Abstract
The Rhox family of homeobox-containing genes maps to three gene dense clusters, α, β, and γ, on the mouse X chromosome. Rhox genes are expressed primarily in reproductive and extra-embryonic tissues and may be regulated by colinear mechanisms. Uniquely among family members, Rhox4 is also expressed in the developing and adult thymus, where its striking restriction to the third pharyngeal pouch has suggested a role in lineage specification. In this article we describe a previously unreported duplication within the Rhox α locus that contains seven copies of Rhox4 and eight copies of Rhox2 and Rhox3 in a tandem array. We further show that all seven Rhox4 copies are expressed, although preferential expression occurs and differs between tissues. In contrast to reproductive tissues, we found no evidence of colinear expression of the Rhox α cluster during thymus development. All subspecies of mice examined contained multiple copies of Rhox4. However, the only predicted ortholog of Rhox4, rat Rhox4, is present in a single copy, suggesting that the duplications arose at the time of rat and mouse lineage divergence. Finally, no changes in Rhox4 expression were detected in mice with defects in thymus organogenesis, placing it upstream or outside of established transcriptional pathways.
Similar content being viewed by others
References
Adkins RM, Gelke EL, Rowe D, Honeycutt RL (2001) Molecular phylogeny and divergence time estimates for major rodent groups: evidence from multiple genes. Mol Biol Evol 18: 777–791
Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, et al. (2002) Recent segmental duplications in the human genome. Science 297: 1003–1007
Blackburn CC, Manley NR (2004) Developing a new paradigm for thymus organogenesis. Nat Rev Immunol 4: 278–289
Blackburn CC, Augustine CL, Li R, Harvey RP, Malin MA, et al. (1996) The nu gene acts cell-autonomously and is required for differentiation of thymic epithelial progenitors. Proc Natl Acad Sci U S A 93: 5742–5746
Bray N, Dubchak I, Pachter L (2003) AVID: A global alignment program. Genome Res 13: 97–102
Gordon J, Bennett AR, Blackburn CC, Manley NR (2001) Gcm2 and Foxn1 mark early parathyroid- and thymus-specific domains in the developing third pharyngeal pouch. Mech Dev 103: 141–143
Gunther T, Chen ZF, Kim J, Priemel M, Rueger, M. et al. 2000. Genetic ablation of parathyroid glands reveals another source of parathyroid hormone. Nature 406: 199–203
Hammond WS (1954) Origin of thymus in the chick embryo. J Morphol 95: 501–613
Hogstrand K, Bohme J (1999) Gene conversion can create new MHC alleles. Immunol Rev 167: 305–317
Jackson M, Baird JW, Cambray N, Ansell JD, Forrester LM, et al. (2002) Cloning and characterisation of EHOX, a novel homeobox gene essential for ES cell differentiation. J Biol Chem 277: 38683–38692
Jackson M, Baird JW, Nichols J, Wilkie R, Ansell JD, et al. (2003) Expression of a novel homeobox gene Ehox in trophoblast stem cells and pharyngeal pouch endoderm. Dev Dyn 228: 740–744
Kmita M, Fraudeau N, Herault Y, Duboule D (2002) Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs. Nature 420: 145–150
Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151–1155
Maclean JA 2nd, Chen MA, Wayne CM, Bruce SR, Rao M, et al. 2005. Rhox: a new homeobox gene cluster. Cell 120: 369–382
Manley NR, Capecchi MR (1995) The role of Hoxa-3 in mouse thymus and thyroid development. Development 121: 1989–2003
Manley NR, Capecchi MR (1998) Hox group 3 paralogs regulate the development and migration of the thymus, thyroid, and parathyroid glands. Dev Biol 195: 1–15
Moore-Scott BA, Gordon J, Blackburn CC, Condie BG, Manley NR (2003) New serum-free in vitro culture technique for midgestation mouse embryos. Genesis 35: 164–168
Nehls M, Pfeifer D, Schorpp M, Hedrich H, Boehm T (1994) New member of the winged-helix protein family disrupted in mouse and rat nude mutations. Nature 372: 103–107
Noonan JP, Grimwood J, Schmutz J, Dickson M, Myers RM (2004) Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Res 14: 354–366
Otting G, Qian YQ, Billeter M, Muller M, Affolter M, et al. (1990) Protein-DNA contacts in the structure of a homeodomain-DNA complex determined by nuclear magnetic resonance spectroscopy in solution. EMBO J 9: 3085–3092
Rozas J, Rozas R (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174–175
Schreier JE, Hamilton JL (1952) An experimental study of the origin of the parathyroid and thymus glands in the chich. J Exp Zool 119: 165–187
Spitz F, Gonzalez F, Duboule D (2003) A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113: 405–417
Springer MS, Murphy WJ, Eizirik E, O’Brien SJ (2003) Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci U S A 100: 1056–1061
Takasaki N, Rankin T, Dean J (2001) Normal gonadal development in mice lacking GPBOX, a homeobox protein expressed in germ cells at the onset of sexual dimorphism. Mol Cell Biol 21: 8197–8202
Wayne CM, MacLean JA, Cornwall G, Wilkinson MF (2002) Two novel human X-linked homeobox genes, hPEPP1 and hPEPP2, selectively expressed in the testis. Gene 301, 1–11
Wolfe KH, Sharp PM (1993) Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. J Mol Evol 37: 441–456
Acknowledgments
The authors thank the Blackburn lab for help with embryo dissections, Edinburgh University School of Biological Sciences Sequence Service for DNA sequencing, N. Manley (University of Georgia, Athens) for the kind gift of the Hoxa3−/− and Gcm2−/−embryos, G. Graham (University of Glasgow) for the Rhox4 probe, A.J.H. Smith (ISCR, Edinburgh) and D. Charlesworth (IEB, Edinburgh) for illuminating discussions, and the Biomed Unit staff for animal care. This work was supported by the Medical Research Council, UK (CCB, JG), The Leukaemia Research Fund, UK (CCB), and the Wellcome Trust (LM, CCB).
Author information
Authors and Affiliations
Corresponding author
Additional information
Nucleotide sequence data reported are available in the EMBL database under accession numbers Rhox4.1, AJ972665; Rhox4.2, AJ972666; Rhox4.3, AJ972667; Rhox4.4, AJ972668; Rhox4.5, AJ972669; Rhox4.6, AJ972670; and Rhox4.7, AJ972671
Electronic Supplementary Material
Rights and permissions
About this article
Cite this article
Morris, L., Gordon, J. & Blackburn, C.C. Identification of a tandem duplicated array in the Rhox α locus on mouse chromosome X. Mamm Genome 17, 178–187 (2006). https://doi.org/10.1007/s00335-005-0138-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00335-005-0138-4