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Echinobase
ECB-ART-41629
BMC Immunol 2010 May 05;11:22. doi: 10.1186/1471-2172-11-22.
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Global characterization of interferon regulatory factor (IRF) genes in vertebrates: glimpse of the diversification in evolution.

Huang B , Qi ZT , Xu Z , Nie P .


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BACKGROUND: Interferon regulatory factors (IRFs), which can be identified based on a unique helix-turn-helix DNA-binding domain (DBD) are a large family of transcription factors involved in host immune response, haemotopoietic differentiation and immunomodulation. Despite the identification of ten IRF family members in mammals, and some recent effort to identify these members in fish, relatively little is known in the composition of these members in other classes of vertebrates, and the evolution and probably the origin of the IRF family have not been investigated in vertebrates. RESULTS: Genome data mining has been performed to identify any possible IRF family members in human, mouse, dog, chicken, anole lizard, frog, and some teleost fish, mainly zebrafish and stickleback, and also in non-vertebrate deuterostomes including the hemichordate, cephalochordate, urochordate and echinoderm. In vertebrates, all ten IRF family members, i.e. IRF-1 to IRF-10 were identified, with two genes of IRF-4 and IRF-6 identified in fish and frog, respectively, except that in zebrafish exist three IRF-4 genes. Surprisingly, an additional member in the IRF family, IRF-11 was found in teleost fish. A range of two to ten IRF-like genes were detected in the non-vertebrate deuterostomes, and they had little similarity to those IRF family members in vertebrates as revealed in genomic structure and in phylogenetic analysis. However, the ten IRF family members, IRF-1 to IRF-10 showed certain degrees of conservation in terms of genomic structure and gene synteny. In particular, IRF-1, IRF-2, IRF-6, IRF-8 are quite conserved in their genomic structure in all vertebrates, and to a less degree, some IRF family members, such as IRF-5 and IRF-9 are comparable in the structure. Synteny analysis revealed that the gene loci for the ten IRF family members in vertebrates were also quite conservative, but in zebrafish conserved genes were distributed in a much longer distance in chromosomes. Furthermore, all ten different members are clustered in respectively different clades; but the IRF-11 was clustered with one in sea urchin. CONCLUSIONS: In vertebrates, the ten well-characterized IRF family members shared a relatively high degree of similarity in genomic structure and syntenic gene arrangement, implying that they might have been evolved in a similar pattern and with similar selective pressure in different classes of vertebrates. Genome and/or gene duplication, and probably gene shuffling or gene loss might have occurred during the evolution of these IRF family members, but arrangement of chromosome or its segment might have taken place in zebrafish. However, the ten IRF family members in vertebrates and those IRF-like genes in non-vertebrate deuterostomes were quite different in those analyzed characters, as they might have undergone different patterns of evolution.

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Species referenced: Echinodermata
Genes referenced: acox1 anln atp6ap2 atp6v1f clcn2 elf2 emc8 exoc2 foxq1 gmds gtf3c1 hey1 irfl kif14 LOC100887844 LOC100888845 LOC100888865 LOC100892016 LOC100892375 LOC100893510 LOC100893907 LOC105439292 LOC105442694 LOC115918340 LOC115919910 LOC115925116 LOC115925415 LOC115925451 LOC115925485 LOC373247 LOC575225 LOC576465 LOC577219 LOC578473 LOC580966 LOC581395 LOC582118 LOC582648 LOC583227 LOC583305 LOC585387 LOC586799 LOC587471 LOC591899 LOC592651 LOC594566 LOC752471 LOC763780 pofut1 ppp2cb psmc6 psmg1 rhol1 skp1 slc25a46 tbc1d4 tnpo3


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References [+] :
Amores, Zebrafish hox clusters and vertebrate genome evolution. 1998, Pubmed