Understanding mutational and selective processes that govern gene duplication in mammals

Abstract : Gene duplication is an essential source of material for the origin of genetic novelties. The reverse transcription of source gene mRNA followed by the genomic insertion of the resulting cDNA - retroposition - has provided the human genome with at least ~3600 detectable retrocopies. We find that ~30% of these retrocopies are transcribed, generally in testes. Their transcription often relies on preexisting regulatory elements (or open chromatin) close to their insertion site, which is illustrated by mRNA molecules containing retrocopies fused to their neighboring genes. Retrocopies appear to have been profoundly shaped by selection. Consistently, human retrocopies with an intact open reading (ORF) are more often transcribed than retropseudogenes, which leads to a minimal estimate of 120 functional retrogenes present in our genome. We also performed an analysis of Ka/Ks for human retrocopies. This analysis demonstrates that several intact retrocopies evolved under purifying selection and yields an estimated formation rate of ~1 retrogene per million year in the primate lineage. Using DNA sequencing and evolutionary simulations, we have identified 7 such primate-specific retrogenes that emerged on the lineage leading to humans In therian genomes, we found an excess of retrogenes with X-linked parents. Expression analyses support the idea that this "out of X" movement was driven by natural selection to produce autosomal functional counterparts for X-linked genes, which are silenced during male meiosis. Phylogenetic dating of this "out of X" movement suggests that our sex chromosomes arose about 180 MYA ago and are thus much younger than previously thought. Finally, we have also analyzed young gene duplications (and deletions) that arose by non allelic-homologous recombination and are not fixed in species. Using wild-caught and laboratory animals, we detected thousands of DNA segments that are polymorphic in copy number in mice. These copy number variants were found to profoundly alter the transcriptome of several mouse tissues. Strikingly, their influence on gene expression is not limited to the gene they contain but seems to extend to genes located up to 1.5 million bases away.

Meiotic drive favors Robertsonian metacentric chromosomes in the common shrew (Sorex araneus, Insectivora, mammalia).

Meiotic drive has attracted much interest because it concerns the robustness of Mendelian segregation and its genetic and evolutionary stability. We studied chromosomal meiotic drive in the common shrew (Sorex araneus, Insectivora, Mammalia), which exhibits one of the most remarkable chromosomal polymorphisms within mammalian species. The open question of the evolutionary success of metacentric chromosomes (Robertsonian fusions) versus acrocentrics in the common shrew prompted us to test whether a segregation distortion in favor of metacentrics is present in female and/or male meiosis. Performing crosses under controlled laboratory conditions with animals from natural populations, we found a clear trend toward a segregation distortion in favor of metacentrics during male meiosis, two chromosome combinations (gm and jl) being significantly preferred over their acrocentric homologs. Apart for one Robertsonian fusion (hi), this trend was absent in female meiosis. We propose a model based on recombination events between twin acrocentrics to explain the difference in transmission ratios of the same metacentric in different sexes and unequal drive of particular metacentrics in the same sex. Pooled data for female and male meiosis revealed a trend toward stronger segregation distortion for larger metacentrics. This is partially in agreement with the frequency of metacentrics occurring in natural populations of a chromosome race showing a high degree of chromosomal polymorphism.

The fixation of metacentric chromosomes during the chromosomal evolution in the common shrew (Sorex araneus, Insectivora)

Rb fusions between acrocentric chromosomes leading to metacentrics tend to become fixed during the chromosomal evolution in the common shrew. Using microsatellite markers preliminary results show that populations are only slightly subdivided and genetic drift seems not to play an important role for the fixation of metacentrics. A significant segregation distortion in favour of metacentric chromosomes was found during male meiosis. This suggests that cytological factors such as facilitated fusion between acrocentric chromosomes or choice-effects at the level of gametes are more likely to play a role for the chromosomal evolution in the common shrew.

Complex meiotic configuration of the holocentric chromosomes: the intriguing case of the scorpion Tityus bahiensis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

2 PERMANENT LINEAR-CHAINS OF SEX-CHROMOSOMES IN NEOTERMES-FULVESCENS AND KARYOTYPES OF 2 OTHER NEOTROPICAL KALOTERMITIDAE SPECIES (INSECTA, ISOPTERA)

Meiosis and (or) mitosis of males and females of Cryptotermes brevis, Eucryptotermes wheeleri, and Neotermes fulvescens, all of them from the neotropical region, were analyzed. Cryptotermes brevis showed a similar karyotype to that obtained by other authors for specimens of the neartic and Australian regions (2n = 36 for females and 2n = 37 for males, with XX and XYY sex mechanisms, respectively). Eucryptotermes wheeleri, the only species that has been described in this genus, showed the lowest number of chromosomes reported for Isoptera (2n = 22) until now. The male meiosis of this species presents a linear chain of six sex chromosomes, three of them being X and three of them Y chromosomes. Neotermes fulvescens showed a diploid number of 40 for males and 42 for females and, in the first male meiosis, two linear chains of chromosomes, both related to sex. One of the chains, named A, presented nine chromosomes and the other, named B, seven chromosomes. Hypotheses to explain these mechanisms are formulated in this paper and putative ancestral relationships with other species of Kalotermitidae are presented.

Cytogenetic analysis of Epicauta atomaria (Meloidae) and Palembus dermestoides (Tenebrionidae) with Xyp sex determination system using standard staining, C-bands, NOR and synaptonemal complex microspreading techniques

The mitotic and meiotic chromosomes of the beetles Epicauta atomaria (Meloidae) and Palembus dermestoides (Tenebrionidae) were analysed using standard staining, C-banding and silver impregnation techniques. We determine the diploid and haploid chromosome numbers, the sex determination system and describe the chromosomal morphology, the C-banding pattern and the chromosome(s) bearing NORs (nucleolar organizer regions). Both species shown 2n = 20 chromosomes, the chromosomal meioformula 9 + Xyp, and regular chromosome segregation during anaphases I and II. The chromosomes of E. atomaria are basically metacentric or submetacentric and P. dermestoides chromosomes are submetacentric or subtelocentric. In both beetles the constitutive heterochromatin is located in the pericentromeric region in all autosomes and in the Xp chromosome; additional C-bands were observed in telomeric region of the short arm in some autosomes in P. dermestoides. The yp chromosome did not show typical C-bands in these species. As for the synaptonemal complex, the nucleolar material is associated to the 7th bivalent in E. atomaria and 3rd and 7th bivalents in P. dermestoides. Strong silver impregnated material was observed in association with Xyp in light and electron microscopy preparations in these species and this material was interpreted to be related to nucleolar material.

The ultrastructure of the pre-meiotic and meiotic stages of spermatogenesis in Plagioscion squamosissimus (Teleostei, Perciformes, Sciaenidae)

Spermatogenesis of 'corvina' P. squamosissimus starts from a stem cell that gives rise to germ cells. These cells are enveloped by Sertoli cells, forming cysts. The germ cells in the cysts are all at the same stage of development and are interconnected by cytoplasmic bridges. Spermatogonia are the largest germ cells. In the cysts, these cells differentiate into primary spermatogonia and secondary spermatogonia. The primary spermatogonia are isolated in the cyst and give rise to the secondary spermatogonia. After several mitotic divisions, they produce spermatocytes I, which can be identified by synaptonemal complexes in the nucleus. The spermatocytes I enter the first phase of meiosis to produce the spermatocytes II. These are not very frequently seen because they rapidly undergo a second phase of meiosis to produce spermatids.

Study of chromosomal and nucleolar aspects in testes of Nysius californicus (Heteroptera: Lygaeidae)

In Nysius californicus (family Lygaeidae, subfamily Orsillinae), a pest commonly known as the seed bug, the chromosome complement is 2n = 16 (12A + 2m + XY), testes are formed by seven seminiferous tubules covered by an orange-colored membrane, and spermatogenesis is cystic. At prophase, sex chromosomes are heteropycnotic and autosomes usually show a chiasma. At metaphase, sex chromosomes along with microchromosomes may be seen located at the center of a ring formed by the remaining autosomes. A characteristic specific of N. californicus was the presence of nucleolar material observed from the cystic cell to the completely differentiated spermatozoon. Variations in size, shape and location of the nucleolar material occur during this process, denoting a variable degree of activity in the different stages. ©FUNPEC-RP.

Spermatogenesis and karyotypes of three species of water striders (Gerridae, Heteroptera).

Although they are of economic importance, there have been few cytogenetic studies of the Gerridae (Heteroptera) in Brazil. We examined spermatogenesis (meiosis and spermiogenesis) and nucleolar behavior in three species of the family Gerridae. Brachymetra albinerva and Halobatopsis platensis were found to have a chromosome complement of 2n = 25 (24A + X0) and Cylindrostethus palmaris 2n = 29 (28A + X0) chromosomes. Fifteen individuals of these species were collected from the reservoir of São José do Rio Preto, SP, using screens and were transported in pots containing water to the laboratory, where cytogenetic preparations were made. The polyploidy nuclei are formed by several heteropyknotic regions; cells in meiotic prophase have a heteropyknotic region that is probably the sex chromosome, and the chromosomes from chiasmata. The spermatids are rounded and have a heteropyknotic region at the periphery of the nucleus; the sperm head is small, with a long tail. Silver impregnation of meiotic cells showed one or more disorganized bodies around the perichromosomal sheath. The round spermatids had two bodies next to each other, but these were elongated; one of the bodies remained in the head and the other migrated to the initial part of the tail at the end of spermagenesis, when the staining was no longer evident. The meiotic cells appear during spermatogenesis and have very similar silver-impregnation patterns in different species of Heteroptera.

Distribution of constitutive heterochromatin in two species of triatomines: Triatoma lenti Sherlock and Serafim (1967) and Triatoma sherlocki Papa, Jurberg, Carcavallo, Cerqueira & Barata (2002)

Triatoma lenti and Triatoma sherlocki are hemipterans that belong to the brasiliensis subcomplex. In triatomines, the constitutive heterochromatin pattern is species-specific and allows, in many cases, for the grouping of species. Thus, we cytogenetically analyzed T. sherlocki and T. lenti using C-banding, and we compared the results with previous ones obtained in other species of the brasiliensis subcomplex. Both species were found to have a male diploid chromosome number of 22 chromosomes (2n = 20A. +. XY) with heterochromatic blocks at one or both chromosomal ends of all autosomal pairs. During early meiotic prophase, they showed a large heteropycnotic chromocenter constituted by the association of both sex chromosomes plus two autosomal pairs and many heterochromatic blocks dispersed inside the nucleus. All of these cytogenetic characteristics are similar to those observed in other species of brasiliensis subcomplex, results which confirm the grouping of T. sherlocki and T. lenti within this subcomplex. However, we emphasize the importance of other approaches, such as molecular analysis, to confirm the placement of T. lenti within the brasiliensis subcomplex. © 2012 Elsevier B.V.

Synaptomenal complex analysis of four breeds of Bos taurus taurus x B. taurus indicus hybrids

The synaptonemal complex (SC) was analyzed in four F1 hybrids of Bos taurus taurus and B. taurus indicus including Gyr-Simmental (G-S), Nelore Simmental (N-S), Gyr-Holstein-Friesian (G-H) and Nelore-Piemontese (N-P). We analysed the frequency of various types of SC abnormalities and the frequency of cells with SC abnormalities. The results were compared with similar observations made on purebred animals. All the animals studied possessed 29 autosomal and one sex bivalent. The frequency of cells with abnormalities in the hybrids were 28.0% in the N-P, 29.1% in the G-S, 33.3% in the N-S and 40.0% in the G-H. The frequency of cells with abnormalities in the four hybrids was 31.5%; 57.9% of these abnormalities occurred in zygotene and 42.0% occurred in pachytene. The comparisons among the hybrids and among the hybrids and their parental breeds showed that the only significant difference was between Gyr and Gyr-Holstein-Friesian animals. Some aspects of the relationship between the frequency of cells with anomalies and the fertility of hybrids are discussed.

A gene spans the pseudoautosomal boundary in mice

The X and Y chromosomes of the mouse, like those of other mammals, are heteromorphic over most of their length, but at the distal ends of the chromosomes is a region of sequence identity, the pseudoautosomal region (PAR), where the chromosomes pair and recombine during male meiosis. The point at which the PAR diverges into X- and Y-specific sequences is called the pseudoautosomal boundary. We have completed a genomic walk from the X-specific Amelogenin gene to the PAR. Analysis of this region revealed that the pseudoautosomal boundary of mice is located within an intron of a transcribed gene that encodes a novel RING finger protein. The first three of the exons of the gene are located on the X chromosome whereas the 3′ exons of the gene are located on both X and Y chromosomes. This unusual arrangement may indicate that the gene is in a state of transition from pseudoautosomal to X-unique and provides evidence for a process of attrition of the pseudoautosomal region on the Y chromosome.

Organization and behavior of the synaptonemal complex during achiasmatic meiosis of four buthid scorpions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Centriole behaviour during meiosis of male germ cells of Dermatobia hominis (Diptera:Cuterebridae)

During the meiotic division of Dermatobia hominis spermatogenesis, the centrioles duplicate only in prophase I, giving rise to short cilia which are exposed on the cellular surface. In metaphase I they are internalized and distributed to the daughter cells. Consequently, the secondary spermatocytes have two centrioles which repeat the cycle of cilia externalization followed by internalization. The spermatids receive only one centriole, which changes into a basal body and originates a flagellum. This centriole behaviour seems to be a general feature in insect male germ cell meiosis.

Targeted gene disruption of Hsp70-2 results in failed meiosis, germ cell apoptosis, and male infertility.

In addition to the five 70-kDa heat shock proteins (HSP70) common to germ cells and somatic tissues of mammals, spermatogenic cells synthesize HSP70-2 during meiosis. To determine if this unique stress protein has a critical role in meiosis, we used gene-targeting techniques to disrupt Hsp70-2 in mice. Male mice homozygous for the mutant allele (Hsp70-2 -/-) did not synthesize HSP70-2, lacked postmeiotic spermatids and mature sperm, and were infertile. However, neither meiosis nor fertility was affected in female Hsp70-2 -/- mice. We previously found that HSP70-2 is associated with synaptonemal complexes in the nucleus of meiotic spermatocytes from mice and hamsters. While synaptonemal complexes assembled in Hsp70-2 -/- spermatocytes, structural abnormalities became apparent in these cells by late prophase, and development rarely progressed to the meiotic divisions. Furthermore, analysis of nuclei and genomic DNA indicated that the failure of meiosis in Hsp70-2 -/- mice was coincident with a dramatic increase in spermatocyte apoptosis. These results suggest that HSP70-2 participates in synaptonemal complex function during meiosis in male germ cells and is linked to mechanisms that inhibit apoptosis.