重复序列及异染色质化在植物性染色体重组抑制中的作用

重组抑制是植物性染色体由常染色体进化而来的前提条件,性别决定位点区域发生的重组抑制使早期的性染色体发生了退化和分化。研究表明,重组抑制的产生和染色体上一系列行为的发生有着密切的关系,如重复序列的累积、异染色质化及DNA的甲基化。转座因子和卫星DNA等重复序列的累积使早期植物性染色体形态和分子结构发生了分化,同时还导致性染色体的异染色质化,抑制了性染色体间的重组的发生。文章综述了这一领域的进展,并对DNA甲基化在植物性染色体重组抑制形成过程中可能的作用进行了简要分析。     

兰州百合B染色体的初步研究

对兰州百合具B染色体的细胞在有丝分裂和减数分裂过程中的行为进行了观察。结果表明,B染色体数在0～3之间变化,在有丝分裂和减数分裂中均高度异染色质化,分离具有不定向性,出现少量累积。通过比较两种生境中B染色体出现的频率,认为B染色体的有或无可能与兰州百合的适应性有关。     

RNA干扰技术及应用的研究进展

RNA干扰(RNAi)是由双链RNA(dsRNA)介导的序列特异的基因沉默现象,RNAi效应具有高特异性和高效性的显著特征,能够在细胞和子代间传递.除诱导同源序列mRNA降解或阻止其翻译而使目的基因表达受阻的转录后基因沉默外,RNA干扰可通过组蛋白甲基化影响染色质结构、通过DNA甲基化在转录水平调节基因表达,在翻译水平调节机体发育,并作为基因组的免疫系统,使转座因子或重复序列区域异染色质化,有效抑制了转座子和重复序列之间的同源重组对基因组可能造成的破坏,使生物基因组在长期进化过程中能保持结构的完整性和遗传的连续性. RNA干扰以阻抑基因的表达来模拟基因敲除技术,为反向遗传学研究基因功能提供了一种快速和简便的方法.RNA干扰技术日趋成熟和完善,为人们迅速准确地分析基因功能提供了极为有用的工具,同时在临床应用和治疗肿瘤和癌症等方面也有着巨大的应用前景.     

转座子衍生基因的演变途径及对生物生长发育的影响

转座子(transposable elements,TEs)是指在基因组上能从同一条染色体的一个位置转移到另一个位置或者从一条染色体转移到另一条染色体上的一段DNA序列。广泛存在于基因组中的转座子通过复制、动员、重组基因片段以及修改原基因结构形成的新基因,被称为转座子衍生基因。该文综述了转座子衍生基因与转座子和常规基因的异同以及转座子衍生基因的演变途径,归纳了转座子衍生基因对宿主基因进化,以及对生物生长发育的影响。     

哺乳动物二倍体性别决定系统的多样性

哺乳动物的大多数物种具有XY染色体性别决定 系统。例如,猩猩(Pongo pygmaeets）的二倍体染色 体数,不论是雌性个体还是雄性个体,均为2n = 44, 一可配为22对。其中21对为常染色体;另一对是决定 性别的性染色体,在雌性为XX,在雄性为XY。这是一 般熟知的情况。     

人类的性別决定

1923年,潘特(Painter)首先提出人类的性别,决定于X和Y两种不同的性染色体。女性的性染色体为XX,男性的性染色体为XY。人类的卵一律含有一个X染色体(另有一组常染色体);而精子却分为二类:一类含有一个X染色体,另一类含有一个Y染色体(此二类精子也都另有一组常染色体)。卵与X精子受精,形成XX合子,则发育为女性,若与Y精子受精,形成XY合子,则发育为男性。潘特所提出的有关人类的性别决定方法,基本上是正确的。不过,他所提出的人类染色体数目是48的     

果蝇限制端粒转座子的分子机制

端粒是保护线性染色体末端的核酸-蛋白复合物。与常见的真核生物短重复序列组成的端粒不同,黑腹果蝇(Drosophila melanogaster)端粒DNA由反转座子组成,其转座行为被果蝇宿主严格限制在端粒,既实现延长端粒的功能,也减少转座子跳跃对基因组的损伤。但果蝇宿主是如何完成如此精确调控的机制尚不明确。目前已知的全基因组范围抑制转座子表达包括H3K9me3参与的异染色质形成途径和piRNA路径,而近期研究发现果蝇端粒保护蛋白参与端粒反转座子的特异调控。本文主要综述了端粒保护蛋白在调控端粒转座子中的具体功能。对果蝇端粒转座子调控的研究有利于更好地理解宿主与转座子协同进化的分子机制。     

性别的决定有新说

人的性別究竟由什么来决定?高中生物课本里的XY型性别决定是这样讲的:如果含有XX染色体的合子发育成雌性个体;如果含有XY染色体的合子发育成雄性个体.随着科学技术的发展,这种性别决定的理论被认为是错误的.新的研究指出:性别的决定不是整个性染色体而是性染色体上的极个别的基因.这个发现是由遗传学家戴维·佩奇为首的研究小组获得的.他们认为,那极个别的基因,虽只代表整个性染色体的千分之一,但这种个别的基因却是决定性别差异的关键.     

黑斑蛙的减数分裂研究

本文研究了黑斑蛙的减数分裂,发现其性染色体所形成的性二价体主要呈末端与末端联接,浓缩期占79.6％,中期Ⅰ占75％,这进一步证明黑斑蛙确实存在XY型性别决定机制,这种XY型性染色体虽形态相同,但已发生了质的分化,可能是同型异质。黑斑蛙的性染色体并不形成性泡,少数二价体有中间交叉。     

两栖动物性染色体的多样性及其 进化机制的研究进展

两栖动物性别决定类型和性染色体具有多样性的特点。在已发现异形性染色体两栖动物中,大部分物种Y或W染色体大于其对应的X或Z染色体,少数物种具有高度分化的Y或W染色体。同时两栖动物类群内基因组大小差异大,性染色体间分子水平上也存在差异。高频转换、偶然重组和染色体重排可能是两栖动物性染色体进化过程中的关键机制。本综述通过对两栖动物性染色体进化的深入探讨,揭示其遗传性别决定的机理,有助于对两栖动物性别人工调控的进一步探索。     

Sequence differentiation associated with an inversion on the neo-X chromosome of Drosophila americana

Sex chromosomes originate from pairs of autosomes that acquire controlling genes in the sex-determining cascade. Universal mechanisms apparently influence the evolution of sex chromosomes, because this chromosomal pair is characteristically heteromorphic in a broad range of organisms. To examine the pattern of initial differentiation between sex chromosomes, sequence analyses were performed on a pair of newly formed sex chromosomes in Drosophila americana. This species has neo-sex chromosomes as a result of a centromeric fusion between the X chromosome and an autosome. Sequences were analyzed from the Alcohol dehydrogenase (Adh), big brain (bib), and timeless (tim) gene regions, which represent separate positions along this pair of neo-sex chromosomes. In the northwestern range of the species, the bib and Adh regions exhibit significant sequence differentiation for neo-X chromosomes relative to neo-Y chromosomes from the same geographic region and other chromosomal populations of D. americana. Furthermore, a nucleotide site defining a common haplotype in bib is shown to be associated with a paracentric inversion [In(4)ab] on the neo-X chromosome, and this inversion suppresses recombination between neo-X and neo-Y chromosomes. These observations are consistent with the inversion acting as a recombination modifier that suppresses exchange between these neo-sex chromosomes, as predicted by models of sex chromosome evolution.     

Reduced sequence variability on the Neo-Y chromosome of Drosophila americana americana.

Sex chromosomes are generally morphologically and functionally distinct, but the evolutionary forces that cause this differentiation are poorly understood. Drosophila americana americana was used in this study to examine one aspect of sex chromosome evolution, the degeneration of nonrecombining Y chromosomes. The primary X chromosome of D. a. americana is fused with a chromosomal element that was ancestrally an autosome, causing this homologous chromosomal pair to segregate with the sex chromosomes. Sequence variation at the Alcohol Dehydrogenase (Adh) gene was used to determine the pattern of nucleotide variation on the neo-sex chromosomes in natural populations. Sequences of Adh were obtained for neo-X and neo-Y chromosomes of D. a. americana, and for Adh of D. a. texana, in which it is autosomal. No significant sequence differentiation is present between the neo-X and neo-Y chromosomes of D. a. americana or the autosomes of D. a. texana. There is a significantly lower level of sequence diversity on the neo-Y chromosome relative to the neo-X in D. a. americana. This reduction in variability on the neo-Y does not appear to have resulted from a selective sweep. Coalescent simulations of the evolutionary transition of an autosome into a Y chromosome indicate there may be a low level of recombination between the neo-X and neo-Y alleles of Adh and that the effective population size of this chromosome may have been reduced below the expected value of 25% of the autosomal effective size, possibly because of the effects of background selection or sexual selection.     

Genomic degradation of a young Y chromosome in Drosophila miranda

Background

Y chromosomes are derived from ordinary autosomes and degenerate because of a lack of recombination. Well-studied Y chromosomes only have few of their original genes left and contain little information about their evolutionary origin. Here, we take advantage of the recently formed neo-Y chromosome of Drosophila miranda to study the processes involved in Y degeneration on a genomic scale.

Results

We obtained sequence information from 14 homologous bacterial artificial chromosome (BAC) clones from the neo-X and neo-Y chromosome of D. miranda, encompassing over 2.5 Mb of neo-sex-linked DNA. A large fraction of neo-Y DNA is composed of repetitive and transposable-element-derived DNA (20% of total DNA) relative to their homologous neo-X linked regions (1%). The overlapping regions of the neo-sex linked BAC clones contain 118 gene pairs, half of which are pseudogenized on the neo-Y. Pseudogenes evolve significantly faster on the neo-Y than functional genes, and both functional and non-functional genes show higher rates of protein evolution on the neo-Y relative to their neo-X homologs. No heterogeneity in levels of degeneration was detected among the regions investigated. Functional genes on the neo-Y are under stronger evolutionary constraint on the neo-X, but genes were found to degenerate randomly on the neo-Y with regards to their function or sex-biased expression patterns.

Conclusion

Patterns of genome evolution in D. miranda demonstrate that degeneration of a recently formed Y chromosome can proceed very rapidly, by both an accumulation of repetitive DNA and degeneration of protein-coding genes. Our data support a random model of Y inactivation, with little heterogeneity in degeneration among genomic regions, or between functional classes of genes or genes with sex-biased expression patterns.     

Sex Chromosome Turnover Contributes to Genomic Divergence between Incipient Stickleback Species

Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL) mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.     

The Epigenome of Evolving Drosophila Neo-Sex Chromosomes: Dosage Compensation and Heterochromatin Formation

Sex chromosomes originated from autosomes but have evolved a highly specialized chromatin structure. Drosophila Y chromosomes are composed entirely of silent heterochromatin, while male X chromosomes have highly accessible chromatin and are hypertranscribed as a result of dosage compensation. Here, we dissect the molecular mechanisms and functional pressures driving heterochromatin formation and dosage compensation of the recently formed neo-sex chromosomes of Drosophila miranda. We show that the onset of heterochromatin formation on the neo-Y is triggered by an accumulation of repetitive DNA. The neo-X has evolved partial dosage compensation and we find that diverse mutational paths have been utilized to establish several dozen novel binding consensus motifs for the dosage compensation complex on the neo-X, including simple point mutations at pre-binding sites, insertion and deletion mutations, microsatellite expansions, or tandem amplification of weak binding sites. Spreading of these silencing or activating chromatin modifications to adjacent regions results in massive mis-expression of neo-sex linked genes, and little correspondence between functionality of genes and their silencing on the neo-Y or dosage compensation on the neo-X. Intriguingly, the genomic regions being targeted by the dosage compensation complex on the neo-X and those becoming heterochromatic on the neo-Y show little overlap, possibly reflecting different propensities along the ancestral chromosome that formed the sex chromosome to adopt active or repressive chromatin configurations. Our findings have broad implications for current models of sex chromosome evolution, and demonstrate how mechanistic constraints can limit evolutionary adaptations. Our study also highlights how evolution can follow predictable genetic trajectories, by repeatedly acquiring the same 21-bp consensus motif for recruitment of the dosage compensation complex, yet utilizing a diverse array of random mutational changes to attain the same phenotypic outcome.     

Evolution of amino-acid sequences and codon usage on the Drosophila miranda neo-sex chromosomes

We have studied patterns of DNA sequence variation and evolution for 22 genes located on the neo-X and neo-Y chromosomes of Drosophila miranda. As found previously, nucleotide site diversity is greatly reduced on the neo-Y chromosome, with a severely distorted frequency spectrum. There is also an accelerated rate of amino-acid sequence evolution on the neo-Y chromosome. Comparisons of nonsynonymous and silent variation and divergence suggest that amino-acid sequences on the neo-X chromosome are subject to purifying selection, whereas this is much weaker on the neo-Y. The same applies to synonymous variants affecting codon usage. There is also an indication of a recent relaxation of selection on synonymous mutations for genes on other chromosomes. Genes that are weakly expressed on the neo-Y chromosome appear to have a faster rate of accumulation of both nonsynonymous and unpreferred synonymous mutations than genes with high levels of expression, although the rate of accumulation when both types of mutation are pooled is higher for the neo-Y chromosome than for the neo-X chromosome even for highly expressed genes.     

Contrasting patterns of molecular evolution of the genes on the new and old sex chromosomes of Drosophila miranda

In organisms with chromosomal sex determination, sex is determined by a set of dimorphic sex chromosomes that are thought to have evolved from a set of originally homologous chromosomes. The chromosome inherited only through the heterogametic sex (the Y chromosome in the case of male heterogamety) often exhibits loss of genetic activity for most of the genes carried on its homolog and is hence referred to as degenerate. The process by which the proto-Y chromosome loses its genetic activity has long been the subject of much speculation. We present a DNA sequence variation analysis of marker genes on the evolving sex chromosomes (neo-sex chromosomes) of Drosophila miranda. Due to its relatively recent origin, the neo-Y chromosome of this species is presumed to be still experiencing the forces responsible for the loss of its genetic activity. Indeed, several previous studies have confirmed the presence of some active loci on this chromosome. The genes on the neo-Y chromosome surveyed in the current study show generally lower levels of variation compared with their counterparts on the neo-X chromosome or an X-linked gene. This is in accord with a reduced effective population size of the neo-Y chromosome. Interestingly, the rate of replacement nucleotide substitutions for the neo-Y linked genes is significantly higher than that for the neo-X linked genes. This is not expected under a model where the faster evolution of the X chromosome is postulated to be the main force driving the degeneration of the Y chromosome.     

Heterogeneous Histories of Recombination Suppression on Stickleback Sex Chromosomes

How consistent are the evolutionary trajectories of sex chromosomes shortly after they form? Insights into the evolution of recombination, differentiation, and degeneration can be provided by comparing closely related species with homologous sex chromosomes. The sex chromosomes of the threespine stickleback (Gasterosteus aculeatus) and its sister species, the Japan Sea stickleback (G. nipponicus), have been well characterized. Little is known, however, about the sex chromosomes of their congener, the blackspotted stickleback (G. wheatlandi). We used pedigrees to obtain experimentally phased whole genome sequences from blackspotted stickleback X and Y chromosomes. Using multispecies gene trees and analysis of shared duplications, we demonstrate that Chromosome 19 is the ancestral sex chromosome and that its oldest stratum evolved in the common ancestor of the genus. After the blackspotted lineage diverged, its sex chromosomes experienced independent and more extensive recombination suppression, greater X–Y differentiation, and a much higher rate of Y degeneration than the other two species. These patterns may result from a smaller effective population size in the blackspotted stickleback. A recent fusion between the ancestral blackspotted stickleback Y chromosome and Chromosome 12, which produced a neo-X and neo-Y, may have been favored by the very small size of the recombining region on the ancestral sex chromosome. We identify six strata on the ancestral and neo-sex chromosomes where recombination between the X and Y ceased at different times. These results confirm that sex chromosomes can evolve large differences within and between species over short evolutionary timescales.     

Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda

The neo-sex chromosomes of Drosophila miranda constitute an ideal system to study the effects of recombination on patterns of genome evolution. Due to a fusion of an autosome with the Y chromosome, one homolog is transmitted clonally. Here, I compare patterns of molecular evolution of 18 protein-coding genes located on the recombining neo-X and their homologs on the nonrecombining neo-Y chromosome. The rate of protein evolution has significantly increased on the neo-Y lineage since its formation. Amino acid substitutions are accumulating uniformly among neo-Y-linked genes, as expected if all loci on the neo-Y chromosome suffer from a reduced effectiveness of natural selection. In contrast, there is significant heterogeneity in the rate of protein evolution among neo-X-linked genes, with most loci being under strong purifying selection and two genes showing evidence for adaptive evolution. This observation agrees with theory predicting that linkage limits adaptive protein evolution. Both the neo-X and the neo-Y chromosome show an excess of unpreferred codon substitutions over preferred ones and no difference in this pattern was observed between the chromosomes. This suggests that there has been little or no selection maintaining codon bias in the D. miranda lineage. A change in mutational bias toward AT substitutions also contributes to the decline in codon bias. The contrast in patterns of molecular evolution between amino acid mutations and synonymous mutations on the neo-sex-linked genes can be understood in terms of chromosome-specific differences in effective population size and the distribution of selective effects of mutations.