Epigenetic aspects of X-chromosome dosage compensation

The X chromosomes of mammals and fruit flies exhibit unusual properties that have evolved to deal with the different dosages of X-linked genes in males (XY) and females (XX). The X chromosome dosage-compensation mechanisms discovered in these species are evolutionarily unrelated, but exhibit surprising parallels in their regulatory strategies. These features include the importance of noncoding RNAs, and epigenetic spreading of chromatin-modifying activities. Sex chromosomes have posed a fascinating puzzle for biologists. The dissimilar organization, gene content, and regulation of the X and Y chromosomes are thought to reflect selective forces acting on original pairs of identical chromosomes (1-3). The result in many organisms is a male-specific Y chromosome that has lost most of its original genetic content, and a difference in dosage of the X chromosome in males (XY) and females (XX).     

Paucity of genes on the Drosophila X chromosome showing male-biased expression

Sex chromosomes are primary determinants of sexual dimorphism in many organisms. These chromosomes are thought to arise via the divergence of an ancestral autosome pair and are almost certainly influenced by differing selection in males and females. Exploring how sex chromosomes differ from autosomes is highly amenable to genomic analysis. We examined global gene expression in Drosophila melanogaster and report a dramatic underrepresentation of X-chromosome genes showing high relative expression in males. Using comparative genomics, we find that these same X-chromosome genes are exceptionally poorly conserved in the mosquito Anopheles gambiae. These data indicate that the X chromosome is a disfavored location for genes selectively expressed in males.     

Temperature sex reversal implies sex gene dosage in a reptile

Sex in reptiles is determined by genes on sex chromosomes or by incubation temperature. Previously these two modes were thought to be distinct, yet we show that high incubation temperatures reverse genotypic males (ZZ) to phenotypic females in a lizard with ZZ and ZW sex chromosomes. Thus, the W chromosome is not necessary for female differentiation. Sex determination is probably via a dosage-sensitive male-determining gene on the Z chromosome that is inactivated by extreme temperatures. Our data invite a novel hypothesis for the evolution of temperature-dependent sex determination (TSD) and suggest that sex chromosomes may exist in many TSD reptiles.     

Extensive gene traffic on the mammalian X chromosome

Mammalian sex chromosomes have undergone profound changes since evolving from ancestral autosomes. By examining retroposed genes in the human and mouse genomes, we demonstrate that, during evolution, the mammalian X chromosome has generated and recruited a disproportionately high number of functional retroposed genes, whereas the autosomes experienced lower gene turnover. Most autosomal copies originating from X-linked genes exhibited testis-biased expression. Such export is incompatible with mutational bias and is likely driven by natural selection to attain male germline function. However, the excess recruitment is consistent with a combination of both natural selection and mutational bias.     

Microinjected DNA from the X chromosome affects sex determination in Caenorhabditis elegans

The signal for sex determination in the nematode Caenorhabditis elegans is the ratio of the number of X chromosomes to the number of sets of autosomes (X/A ratio). By previous genetic tests, elements that feminized chromosomal males appeared to be widespread on the X chromosome, but the nature of these elements was not determined. In experiments to define a feminizing element molecularly, cloned sequences were added to chromosomally male embryos by microinjection into the mother. Three different X-chromosome clones, including part of an actin gene, part of a myosin heavy chain gene, and all of two myosin light chain genes, feminize chromosomal males. Both somatic and germline aspects of sex determination are affected. In contrast, about 40 kilobases of nematode autosomal DNA, phage lambda DNA, and plasmid pBR322 DNA do not affect sex determination. A feminizing region was localized to a maximum of 131 base pairs within an intron of the X-linked actin gene; a part of the gene that does not have this region is not feminizing. The results suggest that short, discrete elements found associated with many X-linked genes may act as signals for sex determination in C. elegans.     

森林草莓糖基转移酶基因家族生物信息学及其表达分析

【目的】对森林草莓糖基转移酶基因（FvUGT）家族进行生物信息学分析及基因表达分析,为深入研究森林草莓UGT基因功能和探索UGT调控草莓果实发育及花色苷及品质形成提供理论依据。【方法】基于Phytozome数据库鉴定得出138个FvUGT基因家族基因,运用生物信息学方法分析其蛋白理化性质、基因结构、保守结构域和进化关系,并采用实时荧光定量PCR对UFGT候选基因在森林草莓（红果和白果2个类型）各组织（根、叶柄、叶和果实）中的表达量进行分析。【结果】FvUGT基因家族可分为12个类群（A、C、D、E、F、G、H、I、J、K、L和N）,每个类群分别包含16、2、23、32、8、1、5、5、7、3、21和4个成员;染色体定位发现FvUGT基因家族成员在除2号染色体之外的其他染色体上均有分布,且分布不均;FvUGT基因内含子长度、外显子位置和数目在不同成员间均存在差异,FvUGT基因家族在进化过程中产生较强的分化。实时荧光定量PCR检测结果表明,FvUFGT70基因在森林草莓白果和红果的叶和叶柄中有较高表达;FvUFGT94基因在各组织中均有表达;FvUFGT67和FvUFGT68基因在根中有较高表达;而FvUFGT95和FvUFGT96基因在果实中有表达,且显著高于其他组织（P<0.05,下同）。同时,在果实的小绿期、转色期和成熟期的表达表现为,成熟期FvUFGT33和FvUFGT95这2个基因在森林草莓红果类型的表达量显著高于白果类型。【结论】7个FvUFGT基因表现出明显的组织差异性,其中FvUFGT33和FvUFGT95基因在果实中有较高表达量,且在森林草莓红果类型表达量显著高于白果类型,故推测其在花色苷合成中发挥作用。     

大豆SBP基因家族的序列特征、表达及进化分析

SBP基因家族是植物所特有的一类重要转录因子,由多个成员组成,主要参与植物生长、发育以及多种生理生化过程.试验在大豆基因组中鉴定49个SBP基因,被命名为GmSBP1~49.基于生物信息学手段,对大豆该基因家族49个成员的基因结构、染色体定位、蛋白保守序列、亚细胞定位、表达情况及进化关系进行分析.序列分析表明,SBP基因家族成员分散于不同染色体上,不同基因具有不同个数的外显子,其数目变异范围为1~14;该家族蛋白含有5个保守基序,尽管与SBP结构域有所重叠,但它们能形成6种不同的组织模式,这说明该基因家族序列变异较为复杂.表达分析结果显示,除GmSBP2和GmSBP11等6个基因没有相应的EST外,其余基因都有转录活性;在具有转录活性的基因中,只有GmSBP46显示出组成型表达模式,剩余基因表现出不同程度的组织特异性表达模式.拟南芥、水稻和大豆SBP蛋白的进化树揭示该家族具有8个类群,其中E类群只包括大豆SBP基因,其他类群中大豆SBP基因数目也是最多,这充分说明大豆SBP基因家族起源与进化的复杂性.研究为大豆SBP基因功能研究提供线索     

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees

The determination of the chimpanzee genome sequence provides a means to study both structural and functional aspects of the evolution of the human genome. Here we compare humans and chimpanzees with respect to differences in expression levels and protein-coding sequences for genes active in brain, heart, liver, kidney, and testis. We find that the patterns of differences in gene expression and gene sequences are markedly similar. In particular, there is a gradation of selective constraints among the tissues so that the brain shows the least differences between the species whereas liver shows the most. Furthermore, expression levels as well as amino acid sequences of genes active in more tissues have diverged less between the species than have genes active in fewer tissues. In general, these patterns are consistent with a model of neutral evolution with negative selection. However, for X-chromosomal genes expressed in testis, patterns suggestive of positive selection on sequence changes as well as expression changes are seen. Furthermore, although genes expressed in the brain have changed less than have genes expressed in other tissues, in agreement with previous work we find that genes active in brain have accumulated more changes on the human than on the chimpanzee lineage.     

黄瓜AQP基因家族的鉴定与生物信息学分析

  目的  深入研究黄瓜Cucumis sativus水通道蛋白(aquaporin, AQP)基因家族(CsAQP)的相关功能。  方法  通过全基因组分析技术鉴定其家族成员,对其蛋白质理化性质、系统进化关系、选择压力、基因结构、保守基序、顺式作用元件、蛋白质互作进行分析。  结果  黄瓜基因组共有33个AQP基因,含有2~5个数量不等的外显子,在染色体上不均匀分布;根据物种进化关系将黄瓜AQP基因家族划分为5个亚家族;基因组重复序列分析表明:5号和6号染色体上各有2~3对基因串联重复;计算这些基因的同义替换(synonymous, K_s)和非同义替换(nonSynonymous, K_a)的比率,结果显示均小于1,表明其进化受纯化选择作用;顺式作用调控元件分析发现,大部分基因启动子区所含元件与激素调节、光响应、胁迫密切相关。  结论  通过黄瓜全基因组扫描,获得黄瓜基因组的33个AQP家族成员,分属于5个亚族,映射于7条染色体上。上游启动子区含逆境相关作用元件,且部分基因参与串联复制,历经纯化选择。图6表4参26     

Genetics. Reprogramming X inactivation

Inactivation of one of the two X chromosomes occurs in all cells of female adult mice so that genes are expressed from only one X chromosome. In a Perspective, Clerc and Avner describe an elegant series of experiments in mouse embryos cloned from adult and embryonic female cell nuclei (Eggan et al.) that reveal how the inactivation state of the X chromosomes is reprogrammed.     

水稻dirigent基因家族生物信息学分析

摘　要：利用现有的水稻生物信息资源,共鉴定出了53个水稻dirigent (OsDIR)基因,它们分布在8条水稻染色体上;基因结构分析显示,有32个OsDIR基因不含内含子,占总数的60.4%;保守功能区域预测表明,OsDIR基因至少含有1个保守的DIR功能域;模块预测显示,水稻DIR蛋白拥有至少10个大小不同的保守模块,且不同模块在基因家族成员中出现的频率有较大的差异;蛋白序列比对表明,该基因家族蛋白保守序列均位于DIR功能域内;蛋白功能预测表明,大多数OsDIR蛋白为稳定的疏水性蛋白,表达于大多数细胞器中,且在细胞壁中表达最为丰富;同源基因分子遗传进化分析表明,OsDIR基因可分为5个亚类,功能域片段与基因的复制特征表明,OsDIR基因可能起源于共同的祖先(基因)。     

Function, developmental genetics, and fitness consequences of a sexually antagonistic trait

Sexual conflict is thought to be a potent force driving the evolution of sexually dimorphic traits. In the water strider Rheumatobates rileyi, we show that elaborated traits on male antennae function to grasp resistant females during premating struggles. Using RNA interference, we uncovered novel roles of the gene distal-less (dll) in generating these male-specific traits. Furthermore, graded reduction of the grasping traits resulted in a graded reduction of mating success in males, thus demonstrating both selection for elaboration of the traits and the role of dll in their evolution. By establishing developmental genetic tools in model systems where sexual selection and conflict are understood, we can begin to reveal how selection can exploit ancient developmental genes to enable the evolution of sexually dimorphic traits.     

荆芥HD-Zip基因家族的全基因组鉴定及分析

【目的】鉴定荆芥Schizonepeta tenuifolia的HD-Zip基因家族,利用生物信息学方法分析其在全基因组中的分布和相关特征以及在不同时期中的表达规律,为该家族基因的进一步研究奠定基础。【方法】根据已经表征的HD-Zip基因,筛选荆芥基因组内的HD-Zip基因序列,利用MEME、PlantCARE、NCBI、MEGA X、MCScanX、Circos等在线网站及软件对蛋白序列进行基本理化性质分析、进化树构建、染色体定位、基因结构分析、共线性基因分析等。【结果】在荆芥全基因组中共鉴定到42条HD-Zip基因序列,它们可被分为4个亚家族,分别含有16、7、5、14个基因,亚家族之间的基因长度、结构及保守基序差异显著,但在亚家族内部保守,荆芥基因组与拟南芥Arabidopsis thaliana基因组共线性分析发现有37对基因,可能具有相似的生物学功能。荆芥的4个亚家族基因的顺式元件中均高频出现了光响应、脱落酸响应、MeJA响应等元件,在不同生长时期的叶片及部位的转录组数据中具有不同的表达趋势,Ⅰ亚家族主要在幼叶中表达,Ⅱ和Ⅲ亚家族主要在根中在表达,Ⅳ亚家族主要在叶中表达。【结...     

Mammalian ZFY sequences exist in reptiles regardless of sex-determining mechanism

In some reptiles, egg incubation temperature determines whether the embryo hatches as male or female; in others, sex chromosomes determine sex. A cloned gene (ZFY) representing the putative testis-determining factor in mammals was hybridized to genomic DNA of reptiles with sex chromosomes and to DNA of reptiles with temperature-dependent sex determination. No sex differences in hybridization patterns were observed. Hybridization of ZFY to polyadenylated RNA indicates that reptilian versions of this gene are expressed in embryos of both sexes during the temperature-sensitive period. If these highly conserved sequences are important in reptilian sex determination, then temperature-dependent and genotypic sex determination may have a similar molecular basis. For reptiles with XX/XY or ZZ/ZW systems, the absence of sex differences in hybridization patterns raises the question of whether the ZFY sequences reside on their sex chromosomes.     

葡萄MPT基因家族鉴定与表达分析

线粒体磷酸转运体(mitochondrial phosphate transporter, MPT)基因家族是位于线粒体内膜上的一种重要的功能蛋白,负责将重要代谢底物无机磷酸通过线粒体内膜从细胞质转移到线粒体基质中,在细胞维持正常功能中起到了关键的生理作用。本研究利用生物信息学工具,系统地分析了葡萄MPT基因家族成员的进化关系、基因结构、蛋白质理化性质和保守基序,以及组织特异性表达和同源基因的相关性。结果表明,葡萄全基因组中鉴定出64个MPT家族基因。根据系统发育树可以分为7组,分布于19条染色体上,其中两对基因存在串联复制现象。保守基序分析表明,所有MPT家族成员都含有保守的Mito_carr结构域。组织特异性表达表明,VvMPT基因在果皮、花、叶中高表达。同源基因分析表明,葡萄VvMPT基因家族可能在花器官发育、维持离子浓度中起到了重要作用。     

Cloning of human androgen receptor complementary DNA and localization to the X chromosome

The androgen receptor (AR) mediates the actions of male sex steroids. Human AR genomic DNA was cloned from a flow-sorted human X chromosome library by using a consensus nucleotide sequence from the DNA-binding domain of the family of nuclear receptors. The AR gene was localized on the human X chromosome between the centromere and q13. Cloned complementary DNA, selected with an AR-specific oligonucleotide probe, was expressed in monkey kidney (COS) cells and yielded a high-affinity androgen-binding protein with steroid-binding specificity corresponding to that of native AR. A predominant messenger RNA species of 9.6 kilobases was identified in human, rat, and mouse tissues known to contain AR and was undetectable in tissues lacking AR androgen-binding activity, including kidney and liver from androgen-insensitive mice. The deduced amino acid sequence of AR within the DNA-binding domain has highest sequence identity with the progesterone receptor.     

甜菜WRKY转录因子全基因组鉴定及其在非生物胁迫下的表达分析

【目的】WRKY转录因子是一类植物响应生物、非生物胁迫,对生长发育都起重要调控作用的转录因子。在甜菜全基因组信息分析的基础上,鉴定WRKY家族基因(Bv WRKYs),解析其组织特异性及盐、热胁迫下的表达情况,为该类基因的功能研究提供参考,为观赏甜菜和石竹目其他观赏植物的基因工程打下基础。【方法】以75条拟南芥WRKY蛋白为参考,根据WRKY保守蛋白序列(PF03106)利用hmm和BLAST同源性搜索对甜菜WRKY家族基因进行鉴定。利用Map Inspect、GSDS2.0、MEGA5.0、DNAMAN5.0、Web Logo 3、MEME生物信息学工具对甜菜WRKY家族基因染色体定位、系统发生关系、基因结构、蛋白质保守结构域、保守元件进行预测和分析。利用RNA-seq和q RT-PCR分析甜菜WRKY组织表达特异性,盐胁迫、热胁迫条件下WRKY表达情况。【结果】甜菜WRKY家族基因包含40个成员,其中39条不均匀地分布在9条染色体上,另外1条定位到随机片段上。根据WRKY保守域特征并与拟南芥WRKY蛋白进化分析,可将40个成员分为Ⅰ、Ⅱ、Ⅲ3类,Ⅰ类有9个成员,Ⅱ类有26个成员,Ⅲ类有5个成员。根据进化关系Ⅱ类可进一步分为Ⅱa(1个)、Ⅱb(4个)、Ⅱc(9个)、Ⅱd(5个)和Ⅱe(7个)5个亚类。基因结构分析发现,甜菜WRKY外显子和内含子数目具有高变异性(2—7个外显子),即使同一亚类内也都差异较大。保守元件分析显示同一类或亚类内成员具有相同的保守元件。WRKY保守域分析发现2个WRKY七肽域变型:WRKYGKK和WRKYGEK。每个WRKY至少在2个组织中表达,30个WRKY在叶中表达,40个WRKY在花序中均有表达,36个WRKY在幼叶中有表达,38个WRKY在直根中有表达,39个WRKY在幼苗中有表达,36个WRKY在种子中有表达。各WRKY表达量差异较大,可分为低表达、高表达基因两类,如Bv WRKY23、Bv WRKY3、Bv WRKY11、Bv WRKY7、Bv WRKY6、Bv WRKY26、Bv WRKY4、Bv WRKY40、Bv WRKY24、Bv WRKY2和Bv WRKY28在各组织中均有较高表达,而Bv WRKY38、Bv WRKY13、Bv WRKY36、Bv WRKY35、Bv WRKY5和Bv WRKY34在各组织中均表达较低。热胁迫条件下Bv WRKY16、Bv WRKY21、Bv WRKY20、Bv WRKY22、Bv WRKY32、Bv WRKY33和Bv WRKY34上调表达;盐胁迫条件下Bv WRKY1、Bv WRKY6、Bv WRKY19、Bv WRKY31和Bv WRKY33呈现不同程度上调表达;Bv WRKY33对热、盐2种胁迫均有明显响应。【结论】甜菜WRKY蛋白结构高度保守,基因序列长度和内含子数量变化很大,在不同组织中呈现出多种表达模式,部分WRKY响应热或盐胁迫,对甜菜逆境生理调控起重要作用。     

苹果MADS-box转录因子的生物信息学及其在不同组织中的表达

【目的】分析已知苹果（Malus×domestica）MADS-box基因基本信息,研究其在不同组织中表达情况。【方法】利用NCBI数据库查询并获得苹果MADS-box基因,采用CLC Combined Workbench version 6、WebLogo 3、MEGA4.1、MapInspect和MEME等软件对其蛋白序列进行生物信息学分析。采用RT-PCR技术研究MdMADS基因在不同组织中的表达情况。【结果】共得到26个苹果MADS-box基因。MADS-box结构域分析显示,氨基酸10（I）、16-19（RQVT）、22-23（KR）、29-31（KKA）、33（E）、37-39（LCD）、42（V）和48（S）是保守不变的。保守元件分析表明,苹果MADS-box基因包含4个保守元件：元件1、3为MADS盒;元件2、4为K盒。所有苹果MADS-box蛋白都包含有MADS盒（除MdMADS9）和K盒。进化树分析结果显示,苹果MADS基因共分为5个亚组。MdMADS1、3、4、6、7、8、11、18属于SEP亚组;MdMADS2、5、12属于AP1亚组;MdMADS10、14、15、19、22和MdAGL属于AG亚组;MdMADS16、17、21、MdSOC1、MdSOC1a和MdSOC1c属于SOC1亚组;MdMADS13、23和MdPI属于AP3亚组;MdMADS20属于SVP亚组。染色体定位分析显示,MdMADS在8号染色体上分布最多,共有4个;其次是染色体2、14和17,均分布3个;染色体1、5、6、7、11和16均分布1个;染色体3、4、12和15则没有分布。RT-PCR结果分析显示,SEP和AGL亚组表达模式较为一致,主要在花和果实中表达;AP1亚组除在花和果实中表达外,在其它组织器官中也有表达。【结论】苹果MADS-box基因结构高度保守,多数成员参与调控花和果实发育过程。