黑色素瘤抗原编码基因家族新成员MAGE-D1的组织表达谱研究

MAGE D1是黑色素瘤抗原编码基因家族 (MAGE)中MAGE D亚家族的新成员 .为了研究该基因的性质及其可能功能 ,采用Northernblot和Dotblot杂交技术研究了其组织表达谱 .结果发现 ,该基因在多种肿瘤组织和正常组织中均广泛表达 .在所检测的 4 8种肿瘤组织中 ,经与对应正常组织进行比较发现 ,该基因在 13种肿瘤组织中的表达显著增高 ,而在 7种肿瘤组织中的表达则显著降低 .进一步分析提示该基因在多种胚胎组织中的表达高于成年组织 .由于MAGE A、 B、 C亚家族均具有在肿瘤组织 睾丸中特异表达的特点 ,而作为MAGE D亚家族成员的MAGE D1并非在肿瘤组织中特异表达 ,提示需要对MAGE基因家族进行深入的功能研究 .     

配对盒基因家族——发育过程中重要的转录因子

在大量的脊椎和无脊椎动物中发现的配对盒转录因子（paired box,PAX）及其同源物,在胚胎发育的许多阶段发挥着关键的作用。该基因家族因其具有保守的成对结构域而得名,除此之外其还具有八肽和同源域。根据结构域的组成和序列的同源性,该基因家族主要分为4个亚家族：PAX1/9（PAX1、PAX9）,PAX2/5/8（PAX2、PAX5、PAX8）,PAX3/7（PAX3、PAX7）,PAX4/6（PAX4、PAX6）。各亚家族具有不同的特征结构,例如PAX1/9亚家族的PD-OP、PAX2/5/8亚家族的PD OP-PTHD、PAX3/7亚家族的PD OP-PTHD以及PAX4/6亚家族的PD和PTHD。其中,PAX家族的3个成员PAX2、PAX4和PAX6在胰腺发育和分化的多个阶段中发挥了重要作用,在调节胰岛激素的合成和分泌中也发挥了关键作用,揭示这些转录因子及其在胰腺中的原始和分化作用,为糖尿病的研究和治疗提供帮助。PAX1/9亚家族与肿瘤细胞的相互作用在癌症诊断和检测中具有重要作用,例如在肿瘤中PAX1的甲基化和PAX9表达程度等,而且PAX基因发挥作用具有时间性和空间性。在多种肿瘤中,发现PAX基因功能和结构异常。PAX3/7是作为骨骼肌发育的肌原性转录因子,PAX基因发挥作用具有时间性和空间性。在多种肿瘤中,发现PAX基因功能和结构异常。本文就上述内容进行综述。     

毛果杨nsLTP基因家族全基因组水平鉴定及其表达特性分析

植物非特异性脂质转移蛋白（non-specific lipid transfer proteins,nsLTP）是一类多基因家族编码碱性蛋白,负责脂肪酸体外结和与膜之间的磷脂转移,在植物生长发育和逆境胁迫响应中扮演着重要角色。目前为止,尚无模式植物毛果杨（Populus trichocarpa）nsLTP家族的研究报导。本研究从全基因组水平对PtrnsLTP家族成员的基因数量、亲缘关系、基因结构、编码蛋白保守基序等特性进行了分析,结果表明：PtrnsLTP家族共由39个基因组成,进化成5个亚家族,其中A亚族含有6个基因、B亚族含有2个、C亚族含有13个、D亚族含有3个、E亚族含有15个。PtrnsLTP家族包含7对旁系同源基因,其中1对大于1,6对Ka/Ks均远小于1,且这6对基因均处于同一个大的进化分支上,进化压力的不同导致基因间的功能出现了分化,编码蛋白均含有Motif 1和 Motif 2保守基序。利用qRT-PCR技术并结合杨树转录组数据对PtrnsLTP的组织表达与盐胁迫响应特性研究发现：各家族成员在毛果杨根、茎和叶中均有表达且经qRT-PCR技术验证后与网站预测结果基本吻合,有11、15和13个成员分别在根、茎和叶中有较高的表达,表明该基因家族参与了杨树不同组织的生长发育;NaCl胁迫下,该家族39个基因中分别有26个成员在根部、14个成员在叶部表达量随着胁迫时间的增加而升高,而32个基因在茎部表现为先升高后降低的趋势。本研究结果对于PtrnsLTP家族基因生物学功能的鉴定与盐胁迫响应基因资源的工作有着积极的推动作用。     

采用RACE技术获得全长人新基因MAGE-D1

 c DNA末端快速扩增 (RACE)技术是快速获得新基因 5′和 3′端未知序列的有效手段 .鉴于新报导的人肿瘤基因 MAGE家族成员之一 MAGE- D1的 c DNA序列不完全 ,从而拟用 RACE技术获得 MAGE- D1的全长 c DNA序列 .结果显示 ,MAGE- D1的 c DNA全长为 2 80 0个碱基 ,编码778个氨基酸 .同时对 RACE技术应用时的一些关键问题进行了讨论 .     

番茄WOX转录因子家族的鉴定及其进化、表达分析

WUSCHEL相关的同源异型盒(WUSCHEL-related homeobox,WOX)是一类植物特异的转录因子家族,具有调控植物干细胞分裂分化动态平衡等重要功能。本研究利用番茄(Solanum lycopersicum)基因组数据,通过建立隐马尔科夫模型并进行检索,鉴定了番茄10个WOX转录因子家族成员。多序列比对发现,番茄WOX转录因子家族成员具有高度保守的同源异型结构域;以拟南芥WOX转录因子家族成员序列为参照,通过邻接法、极大似然法、贝叶斯法重建了系统发育树,三者呈现出类似的拓扑结构,番茄和拟南芥WOX转录因子家族共25个成员被分为3个进化支(Clade)和9个亚家族(Subgroup);利用MEME和GSDS对WOX转录因子家族成员的蛋白保守结构域和基因结构进行了分析,同一亚家族内的WOX转录因子家族成员的保守结构域的种类、组织形式以及基因结构具有高度的一致性;利用Perl和Orthomcl对家族成员的染色体定位和同源性关系进行分析,结果表明串联重复的SlWOX3a和SlWOX3b可能来源于一次复制事件;利用番茄转录组数据和qRT-PCR进行表达分析,结果显示家族成员在不同组织中的表达存在差异,暗示了WOX家族的不同成员在功能上可能具有多样性。本研究对番茄WOX转录因子家族成员进行GO(Gene Ontology)注释和比较分析,结果表明该家族成员作为转录因子,可能在组织器官发育、细胞间通讯等过程中发挥作用。     

毛果杨CNGC家族全基因组鉴定及胁迫响应分析

植物环核苷酸门控离子通道（cyclic nucleotide-gated channels,CNGC）家族具有多种生物学功能,尤其是在植物的生长发育及逆境胁迫响应中发挥着重要的作用。本研究通过生物信息学方法及qRT-PCR对PtrCNGC家族成员蛋白的基本理化性质与结构特征、系统发育、基因结构和保守基序、启动子顺式作用元件,以及基因表达模式进行分析。结果表明：在毛果杨（Populus trichocarpa）全基因组中共鉴定出19个PtrCNGC基因,PtrCNGC家族成员可分为4个亚群（Ⅰ、Ⅱ、Ⅲ和Ⅳ亚群）,其中第Ⅳ亚群分为2个亚组（Ⅳa组和Ⅳb组）。PtrCNGC基因编码的蛋白均为碱性蛋白,此外,该家族仅有1个成员为疏水性蛋白,其余成员全部为亲水性蛋白。19个PtrCNGC不均匀地分布于毛果杨的11条染色体上,剩余8条染色体上没有成员分布。PtrCNGC家族包含7对同源基因且它们之间的K_a/K_s值均远小于1。PtrCNGC家族各亚群成员之间的基因结构、蛋白保守基序分布差异较小。启动子顺式作用元件预测分析发现,PtrCNGC基因序列启动子区域存在响应多种激素以及逆境胁迫相关的作用元件。qRT-PCR结果表明,PtrCNGC家族在不同组织中的表达具有特异性,在茎中的表达量较高,在根和叶中的表达量较低;在盐胁迫和干旱胁迫下,PtrCNGC家族同一分支上的多数成员表现出相似的表达模式。本研究结果为进一步研究毛果杨CNGC家族在非生物胁迫中的功能提供参考。     

果蝇心脏基因一个新人同源基因WNT-10A的研究初报

Ｗｇ基因是控制果蝇心脏前体细胞形成的一个关键基因,根据物种间同源异型基因结构上的保守性与功能上的相似性,我们运用计算机克隆的方法获得了一个新的人同源基因,命名为ＷＮＴ－１０Ａ。该基因有一富集ＧＣ碱基的启动子,ｍＲＮＡ全长约２．４ｋｂ,３′末端包含ＡＴＡＡＡ的加尾信号,编码一段长４１７个氨基酸的蛋白质,与小鼠Ｗｎｔ－１０ａ的编码蛋白高度相似。其心脏ＥＳＴ数目占正常组织ＥＳＴ总数的４５％,表明该基因在心脏组织高度表达,提示其可能与心脏发育有关。该基因与其基因家族成员具有相似的同源框序列,在肿瘤细胞中大量表达（占总ＥＳＴ的３１％）,表明该基因相似于其家族成员,可能与肿瘤的发生有关。     

萝卜TALE转录因子家族的鉴定与分析

TALE (three-amino acid loop extension)转录因子在植物生长发育及细胞分化过程中起重要作用。在多种植物中均已鉴定出TALE转录因子的家族成员,但是萝卜TALE转录因子家族的研究鲜有报道。文中通过生物信息学手段在象牙白萝卜全基因组中鉴定出了分布于9条染色体上的33个TALE家族基因。研究结果显示,该家族中除与拟南芥KNATM同源的基因Rsa10037940外,其余基因均含有编码HOX保守结构域的序列。这些基因含有4–6个外显子。萝卜的33个TALE基因与拟南芥中的17个同源基因存在共线性关系。33个TALE基因启动子区的顺式元件中包含大量逆境响应元件。表达特性分析显示,该基因家族BELL亚家族内有4个基因在根内表达量较高,KNOX亚家族内有2个基因在薹和愈伤中表达量较高。该家族不同亚型成员之间的蛋白3D结构高度相似。编码蛋白均为弱酸、有亲水性。萝卜TALE基因家族在进化上较为保守,分化上与拟南芥存在一致性,与水稻差异较大。本研究为开展萝卜中TALE转录因子的生物学功能研究提供了重要参考。     

丝氨酸蛋白酶抑制剂B亚家族

丝氨酸蛋白酶抑制剂(serine proteinase inhibitor,Serpin)亚家族SERPIN B是第二个大的Serpin亚家族,也被称为卵清蛋白样丝氨酸蛋白酶抑制剂,在人类,至今已发现有13个序列高度同源的成员,在原生动物,植物,及病毒中也发现了SERPIN B亚家族的成员。SERPIN B亚家族成员基因位于6p25和18q21,其表达产物构象与其他Serpin亚家族成员存在3点不同：(1)缺乏可剪切的疏水性分泌信号序列和其他信号序列模体。(2)蛋白质结构中的螺旋C与螺旋D之间的环可能是其发挥某些特定功能的模体。(3)SERPIN B亚家族成员缺乏羧基端的延伸序列。大多数SERPIN B蛋白在细胞内产生作用,定位于细胞质或细胞质和细胞核之中,其作用广泛,参与了许多基本的生命活动,例如纤溶,炎症反应,细胞迁移,细胞分化,调亡等。同其他Serpin一样,SERPIN B也是通过一种成为自杀性底物的机制发挥其作用的。     

马铃薯WOX基因家族的鉴定及在离体再生和非生物胁迫中的表达分析

【目的】WUSCHE-相关同源盒（WUSCHEL-related homeobox, WOX）基因家族是植物特有的转录因子家族,在植物生长发育、干细胞分化调控、逆境胁迫响应等过程中扮演重要角色。开展马铃薯WOX基因家族鉴定与功能研究,将为马铃薯遗传改良提供优良基因资源与理论依据。【方法】基于拟南芥、番茄、烟草和水稻WOX蛋白序列,利用HMMER 3.0和BLASTP鉴定马铃薯WOX基因家族成员,使用MCScanX软件分析WOX基因家族成员在马铃薯种内及种间的共线性,并采用邻接法构建系统发育进化树。利用ExPASy、GSDS等软件分析马铃薯WOX基因家族成员理化性质、基因结构、蛋白motif、启动子区域转录因子结合位点。基于PGSC数据库中马铃薯转录组数据,分析StWOXs在不同组织和非生物胁迫下的表达模式;以可能参与离体再生过程的StWOX5作为候选基因,利用实时荧光定量PCR技术分析该基因在具有不同离体再生能力的4个马铃薯品种（系）再生过程中的表达情况。【结果】鉴定得到11个马铃薯WOX基因家族成员,分布在5条染色体上,分为WUS、中间和古老共3个进化分支,不同分支中StWOXs基因...     

Evolutionary history of the cancer immunity antigen MAGE gene family

The evolutionary mode of a multi-gene family can change over time, depending on the functional differentiation and local genomic environment of family members. In this study, we demonstrate such a change in the melanoma antigen (MAGE) gene family on the mammalian X chromosome. The MAGE gene family is composed of ten subfamilies that can be categorized into two types. Type I genes are of relatively recent origin, and they encode epitopes for human leukocyte antigen (HLA) in cancer cells. Type II genes are relatively ancient and some of their products are known to be involved in apoptosis or cell proliferation. The evolutionary history of the MAGE gene family can be divided into four phases. In phase I, a single-copy state of an ancestral gene and the evolutionarily conserved mode had lasted until the emergence of eutherian mammals. In phase II, eight subfamily ancestors, with the exception for MAGE-C and MAGE-D subfamilies, were formed via retrotransposition independently. This would coincide with a transposition burst of LINE elements at the eutherian radiation. However, MAGE-C was generated by gene duplication of MAGE-A. Phase III is characterized by extensive gene duplication within each subfamily and in particular the formation of palindromes in the MAGE-A subfamily, which occurred in an ancestor of the Catarrhini. Phase IV is characterized by the decay of a palindrome in most Catarrhini, with the exception of humans. Although the palindrome is truncated by frequent deletions in apes and Old World monkeys, it is retained in humans. Here, we argue that this human-specific retention stems from negative selection acting on MAGE-A genes encoding epitopes of cancer cells, which preserves their ability to bind to highly divergent HLA molecules. These findings are interpreted with consideration of the biological factors shaping recent human MAGE-A genes.     

MAGE-F1, a novel ubiquitously expressed member of the MAGE superfamily

Most known members of the MAGE superfamily are expressed in tumors, testis and fetal tissues, which has been described as a cancer/testis or "CT" expression pattern. We have identified a novel member of this superfamily, MAGE-F1, which is expressed in all adult and fetal tissues tested. In addition to normal tissues, MAGE-F1 is expressed in many tumor types including ovarian, breast, cervical, melanoma and leukemia. MAGE-F1 is encoded on chromosome 3, identifying a sixth chromosomal location for a MAGE superfamily gene. The coding region of MAGE-F1 is contained within a single exon and includes a microsatellite repeat. Sequence analysis and expression profiles define a new class of ubiquitously expressed MAGE superfamily genes that includes MAGE-F1, MAGE-D1, MAGE-D2/JCL-1 and NDN. The finding that several MAGE genes are ubiquitously expressed suggests a role for MAGE encoded proteins in normal cell physiology. Furthermore, potential cross-reactivity to these ubiquitously expressed MAGE gene products should be considered in the design of MAGE-targeted immunotherapies for cancer.     

Sequence and expression pattern of the human MAGE2 gene

We reported previously identification of the human MAGE1 gene, which encodes an antigen recognized on human melanoma MZ2-MEL by autologous cytolytic T lymphocytes. In addition to MAGE1, melanoma MZ2-MEL expresses several closely related genes, one of which has been named MAGE2. The complete MAGE2 sequence was obtained and it comprises 3 exons homologous to those of MAGE1 and an additional exon homologous to a region of the first MAGE1 intron. Like the open reading frame of MAGE1, that of MAGE2 is entirely encoded by the last exon. The MAGE1 and MAGE2 sequences of this exon show 82% identity and the putative proteins show 67% identity. The MAGE2 gene is expressed in a higher proportion of melanoma tumors than MAGE1. It is also expressed in many small-cell lung carcinomas and other lung tumors, laryngeal tumors, and sarcomas. No MAGE1 and MAGE2 gene expression was found in a large panel of healthy adult tissues, with the exception of testis.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number L18920.     

Expression of Drosophila MAGE gene encoding a necdin homologous protein in postembryonic neurogenesis

The MAGE (melanoma antigen) family is characterized by a large conserved domain termed MAGE homology domain. Originally identified MAGE genes encoding tumor rejection antigens are expressed only in cancers and male germ cells. Necdin, which contains the MAGE homology domain, is highly expressed in postmitotic cells such as neurons and skeletal muscle cells. The human necdin gene NDN is transcribed only from the paternal allele through genomic imprinting, and its deficiency is implicated in the pathogenesis of the neurodevelopmental disorder Prader-Willi syndrome. Although over 30 MAGE genes have been identified in humans, fruit fly (Drosophila melanogaster) has only a single MAGE gene that encodes a protein similar to necdin homologous MAGE proteins. In this study, we analyzed the spatiotemporal expression patterns of MAGE mRNA and the encoded protein during fly development. Whole-mount embryo in situ hybridization analysis revealed that MAGE mRNA was highly expressed at the syncytial blastoderm stage and in the ventral and procephalic neurogenic regions of the ectoderm during gastrulation. In contrast, MAGE expression was nearly undetectable in postmitotic neurons of the central nervous system at late embryonic stages. During postembryonic neurogenesis, MAGE was highly expressed in neural stem cells (neuroblasts) and their progeny (ganglion mother cells and postmitotic neurons) at larval and pupal stages. MAGE was also expressed in postmitotic neurons including mushroom body neurons and retinal photoreceptors in adulthood. These results indicate that MAGE expression lasts throughout the postembryonic neurogenesis in Drosophila.     

Structural characterization and chromosomal localization of the MAGE-E1 gene

Genes of the melanoma-associated antigen (MAGE) family are characterized by the expression of tumor antigens on a malignant melanoma recognized by autologous cytolytic T lymphocytes. We have previously identified novel members of the MAGE gene family expressed in human glioma and named them MAGE-E1a-c. In the present study, we have revealed the genomic structure of MAGE-E1 by sequence analysis of a human chromosome bacterial artificial chromosome clone containing the MAGE-E1 gene. The MAGE-E1 gene is composed of 13 exons, and three of these (exon 2, exon 3 and exon 12) are alternatively spliced in each variant (E1a-c). The open reading frame encoding the MAGE-E1 peptides initiates in exon 2 and ends in exon 13. We have also demonstrated that the MAGE-E1 gene is located in Xp11 through the analysis of radiation hybrid panels. The genomic structure of MAGE-E1 is markedly similar to that of MAGE-D and its chromosomal locus is also identical to that of MAGE-D, but these features contrast with those of other MAGEs. These results suggest that MAGE-D and -E1 may be evolutionarily distant from other members of the MAGE family, and the two may be ancestral genes for the others.