Chromosome Research最新文献

In the 40 years since the discovery of the CENP proteins, many studies have examined the role of these proteins and their interactions with other chromosomal proteins of the centromere and beyond. Together, these studies have yielded vast amounts of sequencing and proteomics data. Typically, each study has focused on a single question and the majority of each dataset remains largely unexplored. Often the interesting details of publicly deposited data are left behind, buried in archives online, while more and more new data are generated. Reanalysing these databases can represent a new paradigm for investigating diverse biological pathways in unprecedented detail. Here, we explore two publicly available pan-cancer proteomic datasets to compare proteins whose abundance correlates with CENP proteins, with a particular focus on CENP-C. Our analysis confirms an expected link between CENP-C and cohesin levels but reveals a surprising and unexpected correlation between CENP-C and proteins of the inner nuclear membrane and the NuMA protein. This guilt-by-association analysis has the potential to identify proteins that act in common pathways but never associate or colocalize and may not even be expressed at the same time in cells. As an example, we show here that it can reveal unexpected links that expand our conception of centromeric chromatin beyond chromosome segregation.

B chromosomes are nonessential chromosomes and are considered genetically inert. However, the maize B chromosome possesses several genetic properties during male gamete development in anthers. To determine whether the transcriptome of maize anthers is influenced by the B chromosome, we established the correlation between anther length and developmental stage in the maize B73 inbred line and applied complementary DNA-amplified fragment length polymorphism (cDNA-AFLP) analysis to microsporogenetic (MS) anthers, microgametogenetic (MG) anthers and mature pollen (MP) of B73 plants carrying zero (0B) and two B chromosomes (2B). The results revealed that 6.4%, 7.4% and 25.1% of 0B-extra or 2B-extra cDNA-AFLP fragments from MS anthers, MG anthers and MP, respectively, are present between B73 + 0B and B73 + 2B. Twelve out of the 13 2B-extra cDNA-AFLP fragments from MS anthers and MP are A chromosome-located sequences and are transcribed in the presence of the B chromosome. Some of these sequences are functional genes. The remaining 2B-extra cDNA-AFLP fragment isolated from MS anthers is a novel B chromosome-specific repeat, pMS4. On the basis of three B-10L translocations and fluorescence in situ hybridization, pMS4 was mapped to the short arm and the junction between the centromeric knob and the proximal euchromatin of the B chromosome. Reverse transcriptase PCR revealed that pMS4 is transcribed in a B chromosome dosage-dependent and tissue-specific manner. Taken together, our data suggest that the maize B chromosome can transcribe and influence the transcription of A chromosome-located genes in anthers at different developmental stages.

Crepis sensu lato (s.l.) comprises species with remarkable variation in genome size, chromosome number, and karyotype structure, making this genus a valuable model for studying genome and chromosome evolution. Studies in various plant systems have suggested that diversification and speciation may be accompanied by dynamic changes in the repetitive DNA fraction, including satellite DNAs (satDNAs). A complex approach consisting of molecular (cloning, dot-blot and Southern hybridisation), cytogenetic (fluorescent in situ hybridisation) and phylogenetic methods allowed assessing the chromosomal and genomic organisation of three satDNAs in 32 species from Crepis s.l.. In the present study, we posed a question of whether these satDNAs are specific to C. capillaris, supporting the "birth-and-death" hypothesis, or whether they are also present in related species, consistent with the "library hypothesis". Each satDNA family exhibited different evolutionary trajectories. While pCcE9 amplification was specific to C. capillaris, supporting the "birth-and-death" hypothesis, two other analysed satDNAs were present in several related species, consistent with the "library hypothesis". Notably, pCcD29 showed different genomic and chromosomal organisation among C. capillaris and the species from the C. vesicaria group, suggesting that the satDNA evolution model proposed by Ruiz-Ruano et al. for animal systems may also apply to Crepis species. The organisation of the pCcD29 family ranges from numerous small, poorly homogenised loci (C. polymorpha) through organisation in both shorter and longer arrays (C. taraxacifolia) to a few major, highly homogenised loci (C. capillaris), highlighting contrasting evolutionary pathways of satDNAs within closely related species.

The phenotypic similarities and genetic heterogeneity occurring in diverse forms of Ehlers Danlos Syndrome (EDS) subtypes and many heritable connective tissue disorders can pose a diagnostic challenge. In the wake of the growing applications of next-generation sequencing technologies including exome and genome sequencing, opportunities for achieving definitive genetic diagnosis are increasingly arising. We present a 46-year-old man with joint laxity, recurrent joint subluxations, pelvic floor dysfunction, and postural orthostatic tachycardia syndrome (POTS), who was referred for EDS assessment. His medical history included morbid obesity requiring gastric bypass surgery, hearing loss, asthma, retinopathy, myopia, atrial septal defect, narcolepsy with cataplexy, polyneuropathy, folliculitis, lichen simplex chronicus, atopic dermatitis, and hypogonadism. His family history was significant for multiple first- and second-degree relatives who died from cardiac diseases including cases of childhood deaths. Physical examination showed joint laxity with Beighton score of 3/9, bilateral pes planus, hearing loss and macrocephaly. Exome sequencing revealed heterozygous variants LMNA c.1262 T > C p.L421P [classified as likely pathogenic], FLG c.2282_2285del p. S761Cfs*36 [classified as pathogenic], and FLG c.1501 C > T p. R501* [classified as pathogenic]. Mitochondria sequencing revealed a variant of uncertain significance (VUS), MT-ND2 m.5047 T > C p.V193A that is present at 9% heteroplasmy in blood. These findings show co-occurrence of pathogenic sequence variants in neighboring genes located in chromosome 1q2 region [LMNA and FLG] in a patient with features of hereditary connective tissue disorders. Our study highlights the capability of exome sequencing in achieving some actionable diagnosis in cases of co-morbid genetic disorders with overlapping and non-specific symptoms.

Centromeres have been the focus of extensive research for almost a century, so it may come as a surprise that a consistent definition and nomenclature for these structures remains elusive. In recent times, centromeric chromatin is most frequently defined by the presence of nucleosomes containing the H3 variant CENP-A and is typically synonymous with the site of the inner-kinetochore. However, crucial mammalian centromere proteins including CENP-B and INCENP have well defined distributions that show very little overlap with CENP-A. Additional protein localisations spanning the primary constriction or forming a band below CENP-A chromatin have been reported. Together, these observations suggest a complex and multi-layered chromatin organisation that is not well served by the canonical dichotomy of 'centromeric' and 'pericentromeric' chromatin. Strikingly, this is not a new observation but was made soon after the discovery of CENP proteins, including in a 1991 publication titled 'When is the centromere not a kinetochore?'. Here we revisit this question, which has become more pertinent following technical innovations in long-read sequencing and super-resolution microscopy. We present a model of centromere organisation for monocentromeres that incorporates additional complexity. We then use this model to reconceptualise diverse centromere forms in other eukaryotes including regional centromeres, holocentromeres and centromeres that lack key proteins including CENP-A. In this way, we hope to move towards a unified understanding of centromeric chromatin.

Centromeres are fundamental chromosomal structures that ensure accurate chromosome segregation during cell division. Despite their conserved and essential role in maintaining genomic stability, centromeres are subject to rapid evolutionary change. At the heart of centromere identity is the histone H3 variant CENP-A, an epigenetic mark that defines and propagates active centromeres and is essential for their function. Recent evidence supports a rapid evolution of centromere DNA sequences but also suggests a certain degree of flexibility in CENP-A deposition and propagation. The phenomenon of centromere drift, recently observed in humans, highlights how the dynamic repositioning of CENP-A and associated epigenetic environment over time maintains a regulated equilibrium, ensuring centromere function despite positional variation. Understanding these processes is crucial for unraveling centromere dynamics and their broader implications for genome stability and evolution.

Four decades ago, the discovery of centromere protein-A (CENP-A) marked a pivotal breakthrough in chromosome biology, revealing the epigenetic foundation of centromere identity. CENP-A, a histone H3 variant, directs the formation of the microtubule-binding kinetochore complex, designating the chromosomal site for its assembly and underpins the accurate partitioning of genetic material during cell division. Errors in cell division can give rise to DNA instability and aneuploidy, implicated in human diseases such as cancer. Therefore, discovering the underlying pathways and mechanisms responsible for the formation, regulation and maintenance of the centromere is important to our understanding of genome stability, epigenetic inheritance, and in providing the knowledge to help generate possible treatments and therapeutics. Here, we review various molecular pathways and mechanisms implicated in maintaining centromere identity and highlight some of the key outstanding questions with a focus on the human centromere.

During spermatogenesis, chromatin structure is remodelled by the incorporation of distinct histone variants and associated posttranslational modifications, followed by the almost complete replacement of histones by protamines in sperm. However, the dynamics of the centromere-specific histone H3 variant CENP-A have not yet been elucidated during spermatogenesis in mammals. Here we investigate CENP-A localisation dynamics in cattle (Bos taurus). In bovine testis tissue sections, we quantify CENP-A intensity in key germ cell types; spermatogonia (pre-meiotic), primary spermatocytes (meiotic) and spermatids (post-meiotic). Our quantitation shows that spermatogonia harbour the highest amount of CENP-A compared to all other germ cell types. Spermatids have approximately one quarter the amount of CENP-A of spermatogonia indicating that overall, it is reduced and maintained through the two meiotic divisions. Yet, we also observed some unexpected dynamics. CENP-A is asymmetrically distributed such that undifferentiated spermatogonia harbour more CENP-A that differentiated spermatogonia that enter meiosis. We also noted an increase in CENP-A intensity in primary spermatocytes during meiotic prophase I, which is indicative of centromere assembly at this time. We also confirm the specific maintenance of CENP-A, and the absence of the centromeric DNA binding protein CENP-B, on mature bull sperm nuclei that have completed histone-to-protamine exchange. Finally, we present a model for centromere positioning in mature sperm nuclei and propose that centralised clustering of centromeres may serve a protective function during histone-to-protamine exchange.

The centromere is a region present on every human chromosome that is essential for mediating chromosome segregation and maintaining genome stability. However, despite its fundamental role in the process of cell division, the centromere is constantly subjected to a wide range of stresses that can challenge their integrity, causing breakages and aneuploidy. In this review, we will examine the plethora of stresses that challenge the centromere, its stress response and how cells cope with perturbations originating from the intracellular and extracellular microenvironment in order to preserve centromere function and, overall, cellular fitness.

Faithful chromosome segregation is facilitated by the centromeres, specialized genomic loci, which connect chromosomes to microtubules in every cell cycle by recruiting the kinetochore complex. However, a single conserved code does not govern the formation and maintenance of centromeres, as we begin to realize that enormous diversity exists in molecular mechanisms dictating centromere homeostasis across species. The fungal kingdom is a vast resource to study and appreciate the divergent nature of the conserved phenomenon of chromosome segregation. Studies in the fungal kingdom enable researchers to view the evolution of centromeres at the molecular level. While some organisms, such as Saccharomyces cerevisiae, rely on a strict genetically determined centromere establishment, most fungi adopt epigenetically driven mechanisms of centromere propagation. This epigenomic regulation ranges from modifications on the underlying DNA to histones forming the centric and pericentric regions. The centromere DNA sequence, arrangement of sequence elements, its transcription state, and the replication timing, as well as its spatial position in the nucleus, play a major role in determining centromere stability and its function. In this review, we aim to highlight the spectrum of centromere regulatory mechanisms observed in fungi and discuss the gaps in the research that can provide new perspectives on centromere biology.