
Deschamps J and Wijgerde M (1993) Two phases in the establishment of HOX expression domains. Developmental Biology 156 (2): 473–480.
Deschamps J, van den Akker E, Forlani S, et al. (1999) Initiation, establishment and maintenance of Hox gene expression patterns in the mouse. The International Journal of Developmental Biology 43 (7): 635–650.
Deschamps J and Duboule D (2017) Embryonic timing, axial stem cells, chromatin dynamics, and the Hox clock. Genes & Development 31 (14): 1406–1416.
Diez del Corral R and Storey KG (2004) Opposing FGF and retinoid pathways: a signalling switch that controls differentiation and patterning onset in the extending vertebrate body axis. BioEssays 26 (8): 857–869.
Duboule D and Morata G (1994) Colinearity and functional hierarchy among genes of the homeotic complexes. Trends in Genetics 10: 358–364.
Force A, Lynch M, Pickett FB, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151 (4): 1531–1545.
Gaunt SJ (1991) Expression patterns of mouse Hox genes: clues to an understanding of developmental and evolutionary strategies. BioEssays 13 (10): 505–513.
Graham A, Maden M and Krumlauf R (1991) The murine Hox‐2 genes display dynamic dorsoventral patterns of expression during central nervous system development. Development 112 (1): 255–264.
Gross S, Krause Y, Wuelling M and Vortkamp A (2012) Hoxa11 and Hoxd11 regulate chondrocyte differentiation upstream of Runx2 and Shox2 in mice. PLoS One 7 (8): e43553.
Guo T, Mandai K, Condie BG, et al. (2011) An evolving NGF‐Hoxd1 signaling pathway mediates development of divergent neural circuits in vertebrates. Nature Neuroscience 14 (1): 31–36.
Holstege JC, de Graaff W, Hossaini M, et al. (2008) Loss of Hoxb8 alters spinal dorsal laminae and sensory responses in mice. Proceedings of the National Academy of Sciences of the United States of America 105 (17): 6338–6343.
Iimura T and Pourquie O (2006) Collinear activation of Hoxb genes during gastrulation is linked to mesoderm cell ingression. Nature 442 (7102): 568–571.
Jung H, Mazzoni EO, Soshnikova N, et al. (2014) Evolving Hox activity profiles govern diversity in locomotor systems. Developmental Cell 29 (2): 171–187.
Keynes R and Krumlauf R (1994) Hox genes and regionalization of the nervous system. Annual Review of Neuroscience 17: 109–132.
Kmita M and Duboule D (2003) Organizing axes in time and space; 25 years of colinear tinkering. Science 301 (5631): 331–333.
Kondrashov N, Pusic A, Stumpf CR, et al. (2011) Ribosome‐mediated specificity in Hox mRNA translation and vertebrate tissue patterning. Cell 145 (3): 383–397.
Lumsden A (2004) Segmentation and compartition in the early avian hindbrain. Mechanisms of Development 121 (9): 1081–1088.
Maconochie M, Nonchev S, Morrison A and Krumlauf R (1996) Paralogous Hox genes: function and regulation. Annual Review of Genetics 30: 529–556.
Maconochie M, Krishnamurthy R, Nonchev S, et al. (1999) Regulation of Hoxa2 in cranial neural crest cells involves members of the AP‐2 family. Development 126 (7): 1483–1494.
Mainguy G, Koster J, Woltering J, Jansen H and Durston A (2007) Extensive polycistronism and antisense transcription in the mammalian Hox clusters. PLoS One 2 (4): e356.
Mallo M (2018) Reassessing the role of Hox genes during vertebrate development and evolution. Trends in Genetics 34 (3): 209–217.
Mazzoni EO, Mahony S, Peljto M, et al. (2013) Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals. Nature Neuroscience 16 (9): 1191–1198.
Montavon T, Le Garrec JF, Kerszberg M and Duboule D (2008) Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness. Genes & Development 22 (3): 346–359.
Neijts R and Deschamps J (2017) At the base of colinear Hox gene expression: cis‐features and trans‐factors orchestrating the initial phase of Hox cluster activation. Developmental Biology 428 (2): 293–299.
Noordermeer D, Leleu M, Splinter E, et al. (2011) The dynamic architecture of Hox gene clusters. Science 334 (6053): 222–225.
Parker HJ and Krumlauf R (2017) Segmental arithmetic: summing up the Hox gene regulatory network for hindbrain development in chordates. Wiley Interdisciplinary Reviews: Developmental Biology 6 (6): e286.
Parker HJ, Pushel I and Krumlauf R (2018) Coupling the roles of Hox genes to regulatory networks patterning cranial neural crest. Developmental Biology 444 (Suppl 1): S67–S78.
Parker HJ, De Kumar B, Green SA, et al. (2019) A Hox‐TALE regulatory circuit for neural crest patterning is conserved across vertebrates. Nature Communications 10 (1): 1189.
Pascual‐Anaya J, Sato I, Sugahara F, et al. (2018) Hagfish and lamprey Hox genes reveal conservation of temporal colinearity in vertebrates. Nature Ecology and Evolution 2 (5): 859–866.
Philippidou P and Dasen JS (2013) Hox genes: choreographers in neural development, architects of circuit organization. Neuron 80 (1): 12–34.
Pradeepa MM, McKenna F, Taylor GC, et al. (2017) Psip1/p52 regulates posterior Hoxa genes through activation of lncRNA Hottip. PLoS Genetics 13 (4): e1006677.
Rancourt DE, Tsuzuki T and Capecchi MR (1995) Genetic interaction between hoxb‐5 and hoxb‐6 is revealed by nonallelic noncomplementation. Genes & Development 9: 108–122.
Soshnikova N and Duboule D (2009) Epigenetic temporal control of mouse Hox genes in vivo. Science 324 (5932): 1320–1323.
Swinehart IT, Schlientz AJ, Quintanilla CA, Mortlock DP and Wellik DM (2013) Hox11 genes are required for regional patterning and integration of muscle, tendon and bone. Development 140 (22): 4574–4582.
Trainor P and Krumlauf R (2000) Plasticity in mouse neural crest cells reveals a new patterning role for cranial mesoderm. Nature Cell Biology 2 (2): 96–102.
Vinagre T, Moncaut N, Carapuco M, et al. (2010) Evidence for a myotomal Hox/Myf cascade governing nonautonomous control of rib specification within global vertebral domains. Developmental Cell 18 (4): 655–661.
Wacker SA, McNulty CL and Durston AJ (2004) The initiation of Hox gene expression in Xenopus laevis is controlled by Brachyury and BMP‐4. Developmental Biology 266 (1): 123–137.
Xue S, Tian S, Fujii K, et al. (2015) RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation. Nature 517 (7532): 33–38.
Yekta S, Tabin CJ and Bartel DP (2008) MicroRNAs in the Hox network: an apparent link to posterior prevalence. Nature Reviews Genetics 9 (10): 789–796.
Yin Y, Yan P, Lu J, et al. (2015) Opposing roles for the lncRNA haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation. Cell Stem Cell 16 (5): 504–516.
Zákány J, Kmita M, Alarcon P, de la Pompa JL and Duboule D (2001) Localized and transient transcription of Hox genes suggests a link between patterning and the segmentation clock. Cell 106 (2): 207–217.
Further Reading
Carroll SB (1995) Homeotic genes and the evolution of arthropods and chordates. Nature 376: 479–485.
Duboule D (1994) Guidebook to the Homeobox Genes. IRL Press: Oxford.
Duboule D (2007) The rise and fall of Hox gene clusters. Development (Cambridge, England) 134: 2549–2560.
Hrycaj SM and Wellik DM (2016) Hox genes and evolution. F1000Research 5: 859.
Iimura T and Pourquie O (2007) Hox genes in time and space during vertebrate body formation. Development, Growth & Differentiation 49: 265–275.
Krumlauf R (1994) Hox genes in vertebrate development. Cell 78: 191–201.
Krumlauf R (2016) Hox genes and the hindbrain: a study in segments. In: Wassarman PM (ed.) Current Topics in Developmental Biology, vol. 116, pp 581–596. Academic Press: Cambridge, MA.
Pearson JC, Lemons D and McGinnis W (2005) Modulating Hox gene functions during animal body patterning. Nature Reviews Genetics 6: 893–904.
Zakany J and Duboule D (2007) The role of Hox genes during vertebrate limb development. Current Opinion in Genetics & Development 17: 359–366.