Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior

Examining the role of chromatin modifications and gene expression in neurons is critical for understanding how the potential for behaviors are established and maintained. We investigate this question by examining Drosophila melanogaster fru P1 neurons that underlie reproductive behaviors in both sexes. We developed a method to purify cell-type-specific chromatin (Chromatag), using a tagged histone H2B variant that is expressed using the versatile Gal4/UAS gene expression system. Here, we use Chromatag to evaluate five chromatin modifications, at three life stages in both sexes. We find substantial changes in chromatin modification profiles across development and fewer differences between males and females. Additionally, we find chromatin modifications that persist in different sets of genes from pupal to adult stages, which may point to genes important for cell fate determination in fru P1 neurons. We generated cell-type-specific RNA-seq data sets, using translating ribosome affinity purification (TRAP). We identify actively translated genes in fru P1 neurons, revealing novel stage- and sex-differences in gene expression. We also find chromatin modification enrichment patterns that are associated with gene expression. Next, we use the chromatin modification data to identify cell-type-specific super-enhancer-containing genes. We show that genes with super-enhancers in fru P1 neurons differ across development and between the sexes. We validated that a set of genes are expressed in fru P1 neurons, which were chosen based on having a super-enhancer and TRAP-enriched expression in fru P1 neurons.     

小麦杂种及其亲本苗期叶片家族基因差异表达及其与杂种优势关系的初步研究

为探讨小麦杂种优势形成的分子机理,以一套双列杂交组合的苗期叶片为材料,利用mRNA差异显示技术分析了杂种及其亲本间MADS－box、G－ box、Ser/Thr蛋白激酶、EIF－4A、ARF1基因家族共5类家族基因在杂交种和亲本之间的表达差异。并与杂种性状表现和杂种优势进行了相关分析。结果发现,除ARF1家族基因外,其余家族基因在杂种和亲本间存在显著的表达差异,差异表达类型可概括为4种：（1）双亲共沉默;（20单亲表达沉默;（3）杂种特异表达;（4）单亲表达一致。分析发现,MADS－box、G－box和EIF－4A家族基因在杂种和亲本间的差异表达模式相似,均以单亲特异表达和种特异表达类型所占比例最高。相关分析结果表明,以上所有家族基因的总体差异表达程度与所有性状的杂种表现均不相关,MADS－box家族基因中杂种特异表达类型与小穗数、单株产量和单穗产量杂种优势呈显著正相关,双亲共沉默类型与小穗数、千粒重和单穗产量杂种优势呈显著负相关,另外,EIF－4A家族基因中单亲表达一致型与单穗产量杂种优势呈显著正相,但双亲共沉默类型与小穗数和单穗产量杂种优势呈显著负相关,对于G－box基因家族而言,仅小穗数杂种优势和双亲共沉默类型成显著负相关,而蛋白激酶家族基因的各种差异类型与性状杂种优势的相关分析均不显著。这些研究表明,调控基因的差异表达与杂种优势形成有密切关系。     

Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays

Whole genome tiling arrays provide a high resolution platform for profiling of genetic, epigenetic, and gene expression polymorphisms. In this study we surveyed natural genomic variation in cytosine methylation among Arabidopsis thaliana wild accessions Columbia (Col) and Vancouver (Van) by comparing hybridization intensity difference between genomic DNA digested with either methylation-sensitive (HpaII) or -insensitive (MspI) restriction enzyme. Single Feature Polymorphisms (SFPs) were assayed on a full set of 1,683,620 unique features of Arabidopsis Tiling Array 1.0F (Affymetrix), while constitutive and polymorphic CG methylation were assayed on a subset of 54,519 features, which contain a 5'CCGG3' restriction site. 138,552 SFPs (1% FDR) were identified across enzyme treatments, which preferentially accumulated in pericentromeric regions. Our study also demonstrates that at least 8% of all analyzed CCGG sites were constitutively methylated across the two strains, while about 10% of all analyzed CCGG sites were differentially methylated between the two strains. Within euchromatin arms, both constitutive and polymorphic CG methylation accumulated in central regions of genes but under-represented toward the 5' and 3' ends of the coding sequences. Nevertheless, polymorphic methylation occurred much more frequently in gene ends than constitutive methylation. Inheritance of methylation polymorphisms in reciprocal F1 hybrids was predominantly additive, with F1 plants generally showing levels of methylation intermediate between the parents. By comparing gene expression profiles, using matched tissue samples, we found that magnitude of methylation polymorphism immediately upstream or downstream of the gene was inversely correlated with the degree of expression variation for that gene. In contrast, methylation polymorphism within genic region showed weak positive correlation with expression variation. Our results demonstrated extensive genetic and epigenetic polymorphisms between Arabidopsis accessions and suggested a possible relationship between natural CG methylation variation and gene expression variation.     

Perturbation of DNA repair gene expression due to interspecies hybridization

The effect of interspecies hybridization on gene regulation was examined using real-time polymerase chain reaction (RT-PCR) to measure the expression of five base-excision repair genes in brain, eye, gill, liver, and tailfin tissues from Xiphophorus parental species and F(1) hybrids. Relative mRNA levels of uracil N-glycosylase (Ung), Apurinic/apyrimidinic endonuclease (Ape1), polymerase-beta (Polb), flap endonuclease (Fen1), and DNA ligase (Lig1) were measured in three parental Xiphophorus species (X. maculatus Jp 163 B, X. helleri Sarabia, and X. andersi andC) and in two interspecies F(1) hybrids, the Sp-helleri hybrid (X. maculatus Jp 163 BxX. helleri Sarabia) and the Sp-andersi hybrid (X. maculatus Jp 163 BxX. andersi) to identify genes that undergo changes in expression levels upon interspecies hybridization. Significant differences in gene expression were observed between parental animals and their respective F(1) hybrids in both interspecies crosses. Generally, marked increases in DNA repair gene mRNA levels were observed across all tissues in F(1) hybrid animals from the Sp-helleri cross compared to either X. maculatus or X. helleri parents. In contrast, the Sp-andersi F(1) hybrid animals generally exhibited decreased base-excision repair gene expression, although this trend was more specific to individual tissues than observed for Sp-helleri hybrids.     

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid

Microarray analysis of gene expression patterns in immature ear, seedling, and embryo tissues from the maize inbred lines B73 and Mo17 identified numerous genes with variable expression. Some genes had detectable expression in only one of the two inbreds; most of these genes were detected in the genomic DNA of both inbreds, indicating that the expression differences are likely caused by differential regulation rather than by differences in gene content. Gene expression was also monitored in the reciprocal F1 hybrids B73xMo17 and Mo17xB73. The reciprocal F1 hybrid lines did not display parental effects on gene expression levels. Approximately 80% of the differentially expressed genes displayed additive expression patterns in the hybrids relative to the inbred parents. The approximately 20% of genes that display nonadditive expression patterns tend to be expressed at levels within the parental range, with minimal evidence for novel expression levels greater than the high parent or less than the low parent. Analysis of allele-specific expression patterns in the hybrid suggested that intraspecific variation in gene expression levels is largely attributable to cis-regulatory variation in maize. Collectively, our data suggest that allelic cis-regulatory variation between B73 and Mo17 dictates maintenance of inbred allelic expression levels in the F1 hybrid, resulting in additive expression patterns.     

甘蓝型油菜Ogura 雄性不育×白菜的回交杂种后代与亲本之间蕾期基因表达差异比较研究*

以甘蓝型油菜（Brassica napus L, AACC,2n＝38）Ogura细胞质雄性不育材料为母本,以不同白菜（B campestris ssp. chinensis Makino, AA, 2n＝20） 自交系‘新选一号’和‘矮脚黄’为父本进行杂交,获得了杂种F1、BC1、BC2代。利用cDNA-AFLP技术对两种材料的不同回交世代BC1、BC2代与其亲本在蕾期的基因表达进行分析。结果表明,两种白菜回交世代与其亲本的基因表达有明显差异,在质和量上都存在差异。基因表达模式有5类共7种：（1）单亲沉默型（2种）,（2）单亲一致型（2种）,（3）双亲共沉默型,（4）杂种特异型,（5）表达一致型。随着回交世代的增加,回交杂种和亲本的基因表达在单亲沉默型、双亲共沉默型呈增加趋势。而在母本一致型、父本一致型、杂交种特异型、表达一致型呈下降的趋势。两种白菜在F1、BC1、BC2 3个世代与回交亲本花蕾间的基因差异表达有15种类型,其中以在轮回亲本、F1、BC1、BC2中共同出现表达的带的比例最高。Abstract: Crosses between female parent of Ogura male sterility Brassica napus L. and male parents of B. campestris ssp. chinensis Makino were made and F1, BC1 and BC2 generations produced. Gene expression of two Chinese cabbage backcross hybrid BC1, BC2 and their parents at bud stage was analyzed by means of cDNA-AFLP technique. The results indicated that the patterns of gene expression differ significantly between BC1 and BC2 generations and their parents. There were many patterns of gene expression, including gene overexpression and gene silencing. Five patterns (seven kinds) of gene expression were observed, which include: (1) bands occurring in only one parent (two kinds); (2) bands observed in hybrids and one parent (two kinds); (3) bands occurring in only parents (one kind); (4) bands visualized in only hybrids (one kind); (5) bands observed in parents and hybrids (one kind). In accompany with the addition of backcross, the increase trend in backcross hybrids and their parents were described in the aspects of differential gene expression, bands expressed only in one parent and bands expressed only in both parents. The declined trend in backcross hybrids and their parents were observed in the aspects of bands expressed in both hybrids and one parent (two kinds), bands visualized in only hybrids and bands observed in parents and hybrid. Fifteen patterns of gene expression were observed in F1、BC1、BC2 and backcross parents. The percent of bands expressed in F1、BC1、BC2 and backcross was highest.     

玉米杂种与亲本穗分化期功能叶基因差异表达与杂种优势

为探讨玉米杂种优势的分子机理,以10个玉米自交系及其组配的38个杂交种为材料,利用cDNA-AFLP技术,分析杂种与亲本在玉米雌穗小穗分化期功能叶片的基因差异表达类型与主要农艺性状的杂种表现及杂种优势的关系。研究表明：（1）杂种的基因相对于其双亲,存在质和量的表达差异,其中质的差异表达类型包括：单亲沉默表达,双亲沉默表达,亲本显性表达和杂种特异表达等类型。（2）在雌穗小穗分化期,同一差异表达类型中不同杂交组合间差异很大;从总体平均看,杂种特异表达类型占25.22%,亲本显性表达类型占21.46%,双亲沉默表达类型占8.27%,单亲沉默表达类型占33.49%。（3）单亲沉默表达与株高的杂种表现呈显著正相关;双亲沉默表达与穗粗的杂种优势呈显著负相关,显性表达与行粒数和单株粒重的杂种优势呈显著负相关,其余表达类型与所有农艺性状杂种表现及杂种优势均不相关,并对结果进行了讨论。     

Patterns of synonymous codon usage in Drosophila melanogaster genes with sex-biased expression

The nonrandom use of synonymous codons (codon bias) is a well-established phenomenon in Drosophila. Recent reports suggest that levels of codon bias differ among genes that are differentially expressed between the sexes, with male-expressed genes showing less codon bias than female-expressed genes. To examine the relationship between sex-biased gene expression and level of codon bias on a genomic scale, we surveyed synonymous codon usage in 7276 D. melanogaster genes that were classified as male-, female-, or non-sex-biased in their expression in microarray experiments. We found that male-biased genes have significantly less codon bias than both female- and non-sex-biased genes. This pattern holds for both germline and somatically expressed genes. Furthermore, we find a significantly negative correlation between level of codon bias and degree of sex-biased expression for male-biased genes. In contrast, female-biased genes do not differ from non-sex-biased genes in their level of codon bias and show a significantly positive correlation between codon bias and degree of sex-biased expression. These observations cannot be explained by differences in chromosomal distribution, mutational processes, recombinational environment, gene length, or absolute expression level among genes of the different expression classes. We propose that the observed codon bias differences result from differences in selection at synonymous and/or linked nonsynonymous sites between genes with male- and female-biased expression.     

Population differentiation and hybrid success in Campanula americana: geography and genome size

Populations within a species may diverge through genetic drift and natural selection. Few studies report on population differentiation in autopolyploids where multiple gene copies and the ratio of cytoplasmic to nuclear genes differ from diploids and may influence divergence. In autotetraploid Campanula americana we created hybrids between populations that differed in geographic proximity and genome size. Differences in genome size (up to 6.5%) did not influence hybrid performance. In contrast, hybrid performance was strongly influenced by population proximity. F1 hybrids between distant populations performed poorly relative to their parents while hybrids between proximate populations outperformed their parents. Outbreeding depression was strongest for juvenile traits. The expression of outbreeding depression often differed between reciprocal hybrids indicating interactions between nuclear and cytoplasmic genes contribute to population differentiation. Because plants were grown under greenhouse conditions, the outbreeding depression was likely due to genetic (underdominance or loss of additive-by-additive epistasis) rather than ecological factors.     

小麦杂交种与亲本发育早期种子的基因表达差异及其与杂种优势关系的初步研究

为深入探讨小麦杂种优势形成的分子机理,选取3个冬小麦品种(系)为一组亲本,3个为另一组亲本,配制了正反交18个杂交组合,以授粉后6d的杂交和自交种子为材料,应用mRNA差异显示技术(DDRT—PCR)研究了小麦杂交当代种子与其亲本自交种子基因的表达差异,并与杂种优势进行相关分析。为降低DDRT—PCR技术假阳性的不利影响,对每个引物组合均作了两次PCR扩增,在处理数据时,仅统计能重复出现的条带。结果发现：杂交种和亲本之间的基因表达模式有8类共15种：(1)单亲沉默型(2种),(2)单亲一致型(2种),(3)正交或反交沉默型(2种),(4)正交或反交特异型(2种),(5)正交或反交单亲一致型(4种),(6)杂交种特异型(1种),(7)双亲共沉默型(1种),(8)表达一致型(1种)。分析发现,小麦杂交种和亲本间存在显著的表达差异。在差异表达类型中,杂交种特异型和双亲共沉默型比例最低。对上述15种表达模式与杂种优势进行相关分析,结果表明,表达一致型与各产量性状杂种优势之间的相关均不显著,说明杂种优势是由某些有表达差异的基因造成。9个产量性状均能检测到一种以上与其显著或极显著相关的基因表达模式,有些性状受正负相关效应的共同影响;沉默型(包括单亲沉默型、正交或反交沉默型和双亲共沉默型)和正交或反交单亲一致型在杂种优势形成中发挥重要作用。这些研究表明,在种子发育早期,基因的差异表达与杂种优势形成之间可能存在较为复杂的关系。     

Esterase B1 activity variation within and among insecticide resistant, susceptible and heterozygous strains of Culex quinquefasciatus (Diptera: Culicidae)

Amplification of the esterase B1 gene of Culex quinquefasciatus Say results in high titers of an esterase enzyme that confers resistance to organophosphate insecticides. Esterase activity of individuals was measured in samples from an organophosphate resistant strain (Tem-R), a susceptible strain (S-Lb), and their reciprocal F1 progeny. Within-strain variation, as measured by coefficients of variation, was fairly consistent between sexes within strains and among strains (average, 12%). On average, individuals from the Tem-R strain had about 120 times the esterase activity of individuals from the S-Lab strain. The mean esterase activities of the F1 strains were significantly higher than the average of the Tem-R and S-Lab strain mean esterase activities, suggesting enhanced expression of the amplified esterase B1 genes in F1 individuals. Reciprocal F1 strains did not differ significantly in esterase activity or resistance, indicating that maternal effects do not influence either of these measures in these strains. The levels of esterase activity of the strains are discussed in relation to their resistance.     

ESS gene expression of X-linked imprinted genes subject to sexual selection

We define ESS (Evolutionary Stable Strategy) conditions for the evolution of genomic imprinting at an X-linked locus. The system analysed is designed for mammalian imprinting in which X-linked genes typically undergo random X-inactivation and lack Y-linked homologues. We consider two models that map cellular gene expression to fitness in females subject to random X-inactivation. In the first model, female fitness is simply a function of the average gene expression across all cells. In the second model, each cell contributes independently to fitness, and female fitness is assessed as the average of these contributions across all cells. In both models, imprinting readily evolves when sexual selection favours different levels of gene expression in the two sexes. Imprinting is beneficial as it improves adaptation in both sexes. There are limits to the improvement in adaptation when sexual selection is strong and favours greater gene expression in males (the heterogametic sex). We also consider the consequences of an active Y-linked homologue on the evolution of imprinting. Our analysis suggests that restrictive conditions apply for the evolution of polymorphic ESSs at an X-linked imprinted loci.     

DEVELOPMENTAL DECOUPLING OF ALTERNATIVE PHENOTYPES: INSIGHTS FROM THE TRANSCRIPTOMES OF HORN‐POLYPHENIC BEETLES

Developmental mechanisms play an important role in determining the costs, limits, and evolutionary consequences of phenotypic plasticity. One issue central to these claims is the hypothesis of developmental decoupling, where alternate morphs result from evolutionarily independent developmental pathways. We address this assumption through a microarray study that tests whether differences in gene expression between alternate morphs are as divergent as those between sexes, a classic example of developmental decoupling. We then examine whether genes with morph‐biased expression are less conserved than genes with shared expression between morphs, as predicted if developmental decoupling relaxes pleiotropic constraints on divergence. We focus on the developing horns and brains of two species of horned beetles with impressive sexual‐ and morph‐dimorphism in the expression of horns and fighting behavior. We find that patterns of gene expression were as divergent between morphs as they were between sexes. However, overall patterns of gene expression were also highly correlated across morphs and sexes. Morph‐biased genes were more evolutionarily divergent, suggesting a role of relaxed pleiotropic constraints or relaxed selection. Together these results suggest that alternate morphs are to some extent developmentally decoupled, and that this decoupling has significant evolutionary consequences. However, alternative morphs may not be as developmentally decoupled as sometimes assumed and such hypotheses of development should be revisited and refined.