人X染色体长臂(Xq)和短臂(Xp)基因组学比较分析

X染色体发生X染色体失活 ,但是Xp基因有 30 %表现为逃逸 ,而Xq仅不到 3%。为了研究X染色体基因失活和表达逃逸发生和维持的分子机制 ,比较了Xq和XpDNA序列的RNA模拟结合强度。X染色体的核苷酸序列被分为 5 0kb一段 ,对每一段DNA做 7碱基 (7nt)字符串组合分析 (共有 4 7=16 384种组合 ) ,记录每段 5 0kbDNA中每种 7nt字符串的频率。选择生发中心B细胞中的 12 0个高表达基因 ,计算这些基因的内含子 7nt字符串的出现频率 ,称为intron 7nt,以此作为RNAs(RNA群 ,模拟细胞中RNA在小片段的总和 )。已知一段DNA序列的 7nt频率值和intron 7nt,即可以计算该DNA段与intron 7nt的结合强度。每段 5 0kbDNA与intron 7nt的结合强度取决于该DNA段与intron 7nt互补核苷酸的频率 ,互补的核苷酸序列越多 ,结合强度就越大。DNA段与intron 7nt的模拟结合强度称为RNA结合强度 ,试图模拟该段DNA可以结合的RNA小片段的总量。之所以采用 7nt字符串组合分析是考虑到连续 7个核苷酸互补则可以形成相对稳定的结合。研究发现 :1)Xp各DNA段的RNA结合强度均值显著大于Xq (P <0 0 0 1) ;2 )Xp上高结合RNA的DNA段数目显著高于Xq (P <0 0 0 1) ;3)RNA高结合DNA段形成的簇与X染色体基因表达逃逸区关联。有证据表明 ,RNA可以通过改变染色质     

珍珠鸟(Taeniopygia guttata)小染色体基因表达的密码子偏性

从NCBI数据库（http：／／www．ncbi．nlm．nih．gov／projects／mapview／map）下载珍珠鸟全部小染色体基因的cDNA序列,最终共有1586个基因的CDS序列纳入统计分析。密码子的偏性分析使用CodonW（1．4．2）完成,初步确定了UUC、UCC、UCG等27个密码子为珍珠鸟小染色体基因表达的“最优”密码子。对应分析表明,影响珍珠鸟小染色体基因密码子使用的主要因素分别为GC3s、CDS的GC含量基以及因的表达丰度。珍珠鸟小染色体基因的密码子用法受到了基因碱基组成的显著影响,其密码子的偏性是碱基组成及选择等因素综合作用的结果。本研究的目的是系统探究珍珠乌小染色体基因的密码子用法,探究鸟类基因表达的分子调控机制。     

哺乳动物X染色体失活机制

哺乳动物X染色体连锁基因的剂量平衡,是通过雌性胚胎发育早期随机或印记失活一条X染色体来实现的,这是一个复杂的过程,包括：启动、计数、选择、维持等一系列的步骤。X染色体失活中心是X染色体失活的主控开关座位,调节X失活的早期事件,失活发生后,X染色体的失活状态可稳定地存在并传递给后代,这一过程涉及基因组印记的形成。此外,在雄性动物,精原细胞减数分裂早期也存在着短暂的X染色体失活现象。现对哺乳动物X染色体失活机制的最新进展进行综述。     

失活X染色体基因逃逸与系统性红斑狼疮的性别二态性

X染色体失活可平衡女性中两条X染色体的基因剂量。越来越多的证据表明,失活X染色体上存在许多能够逃逸失活的基因。逃逸的机制涉及到DNA、RNA、组蛋白的表观修饰以及众多的调控蛋白和染色质的空间结构。失活X染色体基因逃逸的研究为人类疾病(特别是自身免疫性疾病)性别二态性的研究开辟了新的途径。目前已证实包括TLR7、CD40L、IRAK-1、CXCR3、CXorf21等失活X染色体基因逃逸是系统性红斑狼疮(systemic lupus erythematosus,SLE)女性好发的重要原因。本文主要综述了失活X染色体上基因逃逸以及与SLE性别二态性形成的分子机制。阐明SLE性别二态性形成的分子机制,不仅对疾病的诊断、治疗具有重要意义,而且对深入揭示人类免疫系统的发育及调控机理也有重要的理论意义。     

X染色体失活机理研究

X染色体失活是哺乳动物中为实现雌性XX个体和雄性XY个体间X染色体上基因剂量补偿作用(dosage compensation)而普遍存在的一种现象,表现为雌性个体两条X染色体中的一条结构异固缩和大范围的基因失活。由于失活基因高度甲基化,曾经认为甲基化在这一过程中发挥重要作用并据此提出一些模型,但相反的证据不断积累使人们对甲基化在这一过程中的主导作用发生怀疑。由于X     

孤雌胚胎干细胞基因印迹及X染色体失活状态初步研究

目的:研究孤雌胚胎干细胞(phESC)与受精卵来源胚胎干细胞(hESC)在印迹基因表达、X染色体失活等方面的异同。方法:运用实时荧光相对定量PCR、甲基化特异性PCR和免疫荧光染色等方法检测phESC与hESC在父系印迹基因IGF2R,母系印迹基因SNRPN,IGF2相对表达量及X染色体失活状态。结果:①母系印迹基因SNRPN,IGF2在phESC细胞中不表达,而父系印迹基因IGF2R表达量则相对于hESC有近2倍的上调;②XIST基因在第35代phESC细胞中没有表达,意味着早期的phESC没有进行X染色体失活,而到了第55代,XIST基因开始表达并随着分化时间的延长表达量逐渐上调;③XIST启动子甲基化状态及组蛋白H3赖氨酸27三甲基化免疫荧光染色阳性证实phESC在长期培养后启动了X染色体失活。结论:phESC的X染色体失活状态在培养过程中存在不稳定的情况,建议对phESC进行更深入的表观遗传稳定性研究,以确保这种细胞未来安全、高效的应用。     

微生物基因组的生物信息学研究平台的建立*

随着人类基因组计划及其它测序工作顺利进行,人们已经得到了大量的基因序列。如何阐明这些序列的功能和意义,是功能基因组学的主要任务。生物信息学和比较基因组学为加速这一进程提供了有利的工具。该研究建立了对已经完成全基因组测序和部分测序的25种细菌的基因组的生物信息学研究平台,提供了WEB形式的服务(http://202.116.74.108)。25种细菌的全基因组蛋白质序列可以在NCBI的ftp://ftp.ncbi.nlm.nih.gov/geabank/genomes/bacteria下载。该系统可以按照基     

反义磷脂酶Dγ转基因片段的结构与功能分析及转基因产物预测

目的:从生物信息学角度,对反义磷脂酶Dγ转基因片段的结构、来源进行查找,并预测分析该片段的转录产物、翻译产物,进而推导该片段的最终产物和作用方式。方法:利用http://www.expasy.ch/、http://bioweb.pasteur.fr、http://fasta.bioch.virginia.edu/fasta_www、http://www.ncbi.nlm.nih.gov等在线分析工具。结果:该片段来自拟南芥第4条染色体上磷脂酶Dγ2(NM_117252.4│GI:42566497),转录生成一段400bp、没有稳定二级结构的RNA,且不能翻译产生蛋白质;经查找,有许多转录物因子和micRNA(mRNA干扰互补RNA,反义RNA)查找。结论:该片段最终产物为micRNA,在RNA干扰(RNAi)水平上调控相关基因的表达。     

微生物基因组的生物信息学研究平台的建立

随着人类基因组计划及其它测序工作顺利进行,人们已经得到了大量的基因序列。如何阐明这些序列的功能和意义,是功能基因组学的主要任务,生物信息学和比较基因组学为加速这一进程提供了有利的工具,该研究建立了对已经完成全基因组测序和部分测序的25种细菌的基因组的生物信息学研究平台,提供了WEB形式的服务（http://202.116.74.108)。25种细菌的全基因组蛋白质序列可以在NCBI的ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/bacteria下载,该系统可以按照基因序列号,功能和种属名查询基因序列。根据美国国家信息中心（NCBI）的功能代码表对每个基因进行了自动和手工分类,并可查询分类情况,在此基因上建立了几种亲缘关系相近的种属的同源基因相互注释功能的应用。     

用于基因数据挖掘的基因表达数据库GEO

使用高通量方法学来检测基因表达情况在最近几年已非常普遍。微集芯片技术可同时定量成千上万的基因转录本。基因表达综合数据库（Gene Expression Omnibus 简称GEO）是目前最大的而且完全公开的高通量分子丰度数据库,主要储存基因表达数据。该数据库以一个灵活开放的设计理念,允许用户或科研人员来递呈,保存和检索多种不同类型的数据。本文综合描述一下近年来该数据库在基因表达数据挖掘中的应用,同时介绍一些通过使用用户友好网络界面能有效探索、查询和再现数百个实验和数百万个基因表达谱的工具,以方便数据进行挖掘和可视化。登录GEO公用数据库的网址为：http://www.ncbi.nlm.nih.gov/geo.     

An evolutionary conserved early replicating segment on the sex chromosomes of man and the great apes

Replication studies on prometaphase chromosomes of man, the chimpanzee, the pygmy chimpanzee, the gorilla, and the orangutan reveal great interspecific homologies between the autosomes. The early replicating X chromosomes clearly show a high degree of conservation of both the pattern and the time course of replication. An early replicating segment on the short arm of the X chromosomes of man (Xp22.3) which escapes inactivation can be found on the X chromosomes of the great apes as well. Furthermore, the most early replicating segment on the Y chromosomes of all species tested appears to be homologous to this segment on the X chromosomes. Therefore, these early replicating segments in the great apes may correspond to the pseudoautosomal segment proposed to exist in man. From further cytogenetic characterization of the Y chromosomes it is evident that structural alterations have resulted in an extreme divergence in both the euchromatic and heterochromatic parts. It is assumed, therefore, that, in contrast to the X chromosomes, the Y chromosomes have undergone a rapid evolution within the higher primates.     

Cytologic evidence for three human X-chromosomal segments escaping inactivation

Summary Early replication of prometaphasic human sex chromosomes was studied with the bromodeoxyuridine (BrdU)-replication technique. The studies reveal that two distal segments of Xp, including bands Xp 22.13 and Xp 22.3, replicate early in S-phase and therefore may not be subject to random inactivation. Furthermore, the replication of these distal segments of Xp occurs synchronously with those of the short arm of the Y chromosome including bands Yp 11.2 and Yp 11.32. These segments of Xp and Yp correspond well to the pairing segment of the X and Y chromosomes where a synaptonemal complex forms at early pachytene of human spermatogenesis. The homologous early replication of Yp and the distal portion of Xp may be interpreted as a remnant left untouched by the differentiation of heteromorphic sex chromosomes from originally homomorphic autosomes. A third early replicating segment is situated on the long arm of the X chromosome and corresponds to band Xq 13.1. This segment may be correlated with the X-inactivation center postulated by Therman et al. (1979).     

Karyotype and heterochromatin pattern of the field mouse,Apodemus argenteus Temminck

The field mouse,Apodemus argenteus Temminck, has 46 chromosomes. The autosomes comprise 20 pairs of acrocentrics and 2 pairs of metacentrics. The X chromosome is represented by an outstandingly large submetacentric element, while the Y is an acrocentric corresponding in size to the 5th or 6th pair of autosomes. All of the autosomes and gonosomes can be unequivocally identified by their characteristic Q-band or G-band patterns. The constitutive heterochromatin, as revealed by C-banding, is localized at the centromeric regions of all autosomes, the short arm and the proximal 1/3 of the long arm of the X chromosome, and the entire Y chromosome. The C-band-positive segments which constitute 33.5% of the genome exhibit dark fluorescence after Q-banding, late DNA replication, faint or positive staining reaction to G-banding, fast reassociation of DNA revealed by AO staining, and allocyclic behavior of the sex-bivalent in male meiosis. An exception to the above is the distal segment of the Y which is positive to both C- and Q-banding. The giant X chromosome occupies 13.1% of the genome, leaving 5.6% of euchromatic segments, the latter value being equivalent to that of the original type X.     

The location of highly repetitious DNA in the somatic chromosomes of Drosophila melanogaster

In situ hybridization of Drosophila melanogaster somatic chromosomes has been used to demonstrate the near exact correspondence between the location of highly repetitious DNA and classically defined constitutive heterochromatin. The Y chromosome, in particular, is heavily labeled even by cRNA transcribed from female (XX) DNA templates (i.e., DNA from female Drosophila with 2 Xs and 2 sets of autosomes). This observation confirms earlier reports that the Y chromosome contains repeated DNA sequences that are shared by other chromosomes. In grain counting experiments the Y chromosome shows significantly heavier label than any other chromosome when hybridized with cRNA from XY DNA templates (i.e., DNA from male Drosophila with 1 X and 1 Y plus 2 sets of autosomes). However, the preferential labeling of the Y is abolished if the cRNA is derived from XX DNA. We interpret these results as indicating the presence of a class of Y chromosome specific repeated DNA in D. melanogaster. The relative inefficiency of the X chromosome in binding cRNA from XY and XYY DNA templates, coupled with its ability to bind XX derived cRNA, may also indicate the presence of an X chromosome specific repeated DNA.     

MAMMALIAN CHROMOSOMES IN VITRO : XVIII. DNA Replication Sequence in the Chinese Hamster

The complete DNA replication sequence of the entire complement of chromosomes in the Chinese hamster may be studied by using the method of continuous H³-thymidine labeling and the method of 5-fluorodeoxyuridine block with H³-thymidine pulse labeling as relief. Many chromosomes start DNA synthesis simultaneously at multiple sites, but the sex chromosomes (the Y and the long arm of the X) begin DNA replication approximately 4.5 hours later and are the last members of the complement to finish replication. Generally, chromosomes or segments of chromosomes that begin replication early complete it early, and those which begin late, complete it late. Many chromosomes bear characteristically late replicating regions. During the last hour of the S phase, the entire Y, the long arm of the X, and chromosomes 10 and 11 are heavily labeled. The short arm of chromosome 1, long arm of chromosome 2, distal portion of chromosome 6, and short arms of chromosomes 7, 8, and 9 are moderately labeled. The long arm of chromosome 1 and the short arm of chromosome 2 also have late replicating zones or bands. The centromeres of chromosomes 4 and 5, and occasionally a band on the short arm of the X are lightly labeled.     

Current status of the river buffalo (Bubalus bubalis L.) gene map.

Ninety-nine loci have been assigned to river buffalo chromosomes, 67 of which are coding genes and 32 of which are anonymous DNA segments (microsatellites). Sixty-seven assignments were based on cosegregation of cellular markers in somatic cell hybrids (synteny), whereas 39 were based on in situ hybridization of fixed metaphase chromosomes with labeled DNA probes. Seven loci were assigned by both methods. Of the 67 assignments in somatic cell hybrids, 38 were based on polymerase chain reaction (PCR), 11 on isozyme electrophoresis, 10 on restriction endonuclease digestion of DNA, 4 on immunofluorescence, and 4 on chromosomal identification. A genetic marker or syntenic group has been assigned to each arm of the five submetacentric buffalo chromosomes as well as to the 19 acrocentric autosomes, and the X and Y chromosomes. These same markers map to the 29 cattle autosomes and the X and Y chromosomes, and without exception, cattle markers map to the buffalo chromosome or chromosomal region predicted from chromosome banding similarity.