Inna E. Pristyazhnyuk

Allelic expression and DNA methylation profiles of promoters at the parental Oct4 and Nanog genes in Mus musculus ES cell/Mus caroli splenocyte hybrid cells

Expression of the parental Oct4 and Nanog alleles and DNA methylation of their promoters were studied in a set of Mus musculus embryonic stem (ES) cell/M. caroli splenocyte hybrid cells containing a variable ratio of parental chromosomes 6 and 17. The transcripts of the reactivated splenocyte Oct4 and Nanog genes were revealed in all hybrid cell clones positive for M. caroli chromosomes 6 and 17. We found that 11 CpG sites in the Oct4 promoter were heavily methylated in M. caroli splenocytes (>80%), whereas M. musculus ES cells were essentially unmethylated (<1%). Analysis of the methylation status of the Oct4 promoter in seven hybrid cell clones showed that the splenocyte-derived promoter sequence lost DNA methylation so that its methylation level was comparable with that of the ES cells. Additionally, no preferential de novo methylation was seen in the Oct4 promoters of M. musculus and M. caroli in teratomas developed from two independent hybrid clones. The upstream region of Nanog was heavily methylated in mouse embryonic fibroblasts (66%) and less methylated in M. caroli splenocytes (24%). The Nanog promoter region was completely unmethylated in M. musculus ES cells. We found that both parental alleles of the Nanog gene promoter were essentially unmethylated in five examined hybrid clones. Thus, we have demonstrated that (1) the Oct4 and Nanog genes of splenocytes are activated, and their promoters undergo demethylation in ES cell hybrids; (2) these events are independent of the number and ratio of parental chromosomes carrying these genes.

Visible and “cryptic” segregation of parental chromosomes in embryonic stem hybrid cells

Chromosome segregation of the parental chromosomes was studied in 20 interspecific hybrid clones obtained by fusion of Mus musculus embryonic stem cells with Mus caroli splenocytes. FISH analysis with labeled species specific probes and microsatellite markers was used for identification of the parental chromosomes. Cytogenetic analysis has shown significant intra- and interclonal variability in chromosome numbers and ratios of the parental chromosomes in the hybrid cells: six clones contained all M. caroli chromosomes, nine clones showed moderate segregation of M. caroli chromosomes (from 1 to 7), and five clones showed extensive loss of M. caroli chromosomes (from 12 to complete loss of all M. caroli autosomes). Both methods demonstrated “cryptic” segregation of the somatic partner chromosomes. For instance, five clones with near-tetraploid chromosome sets contained only few M. caroli chromosomes (from 1 to 8). The data obtained suggest that the tetraploid chromosome set per se is not a sufficient criterion for conclusion on the absence of chromosome loss in the hybrid cells. Note that “cryptic” chromosome segregation occurred at a high frequency in the examined hybrid clones. Thus, “cryptic” segregation should be borne in mind for assessing pluripotency and genome reprogramming of embryonic stem hybrid cells.

Ring chromosomes: from formation to clinical potential

Ring chromosomes (RCs) are circular DNA molecules, which occur rarely in eukaryotic nuclear genomes. Lilian Vaughan Morgan first described them in the fruit fly. Human embryos very seldom have RCs, about 1:50,000. Carriers of RCs may have varying degrees of symptoms, from healthy phenotype to serious pathologies in physical and intellectual development. Many authors describe common symptoms of RC presence: short stature and some developmental delay that could be described as a “ring chromosome syndrome.” As a rule, RCs arise de novo through the end-joining of two DNA double-strand breaks, telomere-subtelomere junction, or inv dup del rearrangement in both meiosis and mitosis. There are family cases of RC inheritance. The presence of RCs causes numerous secondary chromosome rearrangements in vivo and in vitro. RCs can change their size, become lost, or increase their copy number and cause additional deletions, duplication, and translocations, affecting both RCs and other chromosomes. In this review, we examine RC inheritance, instability, mechanisms of formation, and potential clinical applications of artificially created RCs for large-scale chromosome rearrangement treatment.

Chromosome composition of interspecies hybrid embryonic stem cells in mice

Chromosome complements of 20 hybrid clones obtained by fusing Mus musculus embryonic stem cells (ESCs) and Mus caroli splenocytes were studied. The use of two-color fluorescence hybridization in situ with chromosome- and species-specific probes has allowed us to reliably reveal the parental origin of homologs of any chromosome in hybrid cells. Depending on the ratio of parental chromosome homologs, all 20 hybrid clones were separated in several groups ranging from the clones that contain cells that are nearly tetraploid with two diploid sets of M. musculus and single M. caroli chromosomes to clones with a marked predominance of the M. caroli chromosome. In eight hybrid cell clones, we observed the pronounced prevalence of chromosomes of the pluripotent partner over chromosomes of the somatic partner in a ratio of 5: 1 to 3: 1. In other hybrid cell clones, the ratio of M. musculus to M. caroli chromosomes was either equal (1: 1; 2: 2) or with the prevalence of the pluripotent (2: 1) or differentiated (1: 2) partner. In three hybrid cell clones, for the first time, we observed the predominant segregation of ESC-derived pluripotent chromosomes. This might indicate the compensation for the epigenetic differences between parental chromosomes of the ESC and splenocyte origin.

Germline-Restricted Chromosome (GRC) is Widespread among Songbirds

The genome of flying birds, the smallest among amniotes, reflects overweight of the extensive DNA loss over the unrestricted proliferation of selfish genetic elements, resulted in a shortage of repeated sequences and lack of B-chromosomes. The only exception of this rule has been described in zebra finch, which possesses a large germ-line restricted chromosome (GRC), transmitted via oocytes, eliminated from male postmeiotic cells and absent in somatic cell. It is considered as a rarity and its origin, content and function remain unclear. We discovered that all songbirds possess GRC: in various size and genetic content it is present in all fifteen songbird species investigated and absent from germ-line genomes of all eight species of other bird orders examined. Our data based on fluorescent in situ hybridization of DNA probes derived from GRCs of four different Passeri species and their sequencing indicate that the GRCs show low homology between avian species. They contain fragments of the somatic genomes, which include various unique and repetitive sequences. We propose that the GRC has formed in the common ancestor of the extant songbirds and undergone subsequent divergence. GRC presence in the germ line of every songbird studied indicate that it could contain genetic element(s) indispensable for gametogenesis, which are yet to be discovered.

Alternative dominance of the parental genomes in hybrid cells generated through the fusion of mouse embryonic stem cells with fibroblasts

For the first time, two types of hybrid cells with embryonic stem (ES) cell-like and fibroblast-like phenotypes were produced through the fusion of mouse ES cells with fibroblasts. Transcriptome analysis of 2,848 genes differentially expressed in the parental cells demonstrated that 34–43% of these genes are expressed in hybrid cells, consistent with their phenotypes; 25–29% of these genes display intermediate levels of expression, and 12–16% of these genes maintained expression at the parental cell level, inconsistent with the phenotype of the hybrid cell. Approximately 20% of the analyzed genes displayed unexpected expression patterns that differ from both parents. An unusual phenomenon was observed, namely, the illegitimate activation of Xist expression and the inactivation of one of two X-chromosomes in the near-tetraploid fibroblast-like hybrid cells, whereas both Xs were active before and after in vitro differentiation of the ES cell-like hybrid cells. These results and previous data obtained on heterokaryons suggest that the appearance of hybrid cells with a fibroblast-like phenotype reflects the reprogramming, rather than the induced differentiation, of the ES cell genome under the influence of a somatic partner.

Direct conversion of somatic cells to neuronal precursors: Problems and outlooks

The generation of multipotent patient-specific neural precursors from human fibroblasts is one of the challenges to regenerative medicine. A recently proposed novel approach allows direct conversion of human and mouse fibroblasts into induced neuronal precursor (iNP) cells by overexpression of a single transcription factor, Sox2. In this work, we have analyzed the Sox2-induced iNP cells and evaluated the possibility of its medical application. Both mouse and human fibroblasts had pronounced morphological changes after lentiviral-mediated Sox2 overexpression. The resulting mouse and human iNP cell cultures are morphologically similar to the neuronal precursors (NPs) derived from the mouse embryonic brain. Both human and mouse iNP cells express NP molecular markers, however, differentiation of mouse iNP cells fails to produce various types of neural cells. Especially, these cells are unable to differentiate into mature neurons. In addition to Sox2, we have treated human fibroblasts with c-Myc in combination with either Ascl or Brn2. One of the produced cell lines displayed a low proliferative potential, while another intensely divided; however, cytogenetic analysis revealed their aberrant karyotype. The observed specific features of both the human and mouse iNP cells produced according to this protocol make them of limited therapeutic use. Thus, these iNP cell cultures are not completely equivalent to natural NPs. Correspondingly, we assume that the published protocol for iNP generation via Sox2 exogenous expression is poorly reproducible.

FISH analysis of regional replication of homologous chromosomes in hybrid cells obtained by fusion of embryonic stem cells with somatic cells

The paper deals with the FISH analysis of the regional replication of homologue of chromosomes 1, 3, and 6 in hybrid cells obtained by the fusion of Mus musculus embryonic stem cells (ESCs) and somatic cells—M. caroli splenocytes. The obtained data showed that, in hybrid cells with near-diploid karyotypes, the parental chromosomes were replicated synchronously in 70–75% of tested cells, similar to in diploid ESCs and diploid fibroblasts. In hybrid cells with near-triploid karyotypes, the asynchronous replication of the parental chromosomes increased to 46–57% of tested cells. However, this is true for hybrid cells with three copies of tested chromosomes, whereas, in triploid cells with two copies, the level of the homolog synchronous replication was close to that of diploid cells. In hybrid cells with near-tetraploid karyotypes, the level of asynchronous replication was observed in more than 50% of cells, which is comparable with the level in tetraploid ESCs and tetraploid fibroblasts. Thus, in hybrid cells with no more than two copies of an individual chromosome, the synchronous replication of homologue that initially had different levels of differentiation and parameters of replications was observed. However, the information value of the method of in situ hybridization on interphase nuclei changes significantly with an increase in the number of copies of individual chromosomes and thereby restricts possibilities of this approach for evaluation of synchronous homolog replication in hybrid cells.