Chromosome Research最新文献

Abstract

Polyploidization is a process which is related to species hybridization and whole genome duplication. It is widespread among angiosperm evolution and is essential for speciation and diversification. Allopolyploidization is mainly derived from interspecific hybridization and is believed to pose chromosome imbalances and genome instability caused by meiotic irregularity. However, the self-compatible allopolyploid in wild nature is cytogenetically and genetically stable. Whether this stabilization form was achieved in initial generation or a consequence of long term of evolution was largely unknown. Here, we synthesized a series of nascent allotetraploid wheat derived from three diploid genomes of A, S*, and D. The chromosome numbers of the majority of the progeny derived from these newly formed allotetraploid wheat plants were found to be relatively consistent, with each genome containing 14 chromosomes. In meiosis, bivalent was the majority of the chromosome configuration in metaphase I which supports the stable chromosome number inheritance in the nascent allotetraploid. These findings suggest that diploidization occurred in the newly formed synthetic allotetraploid wheat. However, we still detected aneuploids in a proportion of newly formed allotetraploid wheat, and meiosis of these materials present more irregular chromosome behavior than the euploid. We found that centromere pairing and centromere clustering in meiosis was affected in the aneuploids, which suggest that aneuploidy may trigger the irregular interactions of centromere in early meiosis which may take participate in promoting meiosis stabilization in newly formed allotetraploid wheat.

Methylation of H3K9 histone residue is a marker of gene silencing in eukaryotes. Three enzymes responsible for adding this modification — G9a, SetDB1/Egg, and Su(var)3-9 — are known in Drosophila. To understand how simultaneous mutations of SetDB1 and Su(var)3-9 may affect the fly development, appropriate combinations were obtained. Double mutants egg; Su(var)3-9 displayed pronounced embryonic lethality, slower larval growth and died before or during metamorphosis. Analysis of transcription in larval salivary glands and wing imaginal disks indicated that the effect of double mutation is tissue-specific. In salivary gland chromosomes, affected genes display low H3K9me2 enrichment and are rarely bound by SetDB1 or Su(var)3-9. We suppose that each of these enzymes directly or indirectly controls its own set of gene targets in different organs, and double mutation results in an imbalanced developmental program. This also indicates that SetDB1 and Su(var)3-9 may affect transcription via H3K9-independent mechanisms. Unexpectedly, in double and triple mutants, amount of di- and tri-methylated H3K9 is drastically reduced, but not completely absent. We hypothesize that this residual methylation implies the existence of additional H3K9-specific methyltransferase in Drosophila.

Eukaryotes have varying numbers and structures of characteristic chromosomes across lineages or species. The evolutionary trajectory of species may have been affected by spontaneous genome rearrangements. Chromosome fusion drastically alters karyotypes. However, the mechanisms and consequences of chromosome fusions, particularly in muntjac species, are poorly understood. Recent research-based advancements in three-dimensional (3D) genomics, particularly high-throughput chromatin conformation capture (Hi-C) sequencing, have allowed for the identification of chromosome fusions and provided mechanistic insights into three muntjac species: Muntiacus muntjak, M. reevesi, and M. crinifrons. This study aimed to uncover potential genome rearrangement patterns in the threatened species Fea's muntjac (Muntiacus feae), which have not been previously examined for such characteristics. Deep Hi-C sequencing (31.42 × coverage) was performed to reveal the 3D chromatin architecture of the Fea's muntjac genome. Patterns of repeated chromosome fusions that were potentially mediated by high-abundance transposable elements were identified. Comparative Hi-C maps demonstrated linkage homology between the sex chromosomes in Fea's muntjac and autosomes in M. reevesi, indicating that fusions may have played a crucial role in the evolution of the sex chromosomes of the lineage. The species-level dynamics of topologically associated domains (TADs) suggest that TAD organization could be altered by differential chromosome interactions owing to repeated chromosome fusions. However, research on the effect of TADs on muntjac genome evolution is insufficient. This study generated Hi-C data for the Fea's muntjac, providing a genomic resource for future investigations of the evolutionary patterns of chromatin conformation at the chromosomal level.

Satellite DNA (satDNA) is a rapidly evolving class of tandem repeats, with some monomers being involved in centromere organization and function. To identify repeats associated with (peri)centromeric regions, we investigated satDNA across Southern and Coastal clades of African annual killifishes of the genus Nothobranchius. Molecular cytogenetic and bioinformatic analyses revealed that two previously identified satellites, designated here as NkadSat01-77 and NfurSat01-348, are associated with (peri)centromeres only in one lineage of the Southern clade. NfurSat01-348 was, however, additionally detected outside centromeres in three members of the Coastal clade. We also identified a novel satDNA, NrubSat01-48, associated with (peri)centromeres in N. foerschi, N. guentheri, and N. rubripinnis. Our findings revealed fast turnover of satDNA associated with (peri)centromeres and different trends in their evolution in two clades of the genus Nothobranchius.

This review investigates the role of aneuploidy and chromosome instability (CIN) in the aging brain. Aneuploidy refers to an abnormal chromosomal count, deviating from the normal diploid set. It can manifest as either a deficiency or excess of chromosomes. CIN encompasses a broader range of chromosomal alterations, including aneuploidy as well as structural modifications in DNA. We provide an overview of the state-of-the-art methodologies utilized for studying aneuploidy and CIN in non-tumor somatic tissues devoid of clonally expanded populations of aneuploid cells.CIN and aneuploidy, well-established hallmarks of cancer cells, are also associated with the aging process. In non-transformed cells, aneuploidy can contribute to functional impairment and developmental disorders. Despite the importance of understanding the prevalence and specific consequences of aneuploidy and CIN in the aging brain, these aspects remain incompletely understood, emphasizing the need for further scientific investigations.This comprehensive review consolidates the present understanding, addresses discrepancies in the literature, and provides valuable insights for future research efforts.

Aneuploidy-the karyotype state in which the number of chromosomes deviates from a multiple of the haploid chromosome set-is common in cancer, where it is thought to facilitate tumor initiation and progression. However, it is poorly tolerated in healthy cells: during development and tissue homeostasis, aneuploid cells are efficiently cleared from the population. It is still largely unknown how cancer cells become, and adapt to being, aneuploid. P53, the gatekeeper of the genome, has been proposed to guard against aneuploidy. Aneuploidy in cancer genomes strongly correlates with mutations in TP53, and p53 is thought to prevent the propagation of aneuploid cells. Whether p53 also participates in preventing the mistakes in cell division that lead to aneuploidy is still under debate. In this review, we summarize the current understanding of the role of p53 in protecting cells from aneuploidy, and we explore the consequences of functional p53 loss for the propagation of aneuploidy in cancer.

Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species present relatively stable karyotypes with 2n = 22 chromosomes, the karyotypes of species of the Leptostachyus group show high rates of structural rearrangements, including a nested chromosome fusion that led to the dysploid chromosome number of the group (2n = 20). We examined the roles of repetitive landscapes in the rearrangements of species of the Leptostachyus group using genome-skimming data to characterize the repeatome in a range of Phaseolus species and compared them to species of that group (P. leptostachyus and P. macvaughii). LTR retrotransposons, especially the Ty3/gypsy lineage Chromovirus, were the most abundant elements in the genomes. Differences in the abundance of Tekay, Retand, and SIRE elements between P. macvaughii and P. leptostachyus were reflected in their total amounts of Ty3/gypsy and Ty1/copia. The satellite DNA fraction was the most divergent among the species, varying both in abundance and distribution, even between P. leptostachyus and P. macvaughii. The rapid turnover of repeats in the Leptostachyus group may be associated with the several rearrangements observed.

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.

Aneuploidy is defined as the cellular state of having a number of chromosomes that deviates from a multiple of the normal haploid chromosome number of a given organism. Aneuploidy can be present in a static state: Down syndrome individuals stably maintain an extra copy of chromosome 21 in their cells. In cancer cells, however, aneuploidy is usually present in combination with chromosomal instability (CIN) which leads to a continual generation of new chromosomal alterations and the development of intratumour heterogeneity (ITH). The prevalence of cells with specific chromosomal alterations is further shaped by evolutionary selection, for example, during the administration of cancer therapies. Aneuploidy, CIN and ITH have each been individually associated with poor prognosis in cancer, and a wealth of evidence suggests they contribute, either alone or in combination, to cancer therapy resistance by providing a reservoir of potential resistant states, or the ability to rapidly evolve resistance. A full understanding of the contribution and interplay between aneuploidy, CIN and ITH is required to tackle therapy resistance in cancer patients. However, these characteristics often co-occur and are intrinsically linked, presenting a major challenge to defining their individual contributions. Moreover, their accurate measurement in both experimental and clinical settings is a technical hurdle. Here, we attempt to deconstruct the contribution of the individual and combined roles of aneuploidy, CIN and ITH to therapy resistance in cancer, and outline emerging approaches to measure and disentangle their roles as a step towards integrating these principles into cancer therapeutic strategy.

We show that specific inactivation of the protein kinase Cdk1/cyclin B (Cdc28/Clb2) triggers exit from mitosis in the budding yeast Saccharomyces cerevisiae. Cells carrying the allele cdc28-as1, which makes Cdk1 (Cdc28) uniquely sensitive to the ATP analog 1NM-PP1, were arrested with spindle poisons and then treated with 1NM-PP1 to inhibit Cdk1. This caused the cells to leave mitosis and enter G1-phase as shown by initiation of rebudding (without cytokinesis), induction of mating projections ("shmoos") by α-factor, stabilization of Sic1, and degradation of Clb2. It is known that Cdk1 must be inactivated for cells to exit mitosis, but our results show that inactivation of Cdk1 is not only necessary but also sufficient to initiate the transition from mitosis to G1-phase. This result suggests a system in which to test requirements for particular gene products downstream from Cdk1 inactivation, for example, by combining cdc28-as1 with conditional mutations in the genes of interest. Using this approach, we demonstrate that protein phosphatase 1 (PPase1; Glc7 in S. cerevisiae) is required for mitotic exit and reestablishment of interphase following Cdk1 inactivation. This system could be used to test the need for other protein phosphatases downstream from Cdk1 inactivation, such as PPase 2A and Cdc14, and it could be combined with phosphoproteomics to gain information about the substrates that the various phosphatases act upon during mitotic exit.