X chromosome inactivation: how human are mice?

Thoughts about SLC16A2, TSIX and XIST gene like sites in the human genome and a potential role in cellular chromosome counting

Background

Chromosome counting is a process in which cells determine somehow their intrinsic chromosome number(s). The best-studied cellular mechanism that involves chromosome counting is ‘chromosome-kissing’ and X-chromosome inactivation (XCI) mechanism. It is necessary for the well-known dosage compensation between the genders in mammals to balance the number of active X-chromosomes (Xa) with regard to diploid set of autosomes. At the onset of XCI, two X-chromosomes are coming in close proximity and pair physically by a specific segment denominated X-pairing region (Xpr) that involves the SLC16A2 gene.

Results

An Ensembl BLAST search for human and mouse SLC16A2/Slc16a2 homologues revealed, that highly similar sequences can be found at almost each chromosome in the corresponding genomes. Additionally, a BLAST search for SLC16A2/TSIX/XIST (genes responsible for XCI) reveled that “SLC16A2/TSIX/XIST like sequences” cover equally all chromosomes, too. With respect to this we provide following hypotheses.

Hypotheses

If a single genomic region containing the SLC16A2 gene on X-chromosome is responsible for maintaining “balanced” active copy numbers, it is possible that similar sequences or gene/s have the same function on other chromosomes (autosomes). SLC16A2 like sequences on autosomes could encompass evolutionary older, but functionally active key regions for chromosome counting in early embryogenesis. Also SLC16A2 like sequence on autosomes could be involved in inappropriate chromosomes pairing and, thereby be involved in aneuploidy formation during embryogenesis and cancer development. Also, “SLC16A2/TSIX/XIST gene like sequence combinations” covering the whole genome, could be important for the determination of X:autosome ratio in cells and chromosome counting.

Conclusions

SLC16A2 and/or SLC16A2/TSIX/XIST like sequence dispersed across autosomes and X-chromosome(s) could serve as bases for a counting mechanism to determine X:autosome ratio and could potentially be a mechanism by which a cell also counts its autosomes. It could also be that such specific genomic regions have the same function for each specific autosome. As errors during the obviously existing process of chromosome counting are one if not the major origin of germline/somatic aneuploidy the here presented hypotheses should further elaborated and experimentally tested.

Electronic supplementary material

The online version of this article (doi:10.1186/s13039-016-0271-7) contains supplementary material, which is available to authorized users.

Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome

Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 22 X-linked genes, including XIST, using 27 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this analysis indicated heterogeneous maintenance of gene silencing along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals.

Triple X syndrome in a patient with partial lipodystrophy discovered using a high-density oligonucleotide microarray: a case report

INTRODUCTION

Patients with lipodystrophy experience selective or generalized atrophy of adipose tissue. The disruption of lipid metabolism results in an increased risk for development of metabolic syndrome and coronary artery disease. Currently, the mutations responsible for approximately half of lipodystrophy patients are known, but new techniques and examination of different types of genetic variation may identify new disease-causing mechanisms.

CASE PRESENTATION

A 53-year-old woman of African descent was referred to a tertiary care endocrinology clinic for treatment of severe insulin resistance, treatment-resistant hypertension and dyslipidemia. After all known lipodystrophy-causing mutations were excluded by DNA sequencing, the patient was found to have triple X syndrome after an initial investigation into copy number variation using a high-density oligonucleotide microarray. The patient also had a previously unobserved duplication of 415 kilobases of chromosome 5q33.2. This is the first case report of a patient with lipodystrophy who also had triple X syndrome.

CONCLUSION

While we cannot make a direct link between the presence of triple X syndrome and partial lipodystrophy, if unrelated, this is an extremely rare convergence of syndromes. This patient poses an interesting possibility regarding the influence triple X syndrome may have on an individual with other underlying lipodystrophy susceptibility. Finally, impending large-scale case-control and cohort copy number variation investigations will, as a by-product, further document the prevalence of triple X syndrome in various patient groups.

Genomic imprinting mechanisms in mammals

Genomic imprinting is a form of epigenetic gene regulation that results in expression from a single allele in a parent-of-origin-dependent manner. This form of monoallelic expression affects a small but growing number of genes and is essential to normal mammalian development. Despite extensive studies and some major breakthroughs regarding this intriguing phenomenon, we have not yet fully characterized the underlying molecular mechanisms of genomic imprinting. This is in part due to the complexity of the system in that the epigenetic markings required for proper imprinting must be established in the germline, maintained throughout development, and then erased before being re-established in the next generation's germline. Furthermore, imprinted gene expression is often tissue or stage-specific. It has also become clear that while imprinted loci across the genome seem to rely consistently on epigenetic markings of DNA methylation and/or histone modifications to discern parental alleles, the regulatory activities underlying these markings vary among loci. Here, we discuss different modes of imprinting regulation in mammals and how perturbations of these systems result in human disease. We focus on the mechanism of genomic imprinting mediated by insulators as is present at the H19/Igf2 locus, and by non-coding RNA present at the Igf2r and Kcnq1 loci. In addition to imprinting mechanisms at autosomal loci, what is known about imprinted X-chromosome inactivation and how it compares to autosomal imprinting is also discussed. Overall, this review summarizes many years of imprinting research, while pointing out exciting new discoveries that further elucidate the mechanism of genomic imprinting, and speculating on areas that require further investigation.

Regulating fragile X gene transcription in the brain and beyond

The past several years have seen remarkable growth in our understanding of the molecular processes underlying fragile X syndrome (FXS). Many studies have provided new insights into the regulation of Fmr1 gene expression and the potential function of its protein product. It is now known that the promoter elements modulating Fmr1 transcription involve a complex array of both cis and trans factors. Moreover, recent studies of epigenetic modification of chromatin have provided novel clues to unlocking the mysteries behind the regulation of Fmr1 expression. Here, we review the latest findings on the regulation of Fmr1 transcription.

Gene trap as a tool for genome annotation and analysis of X chromosome inactivation in human embryonic stem cells

Human embryonic stem (ES) cells were suggested to be an important tool in transplantation medicine. However, they also play a major role in human genetics. Using the gene trap strategy, we have created a bank of clones with insertion mutations in human ES cells. These insertions occurred within known, predicted and unknown genes, and thus assist us in annotating the genes in the human genome. The insertions into the genome occurred in multiple chromosomes with a preference to larger chromosomes. Utilizing a clone where the integration occurred in the X chromosome, we have studied X-chromosome inactivation in human cells. We thus show that in undifferentiated female human ES cells both X chromosomes remain active and upon differentiation one chromosome undergoes inactivation. In the differentiated embryonic cells the inactivation is random, while in the extra-embryonic cells it is non-random. In addition, using a selection methodology, we demonstrate that in a minority of the cells partial inactivation and XIST expression occur even in the undifferentiated cells. We suggest that X chromosome inactivation during human embryogenesis, which coincides with differentiation, may be separated from the differentiation process. The genetic manipulation of human ES cells now opens new ways of analyzing chromosome status and gene expression in humans.

Chromosomal localization of sixty autosomal loci in sheep (Ovis aries, 2n = 54) by fluorescence in situ hybridization and R-banding

Sixty autosomal loci (5 type I and 55 type II) from 24 bovine syntenic groups, and previously FISH-mapped to goat and river buffalo chromosomes, were localized by fluorescence in situ on sheep (OVIS ARIES, 2n = 54) chromosomes, thereby notably extending the cytogenetic map of this economically important species. Caprine BAC clones were hybridized to R-banded chromosome preparations. FITC-signals and RBPI- banding (R-banding by late BrdU-incorporation and propidium iodide staining) were simultaneously visualized and captured by a colour CCD-camera. All mapped loci were localized on homoeologous chromosomes and chromosome regions (bands) of sheep, goat and river buffalo, further supporting chromosome and genetic (loci) homoeologies among bovids.