RESUMEN
It has been repeatedly demonstrated that the centromere-specific histone H3 (CENH3), a key component of the centromere, shows considerable variability between species within taxa. We determined the molecular structure and phylogenetic relationships of CENH3 in 11 Secale species and subspecies that possess distinct pollination systems and are adapted to a wide range of abiotic and biotic stresses. The rye (Secale cereale) genome encodes two paralogous CENH3 genes, which differ in intron-exon structure and are transcribed into two main forms of the protein, αCENH3 and ßCENH3. These two forms differ in size and amino acid substitutions. In contrast to the reported differences in CENH3 structure between species within other taxa, the main forms of this protein in Secale species and subspecies have a nearly identical structure except some nonsynonymous substitutions. The CENH3 proteins are strictly controlled by genetic factors responsible for purifying selection. A comparison between Hordeum, Secale and Triticum species demonstrates that the structure of CENH3 in the subtribes Hordeinae and Triticinae evolved at different rates. The assumption that reticulate evolution served as a factor stabilizing the structure and evolutionary rate of CENH3 and that this factor was more powerful within Secale and Triticum than in Hordeum, is discussed.
Asunto(s)
Centrómero/metabolismo , Cromosomas de las Plantas/metabolismo , Histonas/metabolismo , Hordeum/genética , Secale/genética , Triticum/genética , Empalme Alternativo/genética , Secuencia de Aminoácidos/genética , Estructura Molecular , Filogenia , Secale/clasificación , Alineación de SecuenciaRESUMEN
BACKGROUND: A prominent and distinctive feature of the rye (Secale cereale) chromosomes is the presence of massive blocks of subtelomeric heterochromatin, the size of which is correlated with the copy number of tandem arrays. The rapidity with which these regions have formed over the period of speciation remains unexplained. RESULTS: Using a BAC library created from the short arm telosome of rye chromosome 1R we uncovered numerous arrays of the pSc200 and pSc250 tandem repeat families which are concentrated in subtelomeric heterochromatin and identified the adjacent DNA sequences. The arrays show significant heterogeneity in monomer organization. 454 reads were used to gain a representation of the expansion of these tandem repeats across the whole rye genome. The presence of multiple, relatively short monomer arrays, coupled with the mainly star-like topology of the monomer phylogenetic trees, was taken as indicative of a rapid expansion of the pSc200 and pSc250 arrays. The evolution of subtelomeric heterochromatin appears to have included a significant contribution of illegitimate recombination. The composition of transposable elements (TEs) within the regions flanking the pSc200 and pSc250 arrays differed markedly from that in the genome a whole. Solo-LTRs were strongly enriched, suggestive of a history of active ectopic exchange. Several DNA motifs were over-represented within the LTR sequences. CONCLUSION: The large blocks of subtelomeric heterochromatin have arisen from the combined activity of TEs and the expansion of the tandem repeats. The expansion was likely based on a highly complex network of recombination mechanisms.
Asunto(s)
Elementos Transponibles de ADN , Amplificación de Genes , Heterocromatina/genética , Secale/genética , Secuencias Repetidas en Tándem , Cromosomas Artificiales Bacterianos , Cromosomas de las Plantas/genética , Biblioteca de Genes , Componentes Genómicos , Hibridación Fluorescente in Situ , Análisis de Secuencia por Matrices de Oligonucleótidos , Filogenia , Análisis de Secuencia de ADNRESUMEN
Subtelomeric regions of chromosomes are particularly dynamic and variable parts in the evolution of the eukaryotic genomes. A specific feature of the rye (Secale) chromosomes is large heterochromatin blocks at the arms of all seven pairs of chromosomes. Within the genus Secale, an interspecific variation in the genome size reaches nearly 15% between Secale cereale (cultivated rye) and the ancient species S. silvestre and an increase in the size of subtelomeric heterochromatin regions is the main contributor to these differences. Earlier works have demonstrated that the subtelomeric hetechromatin of rye is enriched for a few multicopy tandemly organized DNA families which form the long arrays of monomers. Here we aimed to clarify the fine large-scale organization and mutual arrangement within the tandem arrays of these families and the flanking genomic nonarray DNA. Restriction analysis of the BAC-clones containing genetic material of the short arm of the first rye chromosome (1RS) showed that within arrays the bulk of monomers is organized in the specific higher-order repeat units (up to hexamers) which are generated in the central part of tandem arrays, while only monomers and dimers are present near the boundaries. Sequencing of the genomic nonarray DNA flanking the tandem arrays has demonstrated that this DNA in the studied BAC-clones consists completely of retrotransposons of various classes which are also present in the wheat and barley genomes. Thus, only an explosive amplificcation ofpSc200 and pSc250 monomers, on the background of a saturated mixture of various retrotransposons, can be regarded as a specific molecular process in formation of subtelomeric hetechromatin during the divergence of rye genome from the common ancestor of cereals. Evidently, this process resulted in the enlargement of subtelomeric hetechromatin of S. cereale and an increasing of its genome size.
Asunto(s)
Cromosomas de las Plantas , Especiación Genética , Genoma de Planta , Heterocromatina , Secuencias Repetitivas de Ácidos Nucleicos , Secale/genética , Telómero , Cromosomas Artificiales Bacterianos , Electroforesis en Gel de Campo Pulsado , Tamaño del Genoma , Hordeum/genética , Retroelementos , Especificidad de la Especie , Triticum/genéticaRESUMEN
X-chromosome inactivation which takes place in early embryogenesis of all higher mammals is largely determined by the Xist gene activity. This gene encodes long untranslated RNA, which provides transcriptional silencing of the genes on chromosome. In the present study, three enhancer and three silencing transcriptional elements were identified in the Xist promoter region. In these regions, location of putative transcription factors was demonstrated, including the ER site, which was discovered in two positions. The effect of estradiol and retinoic acid on the promoter activity was investigated. The estradiol-induced increase of the promoter activity was demonstrated. A model of the estrogen effect on X chromosome inactivation was suggested.
Asunto(s)
Regiones Promotoras Genéticas , ARN no Traducido/genética , Animales , Secuencia de Bases , Elementos de Facilitación Genéticos , Estradiol/farmacología , Estrógenos/farmacología , Fibroblastos/efectos de los fármacos , Fibroblastos/metabolismo , Técnicas In Vitro , Ratones , Datos de Secuencia Molecular , ARN Largo no Codificante , Elementos Silenciadores Transcripcionales , Tretinoina/farmacología , Cromosoma XRESUMEN
BAC library constructed from the short arm of the first rye (Secale cereale L.) chromosome 1R was screened extensively in order to identify clones containing the copies of a tandemly organized repetitive DNA family, pSc200, which is the most abundant in the rye subtelomeric heterochromatin. Molecular organization of the monomers array and adjacent sequences have been studied in BAC 126/C20. The pSc200 array does not demonstrate the higher-order organization under treatment by different restrictases. The DNA adjacent to the pSc200 array consists of the different repeats included retrotransposon derivatives and another tandemly repeated XbaI family with monomer length of 576 bp, 475 of these show 82% similarity to part of the long terminal repeat of known retrotransposon Cereba. The sequencing of the 13 kb region in BAC 126/C20 revealed the direct junction of the pSc200 and XbaI monomers. The junction between these monomers was abrupt in the identical AT-rich site, CAAAAAT. Another recombinational signal is the palindromes in the close proximity to the site ofjunction. The presence of microhomologies promotes the efficiency action of the proteins involved in the mechanisms of double strand DNA break repair. To our knowledge, for the first time we revealed the direct junction of the monomers, which are longer than 100 bp length and belong to distinct families of tandem repeats from plant genomes.
Asunto(s)
Cromosomas de las Plantas/genética , Heterocromatina/genética , Secale/genética , Secuencias Repetidas en Tándem/genética , Cromosomas Artificiales Bacterianos/genética , ADN de Plantas/química , ADN de Plantas/genética , Desoxirribonucleasas de Localización Especificada Tipo II/químicaRESUMEN
Rich in repeated DNA sequences and poor in genes, the heterochromatin is an important functional part of the eukaryotic genome. Heterochromatin exhibits high evolutionary variability, which was revealed on the cytological and molecular levels in malarial mosquito species from the Anopheles maculipennis complex. In this connection, investigation of the heterochromatin molecular composition in species of this complex is of interest.
Asunto(s)
Anopheles/genética , Cromosomas de Insectos/genética , ADN/genética , Heterocromatina/genética , AnimalesRESUMEN
After the radiation of primates and rodents, the evolution of X-chromosome inactivation centers in human and mouse (XIC/Xic) followed two different directions. Human XIC followed the pathway towards transposon accumulation (the repeat proportion in the center constitutes 72%), especially LINEs, which prevail in the center. On the contrary, mouse Xic eliminated long repeats and accumulated species-specific SIN Es (the repeat proportion in the center constitutes 35%). The mechanism underlying inactivation of one of the X chromosomes in female mammals appeared on the basis of trasnsposons. The key gene of the inactivation process, XIST/Xist, similarly to other long noncoding RNA genes, like TSIX/Tsix, JPX/Jpx, and FTX/Ftx, was formed with the involvement of different transposon sequences. Furthermore, two clusters ofmicroRNA genes from inactivation center originated from L2 [1]. In mouse, one of such clusters has been preserved in the form of microRNA pseudogenes. Thus, long ncRNA genes and microRNAs appeared during the period of transposable elements expansion in this locus, 140 to 105 Myr ago, after the radiation of marsupials and placental mammal lineages.
Asunto(s)
Cromosomas Humanos X/genética , Elementos Transponibles de ADN/genética , Evolución Molecular , MicroARNs/genética , Inactivación del Cromosoma X/genética , Animales , Femenino , Humanos , Ratones , Especificidad de la EspecieRESUMEN
The Xist gene belongs to the class of long noncoding regulatory RNA genes which play a key role in the process of inactivation of one of the X chromosomes in females of placental mammals. Based on interspecific comparative sequence analysis performed using a set ofbioinformatic programs and approaches, the exon-intron gene structure was first described in two species, elephant and armadillo, belonging to the most primitive placental mammal groups, Afrotheria and Xenarthra. Using multiple sequence alignment of the species representing all main groups of placental mammals (12 species), consensus sequence of the ancestral gene was reconstructed. In the gene structure four evolutionary conserved regions with the identity level of 90% and the sizes of more than 100 bp were identified. Substantial contribution of transposable elements to the gene origin, as well as mosaic evolution of certain elements of the Xist locus was demonstrated. It is likely that the ancestral gene consisted often exons and was formed before the radiation of placental mammals, in the period from 140 to 105 Myr ago.
Asunto(s)
Armadillos/genética , Elefantes/genética , Evolución Molecular , Exones/genética , Intrones/genética , ARN no Traducido/genética , Cromosoma X/genética , Animales , Elementos Transponibles de ADN/genética , Femenino , Masculino , ARN Largo no Codificante , Alineación de Secuencia/métodos , Especificidad de la EspecieRESUMEN
The Tsix regulatory region was examined in vole Microtus rossiaemeridionalis. The minimal promoter region, three potential enhancer regulatory elements and one transcription suppressor element were identified. The enhancer regions contained potential binding sites of transcription activators, while in the region of putative silencer contained potential binding site of the ARP1 (NR2F2) protein. This protein can play the role of either activator or repressor depending on the promoter context.
Asunto(s)
Arvicolinae/genética , ARN no Traducido/genética , Elementos de Respuesta/genética , Elementos Silenciadores Transcripcionales/genética , Animales , Factor de Transcripción COUP II/genética , Proteínas Represoras/genéticaRESUMEN
Interaction of transcription factor CTCF with the minimal promoter of Xist gene was investigated in intraspecific hybrids ofcommon voles. CTCF was shown to bind with the minimal promoter region in vivo. However, the experiments of the delay in gel resulted in the absence of interaction between the CTCF factor and its potential binding site. Probably, G(-43)A substitution influences binding efficacy of another transcription factor such as activator protein 2, AP2.
Asunto(s)
Quimera/genética , Polimorfismo de Nucleótido Simple , Regiones Promotoras Genéticas/genética , ARN no Traducido/genética , Inactivación del Cromosoma X/genética , Cromosoma X/genética , Animales , Arvicolinae , Factor de Unión a CCCTC , Quimera/metabolismo , Femenino , Masculino , ARN no Traducido/metabolismo , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Cromosoma X/metabolismoRESUMEN
Mouse X chromosome inactivation center contains the DXPas34 minisatellite locus which plays an important role in expression regulation of the Tsix and Xist genes, involved into female dosage compensation. Comparative analysis of the DXPas34 locus from mouse, rat, and four common vole species revealed similar organization of this region in the form of tandem repeat blocks. A search for functionally important elements in this locus showed that all the species examined carried the conservative motif monomers, which could be involved in regulation of X inactivation.
Asunto(s)
Cromosomas de los Mamíferos/genética , ARN no Traducido/genética , Elementos Reguladores de la Transcripción/genética , Secuencias Repetidas en Tándem/genética , Inactivación del Cromosoma X/genética , Cromosoma X/genética , Animales , Arvicolinae , Femenino , Ratones , ARN Largo no Codificante , RatasRESUMEN
Two conserved regions were discovered as a result of interspecific comparison of the 5'-region of the Xist gene, which is the key gene in the process of X-chromosome inactivation in mammalian females. The first region corresponds to the minimal promoter, and the second spans between -480 bp and -400 bp from the start of Xist transcription. Footprinting experiments revealed protected regions corresponding to the potential binding sites for TBP, SP1, API, SRY, ER, and some other transcription factors. They also demonstrated the interaction with the minimal promoter of the human recombinant transcription factor SP1 in vitro and of the transcription factor CTCF in vivo. Experiments with reporter constructs showed that repressors of Xist transcription were located between -100 bp and -200 bp and between -300 bp and -400 bp and activators of Xist transcription were located between -200 bp and -300 bp and between -400 bp and -500 bp.
Asunto(s)
Arvicolinae/genética , Cromosomas de los Mamíferos/genética , ARN no Traducido/genética , Elementos de Respuesta/fisiología , Factores de Transcripción/genética , Cromosoma X/genética , Animales , Arvicolinae/metabolismo , Cromosomas de los Mamíferos/metabolismo , Femenino , Humanos , ARN no Traducido/biosíntesis , Especificidad de la Especie , Factores de Transcripción/metabolismo , Cromosoma X/metabolismoRESUMEN
In eukaryotes, the SMC (Structural Maintenance of Chromosomes) gene family is represented by at least six genes. Some of these genes have tissue-specific homologs. Eukaryotic SMC structural proteins are the members of biochemical complexes responsible for cohesion of sister chromatids, recombination, repair, regulation of gene expression, and formation of mitotic chromosomes. In the present study, the structure of the SMC4 sub-family gene was examined in common vole Microtus arvalis. Comparative analysis of rodent (M. arvalis, Mus musculus. and Rattus norvegicus), human, and Xenopus SMC4 orthologous genes was carried out, and the main patterns of their organization and regulation were established. The SMC4 genes contain 24 exons; open reading frame starts at exon 2. The SMC4 5' regions contain the CpG islands, extending in the region of exon-intron I and exon 2. The SMC4 genes are characterized by the presence of multiple transcription startpoints. The region of the major transcription startpoint contains the INR CCA,1TTTT element. The SMC4 5' region is characterized by the presence of putative binding site for basal transcription factor Sp and factor E2F, typical of the genes induced in the G I/S phase of the cell cycle. The divergence level of the SMC4 coding region was examined. The mean Ka/Ks ratio for the SMC4 genes examined was 0. 123. The region of exon 2 was found to be the most variable (Ka/Ks = 0.715), while the most conservative was the region coding for the C-globular domain, which contained the DA box (Ka/Ks = 0.024).
Asunto(s)
Arvicolinae/genética , Proteínas Cromosómicas no Histona/genética , Evolución Molecular , Animales , Secuencia de Bases , Proteínas Cromosómicas no Histona/metabolismo , Islas de CpG , Factores de Transcripción E2F/metabolismo , Exones , Humanos , Ratones , Datos de Secuencia Molecular , Ratas , Factor de Transcripción Sp1/metabolismo , Activación TranscripcionalRESUMEN
The tandemly arranged MS4 repeat with monomeric units of 4.1 kb is species-specifically distributed in heterochromatin of sex chromosomes of four common vole species of genus Microtus, group arvalis [1, 2]. In this work, we studied the genomic organization of the MS4 homolog in euchromatin of the X chromosome of M. arvalis. It has been shown by analyzing the phage genomic clones that one MS4 copy makes a part of a monomeric unit exceeding 8.5 kb that also includes a new MS7 repeat and, possibly, LINE fragments. MS7 is located together with MS4 in heterochromatin of common vole sex chromosomes, but in a substantially lesser amount. Probably, as a result of an evolutionary transition of an original repeat from euchromatin of the X chromosome to heterochromatin of the Y chromosome, MS4 underwent multiple amplification, and MS7 spread throughout heterochromatin, being surrounded by the MS4 tandem arrays.
Asunto(s)
Arvicolinae/genética , Mapeo Cromosómico , Genoma , Heterocromatina/genética , Secuencias Repetitivas de Ácidos Nucleicos , Animales , Cromosoma X , Cromosoma YRESUMEN
Two long repeats, MS3 and MS4, are predominantly located in sex-chromosomal heterochromatin in common vole species. Their tandem arrangement was revealed by means of the PCR analysis of genomic DNAs of four Microtus species and by restriction mapping of clones selected from a M. rossiaemeridionalis genomic library. Several mobile elements proved incorporated in a monomeric unit of each repeat and amplified together with its other components. In addition, LINE inserts were found in MS4 tandem arrays. The copy number of both repeats per haploid genome was estimated at 100-300 for euchromatin and 20,000-40,000 for the M. rossiaemeridionalis genome. The repeats were assumed to be the major component of sex-chromosomal heterochromatin DNA.