<p>Sex chromosomes are useful for the study of how factors such as mutation, selection, recombination and effective population size affect diversity and divergence.</p><p>A comparison of gametologous introns in seven different bird species revealed a complete lack of diversity on the female-specific W chromosome. In contrast, Z had at least one segregating site in all examined species. This can be explained by the lower mutation rate and lower effective population size of W but also suggests that selection affects diversity levels on the non-recombining W chromosome.</p><p>In a diverse set of chicken breeds, the Z chromosome showed reduced diversity compared to autosomes and significant heterogeneity in levels of variation. High variance in male reproductive success, leading to a reduced Z chromosome effective population size, can partly explain this observation. In addition, we suggest that selective sweeps frequently act on the Z chromosome and are responsible for a significant part of the observed Z reduction. </p><p>Differences in the mutation rate of Z and W chromosome sequences indicate that the time spent in male germ line is important for the mutation rate, but does not exclude a specifically reduced mutation rate on the Z chromosome. Estimates of mutation rate in autosomal, Z- and W-linked chicken and turkey sequences indicate a slight reduction in the rate on Z. However, due to rate heterogeneity among introns this reduction is not significant and we cannot exclude male biased mutation as the single cause of rate variation between the chromosomal classes.</p><p>Analysis of indel mutation rates in avian and mammalian gametologous introns show frequent occurrence of indels on both W and Y, excluding meiotic recombination as the only source of this type of mutation. The different indel rate patterns in birds (Z>W) and mammals (X=Y) suggest that indels are caused by both replication and recombination.</p>

<p>Chicken and Japanese quail are commonly used models in developmental and sex specific neuroendocrine research. There is relatively little known about the mechanisms behind their sex specific brain development, especially regarding the impact of the sex chromosomes (male: ZZ, female ZW) in relation to gonadal hormones. This thesis explores several aspects of these processes. Gene expression analysis with cDNA and Affymetrix arrays on brain tissue from both pre-gonadal embryos and embryos with differentiated gonads indicate a strong sex chromosomal presence in sexual dimorphic somatic tissue development in both chicken and Japanese quail. This sex chromosome pattern seems to remain in adult brain tissue. The data demonstrates that chicken males exhibit a significant level of Z-gene dosage compared to females in both somatic and germ line derived embryonic tissues. Several avian sex determination gene candidates (MHM non-coding RNA, DMRT1, HINTW, and HINTZ) were analyzed by real-time PCR. DMRT1 is dosage compensated in male brain tissue, in contrast to its reported gene dosage in male gonads. Early embryonic ethinylestradiol (EE2) exposure did not affect male or female neural gene expression patterns during later development. A peptidomics analysis on quail embryonic day 12 (ed12) and ed17 diencephalon by LC-MS identified over 60 endogenous peptides and analyzed the expression patterns for 38 of them with regard to age, sex and early EE2 exposure. There was a general upregulation between ed12 and ed17, but no clear sex effects were detected. Multivariate analysis indicates that EE2 exposed individuals differ from control individuals in a gender independent manner, and that Gonadotropin-inhibiting hormone related peptide 2 (GnIH-RP2) is a candidate for EE2 induced peptidomic alterations in male embryonic brain.</p>

Chicken and Japanese quail are commonly used models in developmental and sex specific neuroendocrine research. There is relatively little known about the mechanisms behind their sex specific brain development, especially regarding the impact of the sex chromosomes (male: ZZ, female ZW) in relation to gonadal hormones. This thesis explores several aspects of these processes. Gene expression analysis with cDNA and Affymetrix arrays on brain tissue from both pre-gonadal embryos and embryos with differentiated gonads indicate a strong sex chromosomal presence in sexual dimorphic somatic tissue development in both chicken and Japanese quail. This sex chromosome pattern seems to remain in adult brain tissue. The data demonstrates that chicken males exhibit a significant level of Z-gene dosage compared to females in both somatic and germ line derived embryonic tissues. Several avian sex determination gene candidates (MHM non-coding RNA, DMRT1, HINTW, and HINTZ) were analyzed by real-time PCR. DMRT1 is dosage compensated in male brain tissue, in contrast to its reported gene dosage in male gonads. Early embryonic ethinylestradiol (EE2) exposure did not affect male or female neural gene expression patterns during later development. A peptidomics analysis on quail embryonic day 12 (ed12) and ed17 diencephalon by LC-MS identified over 60 endogenous peptides and analyzed the expression patterns for 38 of them with regard to age, sex and early EE2 exposure. There was a general upregulation between ed12 and ed17, but no clear sex effects were detected. Multivariate analysis indicates that EE2 exposed individuals differ from control individuals in a gender independent manner, and that Gonadotropin-inhibiting hormone related peptide 2 (GnIH-RP2) is a candidate for EE2 induced peptidomic alterations in male embryonic brain.

Sex chromosomes are useful for the study of how factors such as mutation, selection, recombination and effective population size affect diversity and divergence. A comparison of gametologous introns in seven different bird species revealed a complete lack of diversity on the female-specific W chromosome. In contrast, Z had at least one segregating site in all examined species. This can be explained by the lower mutation rate and lower effective population size of W but also suggests that selection affects diversity levels on the non-recombining W chromosome. In a diverse set of chicken breeds, the Z chromosome showed reduced diversity compared to autosomes and significant heterogeneity in levels of variation. High variance in male reproductive success, leading to a reduced Z chromosome effective population size, can partly explain this observation. In addition, we suggest that selective sweeps frequently act on the Z chromosome and are responsible for a significant part of the observed Z reduction. Differences in the mutation rate of Z and W chromosome sequences indicate that the time spent in male germ line is important for the mutation rate, but does not exclude a specifically reduced mutation rate on the Z chromosome. Estimates of mutation rate in autosomal, Z- and W-linked chicken and turkey sequences indicate a slight reduction in the rate on Z. However, due to rate heterogeneity among introns this reduction is not significant and we cannot exclude male biased mutation as the single cause of rate variation between the chromosomal classes. Analysis of indel mutation rates in avian and mammalian gametologous introns show frequent occurrence of indels on both W and Y, excluding meiotic recombination as the only source of this type of mutation. The different indel rate patterns in birds (Z&gt;W) and mammals (X=Y) suggest that indels are caused by both replication and recombination.

What processes contribute to the evolution of reproductive isolation and the coexistence of interfertile species in the same habitat? This thesis investigates the relative roles of species interactions and intraspecific processes in contributing to reproductive isolation. I combine behavioural and genomic approaches to test hypotheses about what mechanisms maintain the general species boundary between two closely related field cricket species: Teleogryllus oceanicus and T. commodus. These species are a classic study system for sexual communication and readily hybridize in the laboratory, however little is known about species interactions in sympatric populations. I examine patterns of geographic variation in two key sexual traits: calling song and cuticular hydrocarbons (CHCs), and the geographic distribution of genetic variation across a broad sample of allopatric and sympatric populations. I test whether X chromosomes play a pronounced role in population divergence and reproductive isolation. Using close range mating trials and hybridization experiments I identify numerous pre-mating and post-mating barriers between the species. The results indicate that the species are currently reproductively isolated and the pattern of population differentiation does not strongly support contemporary species interactions contributing to phenotypic diversity. Numerous barriers exist between the species, in particular hybrid females are sterile in both cross directions, while hybrid males are relatively fertile. This provides a rare exception to Haldane's rule which is central to many genetic theories of speciation. Established theory predicts that X chromosomes should play a pronounced role in the evolution of both pre- and postzygotic barriers. Contrary to this, I found no evidence that X chromosomes contribute to hybrid female sterility. Moreover, X-linked loci exhibited an unexpected pattern of reduced population differentiation within species, but increased species divergence compared to autosomal loci, which may indicate selective sweeps or sex-biased processes. Taken together, the results suggest that the causes and consequences of X chromosome evolution, in particular among XO taxa, may contradict some of the established theories.

Understanding the genetic basis of reproductive isolation is the ultimate goal of the study of speciation. Here I present the results of a study of gene flow and its barriers at sex chromosome markers across the central European portion of the hybrid zone between two house mouse subspecies, Mus musculus musculus and M. m. domesticus. We identified strong introgression of Y musculus chromosome into the domesticus area accompanied by a perturbation of the census sex ratio. In addition, we detected stochastic effects that can distort results of hybrid zone studies. Finally, we confirmed a strong effect of sex chromosomes on reproductive isolation and hence their important role in the process of speciation.

In the present study, the W sex-chromosome of the codling moth was studied by means of fluorescence in situ hybridization (FISH) with probes prepared from bacterial artificial chromosome (BAC), which were isolated from the codling moth BAC library. The BAC library was screened for clones derived from both the W and Z sex chromosomes using three sets of molecular markers of codling moth sex chromosomes. A total of 54 BAC clones have been obtained. In this work, only 3 W-derived BAC clones and 1 Z-derived BAC clone were further characterized by BAC-FISH mapping on chromosome preparations of pachytene oocytes; the other BAC clones have been retained for next studies. Whereas the Z-BAC probe provided a discrete hybridization signal on the Z chromosome, and surprisingly on the W chromosome, the W-BAC probes showed multiple hybridization signals distributed on the whole W chromosome, suggesting that they are mainly composed of repetitive sequences, which occur in multiple clusters on the W chromosome. The specific pattern of W-BAC hybridization signals along with the discrete signal of the Z-BAC enabled us to discriminate left/right orientation of both the W and Z chromosomes and examine specificity of W-Z pairing during meiotic prophase I.

Cromossomos sexuais evoluíram repetidas vezes independentemente nos grandes grupos de vertebrados. Sistemas sexuais altamente diferenciados e antigos são caracterizados por grandes diferenças morfológicas e de conteúdo gênico entre os dois cromossomos homólogos onde a recombinação é restrita a uma pequena região homóloga. Os sistemas recentes característicos de peixes caracterizam-se pela similaridade entre os cromossomos X e Y (ou Z e W), nos quais as diferenças observadas freqüentemente envolvem a presença de heterocromatina, translocações e inversões. A recombinação ocorre entre o par sexual na maior parte de sua extensão, sendo inibida apenas na região diretamente relacionada com a determinação sexual. Notavelmente, sistemas diferentes de determinação podem ser encontrados em espécies, ou mesmo populações. O gênero Eigenmannia compreende grupos de espécies crípticas do ponto de vista morfológico que exibem variação no número cromossômico e podem apresentar sistemas sexuais XY ou ZW, incluindo sistemas múltiplos (com translocação Y-autossomo). Estes sistemas estão entre os mais recentes descritos (<16ma) e estão dispostos de forma desordenada em árvores de relações filogenéticas, sugerindo origens múltiplas. No presente estudo, a técnicas de pintura cromossômica usando sondas obtidas por microdissecção de cromossomos sexuais foram empregadas para testar a homologia de dois sistemas XY encontrados nos citótipos (ou espécies) E. virescens e E. sp.2. Os resultados mostram que, de fato, ambos são não homólogos. A fusão Y-autossomo provavelmente ocorreu após a separação de E. sp.2 com sua espécie irmã, E. sp.1 uma vez que um evento de fusão independente, envolvendo um dos cromossomos homólogos ao Y, foi detectado em E. sp.1. A hibridação in sit&#956; do cromossomo X de E. virescens em sua população mais próxima (também com 38 cromossomos, mas sem cromossomos sexuais heteromórficos) mostrou que o cromossomo X é homólogo a um par de acrocêntricos, condizente com o modelo proposto de diferenciação por acúmulo de heterocromatina. Essa heterocromatina foi caracterizada e mostrou um padrão complexo de seqüências CG-ricas. Dois fragmentos de DNA repetitivo GC-ricos presentes no cromossomo X foram isolados e seqüenciados. Não foram detectadas similaridades em comparações com bases de dados e entre os fragmentos obtidos. Estes mostraram-se concentrados nas regiões cromomicina-positivas de E. virescens, incluindo regiões periteloméricas de sete pares e os dois maiores blocos heterocromáticos (nos cromossomos X e par n. 8), além de um cromossomo acrocêntrico, possivelmente o Y. Curiosamente, essas seqüências foram detectadas em apenas três pares cromossômicos na população mais próxima, incluindo um par acrocêntrico de morfologia semelhante à condição ancestral do X, sugerindo que processos dinâmicos de expansão e homogenização genômica ocorreram após a separação dessas populações / Sex chromosomes have evolved independently several times in all major groups of vertebrates. Highly differentiated sex chromosomes are characterized by extensive differences in morphology and gene content, whereas recombination is restricted to a small homologous region. Recent sex chromosomes are characteristic of fish, and display a high level of homology between X and Y (or Z and W) chromosomes, recombination is restricted only in a small sex determining region. Notably, different sex chromosome systems can be found in closely related groups, such as species or even populations. The genus Eigenmannia comprises a group of morphologically cryptic species that display a variety of diploid numbers and different sex chromosome systems, including XY, ZW and a multiple XY system (with a Y-autosome fusion). These systems are among the most recent known (<16ma) and occur with a lack of phylogenetic pattern, whereas frequently populations bearing heteromorphic sex chromosomes are closest related to populations displaying no sex chromosomes. In the present study, chromosome painting using probes derived from the microdissection of two different sex chromosomes where used to investigate the homology of both systems. Results show that, in fact, they are non-homologous and evolved independently. The Y-autosome hypothesis gained further support from the observation that a chromosome homologous to the Y in a close population is involved in yet a different fusion event. The X chromosome present in the E. virescens karyotype was found to be homologous to acrocentric chromosomes in all populations analyzed, thus supporting the notion that its differentiations is mainly due to the accumulation of heterochromatin. The X heterochromatic block was shown to form a complex pattern of GC-rich sequences, different from what was previously described. Two GC-rich fragments were isolated and sequenced; both showed no similarities to known sequences and to one another. These sequences were shown to be concentrated viii on the two largest heterochromatic blocks, those of the X and n.8 chromosomes besides peri-telomeric regions of seven additional pairs and the putative Y. Curiously, these sequences were detected in only three pairs in the closest population, including an acrocentric pair morphologically similar to undifferentiated sex pair. This suggests that dynamic evolutionary processes of expansion and genomic homogenization have occurred after the separation of these populations.

Orientadores: Andréa Trevas Maciel-Guerra, Vera Lúcia Gil da Silva Lopes / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-23T23:41:30Z (GMT). No. of bitstreams: 1 Latuf_JulianadePaulo_M.pdf: 2398402 bytes, checksum: cbd1c5c98ab12541607b0be2b5ca8120 (MD5) Previous issue date: 2013 / Resumo: Quadros de ambiguidade genital e esterilidade com cariótipo 46,XY podem ser devidos a mosaico com linhagem 45,X não detectável no cariótipo em linfócitos de sangue periférico. Quando essa linhagem não é detectada, esses indivíduos deixam de ser investigados em relação a uma série de problemas clínicos. Este trabalho teve como objetivo verificar se a hibridação in situ com fluorescência (FISH) em células de mucosa oral poderia ser empregada para detectar criptomosaicismo com linhagem 45,X em indivíduos com cariótipo 46,XY. A casuística foi composta por 19 homens saudáveis com idades entre 20 e 30 anos e cinco pacientes com distúrbios da diferenciação do sexo (DDS) com idades entre 5 e 23 anos, quatro com mosaico 45,X/46,XY e um com disgenesia testicular 46,XY associada a déficit de crescimento. Após confirmar que os jovens saudáveis tinham cariótipo 46,XY em 50 metáfases de linfócitos de sangue periférico, foi realizada análise por FISH com sondas específicas para os cromossomos X e Y em 1.000 núcleos interfásicos de linfócitos de sangue periférico e 1.000 de mucosa oral, seguida de comparação da proporção de núcleos contendo apenas o sinal do cromossomo X nos dois tecidos. A mesma análise foi feita nos cinco pacientes com DDS. A distribuição da proporção dos núcleos interfásicos de linfócitos e mucosa oral contendo apenas o sinal do X nos jovens saudáveis foi compatível com a distribuição normal, e número superior a 12:1.000 em linfócitos e 13:1.000 em mucosa oral devem ser considerados indicativos de mosaicismo em nosso laboratório. A frequência desses núcleos nos dois tecidos não diferiu significativamente (p=0,6855). Nos cinco pacientes com DDS a frequência de núcleos contendo apenas o sinal do X diferiu significativamente da observada em indivíduos normais em linfócitos (p=0,0008) e mucosa oral (p=0,0008). No paciente com cariótipo prévio 46,XY a linhagem 45,X foi confirmada por FISH em metáfases, e em um dos casos de mosaicismo foram detectadas linhagens celulares adicionais. Também não houve diferença significativa entre a frequência de núcleos contendo apenas o sinal do X nos dois tecidos desses pacientes (p=0,3750). Estes resultados indicam que a pesquisa de mosaicismo com linhagem 45,X em indivíduos com DDS ou esterilidade e cariótipo 46,XY pode ser feita por meio de FISH em mucosa oral, com vantagens evidentes em termos de custo e rapidez, além de ser feita a partir de tecido obtido de modo não invasivo / Abstract: Ambiguous genitalia and sterility with a 46,XY karyotype may be due to mosaicism with a 45, X karyotype not detectable in peripheral blood lymphocytes. When this cell line is not detected, these individuals fail to be investigated over a range of clinical problems. This study aimed to verify whether fluorescence in situ hybridization (FISH) in cells from buccal smear could be employed to detect cryptomosaicism with a 45,X cell line in individuals with a 46,XY karyotype. The sample consisted of 19 healthy men aged 20 to 30 years and five patients with disorders of sex development (DSD) aged 5 to 23 years, four with mosaicism 45,X/46,XY and one with testicular dysgenesis 46, XY associated with growth deficiency. After confirming that the healthy young men had a 46,XY karyotype in 50 metaphases from peripheral blood lymphocytes, FISH analysis with probes specific for chromosomes X and Y was done in 1,000 nuclei from peripheral blood lymphocytes and 1,000 from buccal smear, followed by comparison of the proportion of nuclei containing only the signal of the X chromosome in these tissues. The same analysis was performed in five patients with DDS. The distribution of the proportion of interphase nuclei of lymphocytes and buccal smear containing only the X signal in healthy young was consistent with normal distribution; a number greater than 12:1,000 in lymphocytes and 13:1,000 in buccal smear should be considered indicative of mosaicism in our laboratory. The frequency of these nuclei in both tissues did not differ significantly (p = 0.6855). In patients with DDS the frequency of nuclei containing only the X signal differed significantly from that observed in normal individuals both in lymphocytes (p = 0.0008) and buccal smear (p = 0.0008). In the patient with a prior 46,XY karyotype, a 45,X cell line was confirmed by FISH in metaphases, and in one case of mosaicism additional cell lines were detected. There was also no significant difference between the frequency of nuclei containing only the X signal in the two tissues of these patients (p = 0.3750). These results indicate that investigation of mosaicism with 45,X cell line in individuals with 46,XY DSD or sterility can be done by FISH in cells from buccal smear, with obvious advantages in terms of cost and speed, using a tissue obtained noninvasively / Mestrado / Ciencias Biomedicas / Mestra em Ciências Médicas

Meiosis is a specialized cell division that produces haploid cells (gametes) from diploid progenitors. During meiosis parental chromosomes (homologs) need to pair, synapse and eventually segregate. Faithful chromosome segregation depends on chromosome recombination. In the beginning of prophase I programmed double strand breaks (DSBs) are introduced in meiotic cells by SPO11 enzyme. DSBs are positioned at hotspot sites that are specified by that action of DNA-binding histone methyltransferase PRDM9. Specific enzymes act at the site of breaks to create 5’ single stranded DNA ends. With the assistance of the strand exchange proteins DMC1 and RAD51 these ends invade homologous DNA sequence and DSB repair is initiated. DSB repair can be completed either as a crossover (reciprocal exchange of DNA) or as a non-crossover. Crossover events lead to the formation of chiasmata between homologs and ensure proper segregation during the first meiotic division. An interesting feature in male meiosis is the XY chromosomes. The shared region between sex chromosomes is short and is called pseudoautosomal region (PAR). Due to their large non synapsed region, XY chromosomes need to be transcriptionally silenced. Thus they are covered with the phosphorylated histone variant H2AX (γH2AX) forming the so called sex body. PAR region has higher density of DSBs than autosomes and it had been shown that sex chromosomes undergo delayed homologous pairing. Nevertheless little is known how meiotic recombination is regulated in PAR region of sex chromosomes. In close proximity with sex body it has been found a structure named dense body (DB). There are few reports suggesting that DB contains RNAs/proteins but no DNA. Its role in meiosis was unclear because no structural component had been described. In the present thesis the role of two meiotic expressed genes is described. In our group after performing RNA screens we identified several genes that are highly expressed during meiotic prophase I. Based on the expression profile we selected polycomb-related sex comb on midleg like 1 (Scml1) gene and the ankyrin repeat domain 31 (Ankrd31) to study their role in mammalian meiosis.:List of figures i List of abbreviations ii 1. Introduction 1 1.1 Gametogenesis 1 1.2 Meiotic prophase I 2 1.2.1 Meiotic recombination 4 1.2.2 Regulation of meiotic recombination 7 1.2.2.1 Meiotic recombination hotspots and PRDM9 activity 7 1.2.2.2 Meiotic surveillance mechanisms 8 1.3 Unique properties of XY recombination 9 1.4 Sex chromatin associated structure: The dense body 10 1.5 Aim of the thesis 11 2. Publications 12 3. Discussion 92 4. Summary 98 5. References 102 Acknowledgements 108 Declarations 109