Global characterization of interferon regulatory factor (IRF) genes in vertebrates: glimpse of the diversification in evolution.
Global characterization of interferon regulatory factor (IRF) genes in vertebrates: glimpse of the diversification in evolution.
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DOI：
10.1186/1471-2172-11-22
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发表时间：
2010-05-05
期刊：
影响因子：
3
通讯作者：
Nie P
中科院分区：
文献类型：
--
作者：
Huang B;Qi ZT;Xu Z;Nie P
干扰素调节因子（Interferon regulatory factors，IRFs）是一类具有螺旋-转角-螺旋DNA结合结构域（helix-turn-helix DNA binding domain，DBD）的转录因子，参与机体免疫应答、造血分化和免疫调节。尽管在哺乳动物中鉴定了10个IRF家族成员，并且最近努力在鱼类中鉴定这些成员，但对其他脊椎动物中这些成员的组成知之甚少，并且尚未在脊椎动物中研究IRF家族的进化和可能的起源。基因组数据挖掘已被用于识别人类、小鼠、狗、鸡、变色蜥蜴、青蛙和一些硬骨鱼（主要是斑马鱼和棘鱼）以及非脊椎动物后口动物（包括半索动物、头索动物、尾索动物和棘皮动物）中任何可能的IRF家族成员。在脊椎动物中，IRF-1 ~ IRF-10共10个成员，除斑马鱼中存在3个IRF-4基因外，鱼类和蛙中分别存在2个IRF-4和IRF-6基因。令人惊讶的是，在硬骨鱼中发现了IRF家族的另一个成员IRF-11。在非脊椎动物后口动物中检测到2 ~ 10个IRF样基因，基因组结构和系统发育分析表明，它们与脊椎动物中的IRF家族成员相似性很小。然而，IRF-1至IRF-10这10个IRF家族成员在基因组结构和基因同线性方面表现出一定程度的保守性。特别是IRF-1、IRF-2、IRF-6、IRF-8在所有脊椎动物中的基因组结构相当保守，并且在较小程度上，一些IRF家族成员，如IRF-5和IRF-9在结构上是可比的。同线性分析表明，IRF家族10个成员在脊椎动物中的基因位点也相当保守，但在斑马鱼中保守基因在染色体上的分布距离要远得多。此外，所有10个不同的成员分别聚集在不同的分支，但IRF-11与海胆中的一个聚类。在脊椎动物中，10个特征良好的IRF家族成员在基因组结构和同线基因排列方面具有相对较高的相似性，这意味着它们可能在不同类别的脊椎动物中以相似的模式和相似的选择压力进化。在IRF家族成员的进化过程中可能发生了基因组和/或基因的复制，可能还发生了基因重排或基因丢失，但在斑马鱼中可能发生了染色体或其片段的重排。然而，脊椎动物中的10个IRF家族成员和非脊椎动物后口动物中的IRF样基因在所分析的性状上存在很大差异，可能经历了不同的进化模式。
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. 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. 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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影响因子：
3.5
作者：
Dougherty, Dawne C.;Park, Hyi-Man;Sanders, Michel M.
通讯作者：
Sanders, Michel M.
影响因子：
3.6
作者：
Holland, J. W.;Bird, S.;Secombes, C. J.
通讯作者：
Secombes, C. J.
影响因子：
4.1
作者：
Stellacci, E;Testa, U;Battistini, A
通讯作者：
Battistini, A
DOI：
10.1038/nsb1002
发表时间：
2003-11-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
Qin, BY;Liu, C;Lin, K
通讯作者：
Lin, K
影响因子：
7
作者：
Huang, Shengfeng;Yuan, Shaochun;Xu, Anlong
通讯作者：
Xu, Anlong