Modeling Cell Biological Features of Meiotic Chromosome Pairing

During meiosis, homologous chromosomes become associated side by side in a process known as homologous chromosome pairing. Pairing requires long range chromosome motion through a nucleus that is full of other chromosomes. It remains unclear how the cell manages to align each pair of chromosomes quickly while mitigating and resolving interlocks. Here, we use a coarse-grained molecular dynamics model to investigate how specific features of meiosis, including motor-driven telomere motion, nuclear envelope interactions, and increased nuclear size, affect the rate of pairing and the mitigation/resolution of interlocks. By creating in silico versions of three yeast strains and comparing the results of our model to experimental data, we find that a more distributed placement of pairing sites along the chromosome is necessary to replicate experimental findings. Active motion of the telomeric ends speeds up pairing only if binding sites are spread along the chromosome length. Adding a meiotic bouquet significantly speeds up pairing but does not significantly change the number of interlocks. An increase in nuclear size slows down pairing while greatly reducing the number of interlocks. Interestingly, active forces increase the number of interlocks, which raises the question: How do these interlocks resolve? Our model gives us detailed movies of interlock resolution events which we then analyze to build a step-by-step recipe for interlock resolution. In our model, interlocks must first translocate to the ends, where they are held in a quasi-stable state by a large number of paired sites on one side. To completely resolve an interlock, the telomeres of the involved chromosomes must come in close proximity so that the cooperativity of pairing coupled with random motion causes the telomeres to unwind. Together our results indicate that computational modeling of homolog pairing provides insight into the specific cell biological changes that occur during meiosis.

Ploidy Level, Karyotype, and Genome Size of Bletilla Species (Orchidaceae) From China

Bletilla is an Orchidaceae genus with high medical value, including detumescence, antibacterial, and hemostasis. In this study, detailed estimates of ploidy level, karyotype, and genome size were first obtained, and a comprehensive cytological analysis was carried out to better understand the evolution of the genus. The karyotypes of Bletilla were mainly composed of metacentric and submetacentric chromosomes with lengths ranging from 1.25 to 4.93 μm. There was moderate cytological variation in Bletilla (chromosome number 2n = 32 to 76). Diploid with 2n = 34 and 2n = 36 was detected in Bletilla ochracea and Bletilla formosana, respectively, whereas diploid (2n = 32) was dominant in Bletilla striata, dysploidy (2n = 34, 2n = 36) and polyploid (2n = 48, 51, 64, 76) variations were also observed. Three species had a relatively symmetric karyotype, and which of B. ochracea was more asymmetry. The genome size (1C-values) varied from 2.94 pg (B. striata) to 3.33 pg (B. ochracea), of which B. ochracea was significantly larger than the others (P < 0.05). A positive correlation (P < 0.01) between 1Cx vs. haploid chromosome length (HCL) and asymmetry coefficient of karyotypes (AsK%) was observed.

Karyotype and genome size variation in white-flowered Eranthis sect. Shibateranthis (Ranunculaceae)

Comparative karyomorphological analyses of six out of the eight white-flowered species of Eranthis sect. Shibateranthis have been carried out. All studied specimens of E. byunsanensis, E. lobulata, E. pinnatifida, and E. stellata had a somatic chromosome number 2n = 16 with basic chromosome number x = 8. On the contrary, E. tanhoensis and E. sibirica had a basic chromosome number x = 7. The specimens of E. tanhoensis were diploid with 2n = 14, while the specimens of E. sibirica were polyploid with 2n = 42. Monoploid chromosome sets of the investigated diploid species had 4–5 metacentric chromosomes and 2–4 submetacentric/subtelocentric/acrocentric chromosomes. The highest level of interchromosomal asymmetry, estimated via CVCL, was found in E. byunsanensis and E. pinnatifida. The highest levels of intrachromosomal asymmetry (MCA) and heterogeneity in centromere position (CVCI) were found in E. lobulata and E. byunsanensis, while E. sibirica had the most symmetric karyotype. A multivariate PCoA analysis of basic karyotype parameters (2n, x, THL, CVCL, MCA, and CVCI) highlighted no overlap among species accessions, which was also confirmed by LDA. The average absolute monoploid DNA content (1Cx) of the 23 investigated samples of six Eranthis species varied from 9.26 ± 0.25 pg in E. sibirica to 15.93 ± 0.32 pg in E. stellata. Overall karyological affinity was highlighted between E. lobulata and E. stellata, on one side, and between E. byunsanensis and E. pinnatifida, on the other side. Interestingly, there was no significant correlation between total haploid (monoploid) chromosome length (THL) and 1Cx values in these species.

TOP-2 is differentially required for the proper maintenance of cohesin on meiotic chromosomes in C. elegans spermatogenesis and oogenesis

During meiotic prophase I, accurate segregation of homologous chromosomes requires the establishment of a chromosomes with a meiosis-specific architecture. Sister chromatid cohesins and the enzyme Topoisomerase II are important components of meiotic chromosome axes, but the relationship of these proteins in the context of meiotic chromosome segregation is poorly defined. Here, we analyzed the role of Topoisomerase II (TOP-2) in the timely release of sister chromatid cohesins during spermatogenesis and oogenesis of Caenorhabditis elegans. We show that there is a different requirement for TOP-2 in meiosis of spermatogenesis and oogenesis. The loss-of-function mutation top-2(it7) results in premature REC-8 removal in spermatogenesis, but not oogenesis. This is due to a failure to maintain the HORMA-domain proteins HTP-1 and HTP-2 (HTP-1/2) on chromosome axes at diakinesis and mislocalization of the downstream components that control sister chromatid cohesion release including Aurora B kinase. In oogenesis, top-2(it7) causes a delay in the localization of Aurora B to oocyte chromosomes but can be rescued through premature activation of the maturation promoting factor via knock-down of the inhibitor kinase WEE-1.3. The delay in Aurora B localization is associated with an increase in the length of diakinesis chromosomes and wee-1.3 RNAi mediated rescue of Auorora B localization in top-2(it7) is associated with a decrease in chromosome length. Our results imply that the sex-specific effects of Topoisomerase II on sister chromatid cohesion release are due to differences in the temporal regulation of meiosis and chromosome structure in late prophase I in spermatogenesis and oogenesis.

A Karyological Study of Tenualosa Ilisha (Hamilton, 1822) From the Confluence of Padma and Meghna River of Bangladesh

Tenualosa ilisha (Hamilton, 1822), commonly known as Hilsha shad is a valuable and highly acceptable species in terms of their high flavored properties. Hilsha shad has striking morpho-genetical adaptation to heterogeneous habitats across their migratory routes. Cytogenetic analysis demonstrates the changes in chromosomes. But none was focused on the cytogenetic analysis of T. ilisha in Bangladesh. T. ilisha was found to possess 2n = 42 number of chromosomes along with a karyotype formula: 1M + 31m + 8sm + 2st using giemsa staining technique. The results demonstrated ‘diffuse type of interphase nuclei, co-existence of continuous type and interstitial type of prophase chromosomes respectively. No heteromorphic sex chromosomes were determined cytologically. The presence of diverse types of chromosomes based on centromeric position, gradual decrease in total haploid chromosome complement, mean centromeric asymmetry, coefficient of variation of chromosome length and Stebbins’s classification highlighted its asymmetry in karyotype with advance nature. Therefore, the elemental karyological data will offer information for the proper identification, cytotaxonomical classification, expanding productivity and preservation of genetic resources ofT. ilisha. Bangladesh J. Zool. 49 (2): 243-255, 2021

Chromosome length and gene density contribute to micronuclear membrane stability

Micronuclei are derived from missegregated chromosomes and frequently lose membrane integrity, leading to DNA damage, innate immune activation, and metastatic signaling. Here, we demonstrate that two characteristics of the trapped chromosome, length and gene density, are key contributors to micronuclei membrane stability and determine the timing of micronucleus rupture. We demonstrate that these results are not due to chromosome-specific differences in spindle position or initial protein recruitment during post-mitotic nuclear envelope assembly. Micronucleus size strongly correlates with lamin B1 levels and nuclear pore density in intact micronuclei, but, unexpectedly, lamin B1 levels do not completely predict nuclear lamina organization or membrane stability. Instead, small gene-dense micronuclei have decreased nuclear lamina gaps compared to large micronuclei, despite very low levels of lamin B1. Our data strongly suggest that nuclear envelope composition defects previously correlated with membrane rupture only partly explain membrane stability in micronuclei. We propose that an unknown factor linked to gene density has a separate function that inhibits the appearance of nuclear lamina gaps and delays membrane rupture until late in the cell cycle.

State of Shark and Ray Genomics in an Era of Extinction

Chondrichthyan species (sharks, rays, skates, and chimeras) are a class of high ecological, economic, and cultural significance, and yet they are the most threatened taxa in the marine environment. The creation of reference chromosome-length genome assemblies allows for conservation genomics methods, such as population and ecological genomics, to be utilized. Despite being greatly threatened and of great importance in maintaining ecosystem function, chondrichthyan species have been repeatedly absent from conservation-based genome sequencing projects. Less than 1% of these species have a genome sequence, despite their almost 50% either threatened or Data Deficient conservation status. Most notably, there are seven orders within this class without any genome representation. In this review, we identify gaps in chondrichthyan genomic resources and demonstrate how the lack of genomic resources for this major taxonomic class is limiting the conservation of these already difficult to conserve species. We highlight other applications for chondrichthyans genomics, such as evolutionary and developmental biology. Likely, the mismatching sampling protocols and limited computational skills and communication between fields have been preventing the integration of marine and molecular sciences. Here, we propose that this field is in dire need to move forward quickly to increase protection for marine species and ecosystems through improved collaboration between marine, molecular, and computer sciences.

Disruption of Chromatin Dynamics by Hypotonic Stress Suppresses HR and Shifts DSB Processing to Error-Prone SSA

The processing of DNA double-strand breaks (DSBs) depends on the dynamic characteristics of chromatin. To investigate how abrupt changes in chromatin compaction alter these dynamics and affect DSB processing and repair, we exposed irradiated cells to hypotonic stress (HypoS). Densitometric and chromosome-length analyses show that HypoS transiently decompacts chromatin without inducing histone modifications known from regulated local chromatin decondensation, or changes in Micrococcal Nuclease (MNase) sensitivity. HypoS leaves undisturbed initial stages of DNA-damage-response (DDR), such as radiation-induced ATM activation and H2AX-phosphorylation. However, detection of ATM-pS1981, γ-H2AX and 53BP1 foci is reduced in a protein, cell cycle phase and cell line dependent manner; likely secondary to chromatin decompaction that disrupts the focal organization of DDR proteins. While HypoS only exerts small effects on classical nonhomologous end-joining (c-NHEJ) and alternative end-joining (alt-EJ), it markedly suppresses homologous recombination (HR) without affecting DNA end-resection at DSBs, and clearly enhances single-strand annealing (SSA). These shifts in pathway engagement are accompanied by decreases in HR-dependent chromatid-break repair in the G2-phase, and by increases in alt-EJ and SSA-dependent chromosomal translocations. Consequently, HypoS sensitizes cells to ionizing radiation (IR)-induced killing. We conclude that HypoS-induced global chromatin decompaction compromises regulated chromatin dynamics and genomic stability by suppressing DSB-processing by HR, and allowing error-prone processing by alt-EJ and SSA.

Stage-resolved Hi-C analyses reveal meiotic chromosome organizational features influencing homolog alignment

During meiosis, chromosomes exhibit dramatic changes in morphology and intranuclear positioning. How these changes influence homolog pairing, alignment, and recombination remain elusive. Using Hi-C, we systematically mapped 3D genome architecture throughout all meiotic prophase substages during mouse spermatogenesis. Our data uncover two major chromosome organizational features varying along the chromosome axis during early meiotic prophase, when homolog alignment occurs. First, transcriptionally active and inactive genomic regions form alternating domains consisting of shorter and longer chromatin loops, respectively. Second, the force-transmitting LINC complex promotes the alignment of ends of different chromosomes over a range of up to 20% of chromosome length. Both features correlate with the pattern of homolog interactions and the distribution of recombination events. Collectively, our data reveal the influences of transcription and force on meiotic chromosome structure and suggest chromosome organization may provide an infrastructure for the modulation of meiotic recombination in higher eukaryotes.