Sex- and tissue-specific Bkm(GATA)-binding protein in the germ cells of heterogametic sex

MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes

Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, "MicrosatNavigator", a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.

STRs: Ancient Architectures of the Genome beyond the Sequence

Short tandem repeats (STRs) are commonly defined as short runs of repetitive nucleotides, consisting of tandemly repeating 2-6- bp motif units, which are ubiquitously distributed throughout genomes. Functional STRs are polymorphic in the population, and their variations influence gene expression, which subsequently may result in pathogenic phenotypes. To understand STR phenotypic effects and their functional roles, we describe four different mutational mechanisms including the unequal crossing-over model, gene conversion, retrotransposition mechanism and replication slippage. Due to the multi-allelic nature, small length, abundance, high variability, codominant inheritance, nearly neutral evolution, extensive genome coverage and simple assaying of STRs, these markers are widely used in various types of biological research, including population genetics studies, genome mapping, molecular epidemiology, paternity analysis and gene flow studies. In this review, we focus on the current knowledge regarding STR genomic distribution, function, mutation and applications.

Evolutionary Insights of the ZW Sex Chromosomesin Snakes: A New Chapter Added by the AmazonianPuffing Snakes of the Genus Spilotes

Amazonian puffing snakes (Spilotes; Colubridae) are snakes widely distributed in the Neotropical region. However, chromosomal data are scarce in this group and, when available, are only limited to karyotype description using conventional staining. In this paper, we focused on the process of karyotype evolution and trends for sex chromosomes in two Amazonian Puffer Snakes (S. pulllatus and S. sulphureus). We performed an extensive karyotype characterization using conventional and molecular cytogenetic approaches. The karyotype of S. sulphureus (presented here for the first time) exhibits a 2n = 36, similar to that previously described in S. pullatus. Both species have highly differentiated ZZ/ZW sex chromosomes, where the W chromosome is highly heterochromatic in S. pullatus but euchromatic in S. sulphureus. Both W chromosomes are homologous between these species as revealed by cross-species comparative genomic hybridization, even with heterogeneous distributions of several repetitive sequences across their genomes, including on the Z and on the W chromosomes. Our study provides evidence that W chromosomes in these two species have shared ancestry.

Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes

Microsatellite repeat DNA is best known for its length mutability, which is implicated in several neurological diseases and cancers, and often exploited as a genetic marker. Less well-known is the body of work exploring the widespread and surprisingly diverse functional roles of microsatellites. Recently, emerging evidence includes the finding that normal microsatellite polymorphism contributes substantially to the heritability of human gene expression on a genome-wide scale, calling attention to the task of elucidating the mechanisms involved. At present, these are underexplored, but several themes have emerged. I review evidence demonstrating roles for microsatellites in modulation of transcription factor binding, spacing between promoter elements, enhancers, cytosine methylation, alternative splicing, mRNA stability, selection of transcription start and termination sites, unusual structural conformations, nucleosome positioning and modification, higher order chromatin structure, noncoding RNA, and meiotic recombination hot spots.

Repetitive Sequence and Sex Chromosome Evolution in Vertebrates

Sex chromosomes are the most dynamic entity in any genome having unique morphology, gene content, and evolution. They have evolved multiple times and independently throughout vertebrate evolution. One of the major genomic changes that pertain to sex chromosomes involves the amplification of common repeats. It is hypothesized that such amplification of repeats facilitates the suppression of recombination, leading to the evolution of heteromorphic sex chromosomes through genetic degradation of Y or W chromosomes. Although contrasting evidence is available, it is clear that amplification of simple repetitive sequences played a major role in the evolution of Y and W chromosomes in vertebrates. In this review, we present a brief overview of the repetitive DNA classes that accumulated during sex chromosome evolution, mainly focusing on vertebrates, and discuss their possible role and potential function in this process.

Cytogenetic analysis in Polypterus ornatipinnis (Actinopterygii, Cladistia, Polypteridae) and 5S rDNA

Polypteridae is a family of archaic freshwater African fish that constitute an interesting subject for the study of the karyological evolution in vertebrates, on account of their primitive morphological characters and peculiar relationships with lower Osteichthyans. In this paper, a cytogenetic analysis on twenty specimens of both sexes of Polypterus ornatipinnis the ornate "bichir", coming from the Congo River basin, was performed by using both classical and molecular techniques. The karyotypic formula (2n=36; FN=72) was composed of 26 M+10 SM. The Alu I banding, performed to characterize heterochromatin in this species, was mainly centromeric. Both the chromosome location of the ribosomal 5S and 18S rRNA genes were examined by using Ag-NOR, classical C-banding, CMA(3) staining and FISH. CMA(3) marked all centromerical regions and showed the presence of two GC rich regions on the p arm of the chromosome pair n°1 and on the q arm of the pair n°14. Staining with Ag-NOR marked the only telomeric region of the chromosome n°1 p arm. After PCR, the 5S rDNA in this species was cloned, sequenced and analyzed. In the 665bp 5S rDNA sequence of P.ornatipinnis, a conserved 120bp gene region for the 5S rDNA was identified, followed by a non-transcribed variable spacer (NTS) which included simple repeats, microsatellites and a fragment of a non-LTR retrotransposon R-TEX. FISH with 5S rDNA marked the subtelomeric region of the q arm of the chromosome pair n°14, previously marked by CMA(3). FISH with 18S rDNA marked the telomeric region of the p arm of the pair n°1, previously marked both by Ag-NOR and CMA(3). The (GATA)(7) repeats marked the telomeric regions of all chromosome pairs, with the exclusion of the n°1, n°3 and n°14; hybridization with telomeric probes (TTAGGG)(n) showed signals at the end of all chromosomes. Karyotype evolution in Polypterus genus was finally discussed, including the new data obtained.

Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis

BACKGROUND

Simple sequence repeats (SSRs) of GACA/GATA have been implicated with differentiation of sex-chromosomes and speciation. However, the organization of these repeats within genomes and transcriptomes, even in the best characterized organisms including human, remains unclear. The main objective of this study was to explore the buffalo transcriptome for its association with GACA/GATA repeats, and study the structural organization and differential expression of the GACA/GATA repeat tagged transcripts. Moreover, the distribution of GACA and GATA repeats in the prokaryotic and eukaryotic genomes was studied to highlight their significance in genome evolution.

RESULTS

We explored several genomes and transcriptomes, and observed total absence of these repeats in the prokaryotes, with their gradual accumulation in higher eukaryotes. Further, employing novel microsatellite associated sequence amplification (MASA) approach using varying length oligos based on GACA and GATA repeats; we identified and characterized 44 types of known and novel mRNA transcripts tagged with these repeats from different somatic tissues, gonads and spermatozoa of water buffalo Bubalus bubalis. GACA was found to be associated with higher number of transcripts compared to that with GATA. Exclusive presence of several GACA-tagged transcripts in a tissue or spermatozoa, and absence of the GATA-tagged ones in lung/heart highlights their tissue-specific significance. Of all the GACA/GATA tagged transcripts, approximately 30% demonstrated inter-tissue and/or tissue-spermatozoal sequence polymorphisms. Significantly, approximately 60% of the GACA-tagged and all the GATA-tagged transcripts showed highest or unique expression in the testis and/or spermatozoa. Moreover, approximately 75% GACA-tagged and all the GATA-tagged transcripts were found to be conserved across the species.

CONCLUSION

Present study is a pioneer attempt exploring GACA/GATA tagged transcriptome in any mammalian species highlighting their tissue, stage and species-specific expression profiles. Comparative analysis suggests the gradual accumulation of these repeats in the higher eukaryotes, and establishes the GACA richness of the buffalo transcriptome. This is envisaged to establish the roles of integral simple sequence repeats and tagged transcripts in gene expression or regulation.

Distribution of polymorphic and non-polymorphic microsatellite repeats in Xenopus tropicalis

The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.

Characterization of novel DNA-binding proteins expressed in snake oocyte cDNA library

DNA-binding proteins play pivotal roles in transcription, DNA-replication, recombination/repair and determine cell-fate in all physiological conditions of differentiation, development and disease. As they are present in extremely small amounts in cells, their isolation/identification, particularly from scarce tissues is impracticable. We cloned the cDNA pool of snake (Ptyas mucosus) oocytes (a scarce tissue) in bacteria, overexpressed total library, purified and identified DNA-binding proteins expressed in the library. Although snake databases do not exist, we identified 23 DNA-binding proteins, obtained 10-15 amino acids internal sequence tags of six of them and succeeded in PCR amplification of the cDNAs of five proteins. We employed electro spray ionization mass spectrometry, matrix assisted laser desorption/ionization time of flight and analyzed the results by peptide mass fingerprint (PMF) and various sequence BLAST analyses. Proteins identified were largely unanimous between the PMF and BLAST analyses. We expect these proteins to play important roles in snake embryonic development and differentiation. We arrived at homologous mouse proteins to some of the identified snake proteins and are working towards characterizing their structure and physiological function. Similar approaches shall prove valuable in isolation and identification of important factors from scarce carcinoma tissues, mammalian oocytes and early embryos, which might be involved in important functions like nuclear reprogramming, embryonic development and differentiation.

A GATA-binding protein expressed predominantly in the pupal ovary of the silkworm, Bombyx mori

Preferential localization of Bkm (Banded krait minor-satellite) DNA sequences on Y/W chromosomes of higher eukaryotes, which remain highly condensed in somatic cells but undergo extensive decondensation in the germ cells during early stages of development, led to the postulation for the existence of a sex- and tissue-specific Bkm-binding protein (BBP). Accordingly, we purified and characterized a BmBBP expressed predominantly in pupal ovary of the silkworm (Bombyx mori). 2D-PAGE revealed BmBBP as moderately basic (pI 7.8-8, in the range expected for DNA-binding proteins) and Matrix Assisted Laser Desorption/Ionization Time of Flight exhibited a value of 37.5-kDa. BmBBP neither contains nor requires divalent metal ions for its DNA-binding activity, suggesting that it does not belong to the well-studied GATA-family of transcription factors. BmBBP is unusually strong in its DNA-binding characteristics to Bkm (GATA-repeats), which suggests its probable role in bringing about coordinated chromatin conformational changes to activate genes present in associated chromosomal domains. Fluorescence immuno-localization studies employing specific anti-BmBBP antibodies revealed its presence in the follicle cells and in the ooplasm, as well as the nucleus of different developmental stages of oocytes.

Interaction of nuclear proteins with repeat sequences in the 5' flanking region of mouse muscle creatine kinase gene during aging

The 5' flanking region of the mouse muscle creatine kinase (MCK) gene contains two repeat sequences-a mononucleotide repeat, (A)(22) (-2694 to -2673), and a tetranucleotide repeat, (GTTT)(8) (-2962 to -2931). We show here that these repeats in the mouse MCK gene bind to specific nuclear protein factors. Some of the factors interacting with these sequences are tissue-specific and show age-related decrease in the binding activity. Nonspecific competitor and heterologous DNA probes failed to compete out the complexes showing that the interaction is specific to the repeat sequences. These proteins may have a role in the expression of the gene during aging.

GATA factors differentially activate multiple gonadal promoters through conserved GATA regulatory elements

The GATA factors are a group of transcriptional regulators that play essential roles in cell differentiation, organ morphogenesis, and tissue-specific gene expression during development. The six vertebrate GATA factors are expressed in a broad spectrum of tissues, including the hemopoietic system, heart, gut, brain, placenta, pituitary, and gonads. Interestingly, GATA-like DNA-binding proteins are found in the gonads of several species, ranging from lower invertebrates to humans, thus supporting an evolutionary conserved and crucial role for these factors in gonadal development and function. Indeed, GATA factors are expressed from the onset of gonadal development and are later found in multiple cell lineages of both the testis and ovary. We now report that GATA-4 differentially activates transcription of several genes expressed in the gonads that encode either steroidogenic enzymes (steroidogenic acute regulatory protein and aromatase), hormones (inhibin alpha and Müllerian inhibiting substance) and a transcription factor (SF-1) known to be essential for gonadal development and function. Thus, our results identify GATA-4 as an important regulator of gonadal gene transcription where its specificity of action is mediated through synergistic interactions with other transcription factors such as SF-1.

Transcription factor GATA-4 is expressed in a sexually dimorphic pattern during mouse gonadal development and is a potent activator of the Mullerian inhibiting substance promoter

Mammalian gonadal development and sexual differentiation are complex processes that require the coordinated expression of a specific set of genes in a strict spatiotemporal manner. Although some of these genes have been identified, the molecular pathways, including transcription factors, that are critical for the early events of lineage commitment and sexual dimorphism, remain poorly understood. GATA-4, a member of the GATA family of transcription factors, is present in the gonads and may be a regulator of gonadal gene expression. We have analyzed the ontogeny of gonadal GATA-4 expression by immunohistochemistry. GATA-4 protein was detected as early as embryonic day 11.5 in the primitive gonads of both XX and XY mouse embryos. In both sexes, GATA-4 specifically marked the developing somatic cell lineages (Sertoli in testis and granulosa in ovary) but not primordial germ cells. Interestingly, abundant GATA-4 expression was maintained in Sertoli cells throughout embryonic development but was markedly down-regulated shortly after the histological differentiation of the ovary on embryonic day 13.5. This pattern of expression suggested that GATA-4 might be involved in early gonadal development and possibly sexual dimorphism. Consistent with this hypothesis, we found that the Mullerian inhibiting substance promoter which harbors a conserved GATA element is a downstream target for GATA-4. Thus, transcription factor GATA-4 may be a new factor in the cascade of regulators that control gonadal development and sex differentiation in mammals.

Simple repetitive sequences in the genome: structure and functional significance

The current explosion of DNA sequence information has generated increasing evidence for the claim that noncoding repetitive DNA sequences present within and around different genes could play an important role in genetic control processes, although the precise role and mechanism by which these sequences function are poorly understood. Several of the simple repetitive sequences which occur in a large number of loci throughout the human and other eukaryotic genomes satisfy the sequence criteria for forming non-B DNA structures in vitro. We have summarized some of the features of three different types of simple repeats that highlight the importance of repetitive DNA in the control of gene expression and chromatin organization. (i) (TG/CA)n repeats are widespread and conserved in many loci. These sequences are associated with nucleosomes of varying linker length and may play a role in chromatin organization. These Z-potential sequences can help absorb superhelical stress during transcription and aid in recombination. (ii) Human telomeric repeat (TTAGGG)n adopts a novel quadruplex structure and exhibits unusual chromatin organization. This unusual structural motif could explain chromosome pairing and stability. (iii) Intragenic amplification of (CTG)n/(CAG)n trinucleotide repeat, which is now known to be associated with several genetic disorders, could down-regulate gene expression in vivo. The overall implications of these findings vis-à-vis repetitive sequences in the genome are summarized.

Biological significance of minisatellites

Minisatellites are tandemly repeated, highly variable DNA sequences found in most higher eukaryotes. These contain a core sequence resembling the chi sequence of Escherichia coli, which is a binding site for recombination proteins. Based on this, a generalized function of minisatellites to provide binding sites for recombination proteins in eukaryotes has also been suggested. However, recent discoveries of trinucleotide repeat expansion mutations associated with at least four human genetic diseases, several short repeats acting as motifs for binding of various transcription factors, and several minisatellite-binding nuclear proteins, which are expressed in specific tissues and bind to specific sequences, strongly suggest that different families of minisatellites may have different functions. A banded krait minor (Bkm) satellite DNA, consisting of highly conserved GATA repeats, which is arranged in a sex-specific manner, is hypervariable. We have found a sex- and tissue-specific factor designated as Bkm-binding protein (BBP), which specifically binds to Bkm (GATA), in the germ cells of the heterogametic sex [ovary, in the case of female heterogamety (in snakes); and testis, in the case of male heterogamety (in mice, rats and humans)]. It is in these tissues that decondensation of the W and Y chromosomes occurs. We suggest that GATA repeats of Bkm bring about a coordinated decondensation of the W and Y sex chromosomes in the germ cells in response to BBP, which may serve as a "switch" for the activation of the genes present on the W and Y sex chromosomes. Since the number of GATA repeats, in tandem, necessary for the binding of BBP is flexible, there is no selection pressure on the maintenance of the exact length of the repeats, unless it is reduced below a threshold at which the binding is completely abolished.