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IEEE/ACM Transactions on Computational... Jun 2024Much evidence from biological theory and empirical data indicates that, gene trees, phylogenetic trees reconstructed from different genes (loci), do not have to have...
Much evidence from biological theory and empirical data indicates that, gene trees, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees might be caused by some "unusual" evolutionary events, such as meiotic sexual recombination in eukaryotes or horizontal transfers of genetic material in prokaryotes. However, most of the gene trees are constrained by the tree topology of the underlying species tree, that is, the phylogenetic tree depicting the evolutionary history of the set of species under consideration. In order to discover "outlying" gene trees which do not follow the "main distribution(s)" of trees, we propose to apply the "tropical metric" with the max-plus algebra from tropical geometry to a non-parametric estimation of gene trees over the space of phylogenetic trees. In this research we apply the "tropical metric," a well-defined metric over the space of phylogenetic trees under the max-plus algebra, to non-parametric estimation of gene trees distribution over the tree space. Kernel density estimator (KDE) is one of the most popular non-parametric estimation of a distribution from a given sample, and we propose an analogue of the classical KDE in the setting of tropical geometry with the tropical metric which measures the length of an intrinsic geodesic between trees over the tree space. We estimate the probability of an observed tree by empirical frequencies of nearby trees, with the level of influence determined by the tropical metric. Then, with simulated data generated from the multispecies coalescent model, we show that the non-parametric estimation of the gene tree distribution using the tropical metric performs better than one using the Billera-Holmes-Vogtmann (BHV) metric developed by Weyenberg et al. in terms of computational times and accuracy. We then apply it to Apicomplexa data.
PubMed: 38941208
DOI: 10.1109/TCBB.2024.3420815 -
Genes To Cells : Devoted To Molecular &... Jun 2024Interhomolog recombination in meiosis is mediated by the Dmc1 recombinase. The Mei5-Sae3 complex of Saccharomyces cerevisiae promotes Dmc1 assembly and functions with...
Interhomolog recombination in meiosis is mediated by the Dmc1 recombinase. The Mei5-Sae3 complex of Saccharomyces cerevisiae promotes Dmc1 assembly and functions with Dmc1 for homology-mediated repair of meiotic DNA double-strand breaks. How Mei5-Sae3 facilitates Dmc1 assembly remains poorly understood. In this study, we created and characterized several mei5 mutants featuring the amino acid substitutions of basic residues. We found that Arg97 of Mei5, conserved in its ortholog, SFR1 (complex with SWI5), RAD51 mediator, in humans and other organisms, is critical for complex formation with Sae3 for Dmc1 assembly. Moreover, the substitution of either Arg117 or Lys133 with Ala in Mei5 resulted in the production of a C-terminal truncated Mei5 protein during yeast meiosis. Notably, the shorter Mei5-R117A protein was observed in meiotic cells but not in mitotic cells when expressed, suggesting a unique regulation of Dmc1-mediated recombination by posttranslational processing of Mei5-Sae3.
PubMed: 38924305
DOI: 10.1111/gtc.13138 -
BioRxiv : the Preprint Server For... Mar 2024When germ cells transition from the mitotic cycle into meiotic prophase I (MPI), chromosomes condense into an array of chromatin loops that are required to promote...
When germ cells transition from the mitotic cycle into meiotic prophase I (MPI), chromosomes condense into an array of chromatin loops that are required to promote homolog pairing and genetic recombination. To identify the changes in chromosomal conformation, we isolated nuclei on a trajectory from spermatogonia to the end of MPI. At each stage along this trajectory, we built genomic interaction maps with the highest temporal and spatial resolution to date. The changes in chromatin folding coincided with a concurrent decline in mitotic cohesion and a rise in meiotic cohesin complexes. We found that the stereotypical large-scale A and B compartmentalization was lost during meiotic prophase I alongside the loss of topological associating domains (TADs). Still, local subcompartments were detected and maintained throughout meiosis. The enhanced Micro-C resolution revealed that, despite the loss of TADs, higher frequency contact sites between two loci were detectable during meiotic prophase I coinciding with CTCF bound sites. The pattern of interactions around these CTCF sites with their neighboring loci showed that CTCF sites were often anchoring the meiotic loops. Additionally, the localization of CTCF to the meiotic axes indicated that these anchors were at the base of loops. Strikingly, even in the face of the dramatic reconfiguration of interphase chromatin into a condensed loop-array, the interactions between regulatory elements remained well preserved. This establishes a potential mechanism for how the meiotic chromatin maintains active transcription within a highly structured genome. In summary, the high temporal and spatial resolution of these data revealed previously unappreciated aspects of mammalian meiotic chromatin organization.
PubMed: 38903112
DOI: 10.1101/2024.03.25.586627 -
Current Medical Science Jun 2024Abnormal expression of T-lymphokine-activated killer cell-originated protein kinase (TOPK) was reported to be closely related to the resistance of prostate cancer to...
OBJECTIVE
Abnormal expression of T-lymphokine-activated killer cell-originated protein kinase (TOPK) was reported to be closely related to the resistance of prostate cancer to radiotherapy and to targeted drug resistance in lung cancer. However, the role of TOPK inhibition in enhancing radiosensitivity of colorectal cancer (CRC) cells is unclear. This study aimed to evaluate the radiosensitization of TOPK knockdown in CRC cells.
METHODS
The expression of TOPK was detected in CRC tissues by immunohistochemistry, and the effect of TOPK knockdown was detected in CRC cells by Western blotting. CCK-8 and clonogenic assays were used to detect the growth and clonogenic ability of CRC cells after TOPK knockdown combined with radiotherapy in CRC cells. Furthermore, proteomic analysis showed that the phosphorylation of TOPK downstream proteins changed after radiotherapy. DNA damage was detected by the comet assay. Changes in the DNA damage response signaling pathway were analyzed by Western blotting, and apoptosis was detected by flow cytometry.
RESULTS
The expression of TOPK was significantly greater in CRC tissues at grades 2-4 than in those at grade 1. After irradiation, CRC cells with genetically silenced TOPK had shorter comet tails and reduced expression levels of DNA damage response-associated proteins, including phospho-cyclin-dependent kinase 1 (p-CDK1), phospho-ataxia telangiectasia-mutated (p-ATM), poly ADP-ribose polymerase (PARP), and meiotic recombination 11 homolog 1 (MRE11).
CONCLUSIONS
TOPK was overexpressed in patients with moderately to poorly differentiated CRC. Moreover, TOPK knockdown significantly enhanced the radiosensitivity of CRC cells by reducing the DNA damage response.
Topics: Humans; Colorectal Neoplasms; DNA Damage; Radiation Tolerance; Cell Line, Tumor; Apoptosis; Male; Gene Knockdown Techniques; Middle Aged; Gene Expression Regulation, Neoplastic; Signal Transduction; Female; Phosphorylation; Mitogen-Activated Protein Kinase Kinases
PubMed: 38900386
DOI: 10.1007/s11596-024-2884-0 -
Experimental Cell Research Jul 2024Mouse HORMAD1 is a phospho-protein involved in multiple functions during meiotic prophase I. To obtain insight into the significance of its phosphorylation, we generated...
Mouse HORMAD1 is a phospho-protein involved in multiple functions during meiotic prophase I. To obtain insight into the significance of its phosphorylation, we generated phospho-specific antibodies against two serine residues, Ser307 and Ser378, representing each of two serine clusters in mouse HORMAD1. The Ser307 phosphorylation is detectable from early leptotene substage in both wild-type and Spo11 spermatocytes, indicating that Ser307 is a primary and SPO11-independent phosphorylation site. In contrast, the Ser378 phosphorylation is negligible at earlier substages in wild-type and Spo11 spermatocytes. After mid-zygotene substage, the Ser378 phosphorylation is abundant on unsynapsed chromosome axes in wild-type spermatocytes and is detected only in a part of unsynapsed chromosome axes in Spo11 spermatocytes. We also generated a non-phosphorylated Ser307-specific antibody and found that Ser307 is phosphorylated on sex chromosome axes but is almost entirely unphosphorylated on desynapsed chromosome axes in diplotene spermatocytes. These results demonstrated a substage-specific phosphorylation status of mouse HORMAD1, which might be associated with multiple substage-specific functions.
Topics: Animals; Meiotic Prophase I; Phosphorylation; Male; Mice; Serine; Spermatocytes; Endodeoxyribonucleases; Mice, Inbred C57BL; Cell Cycle Proteins; Mice, Knockout; Sex Chromosomes
PubMed: 38897409
DOI: 10.1016/j.yexcr.2024.114133 -
Cell Proliferation Jun 2024In the meiotic prophase, programmed SPO11-linked DNA double-strand breaks (DSBs) are repaired by homologous recombination (HR). The MRE11-RAD50-NBS1 (MRN) complex is...
In the meiotic prophase, programmed SPO11-linked DNA double-strand breaks (DSBs) are repaired by homologous recombination (HR). The MRE11-RAD50-NBS1 (MRN) complex is essential for initiating DNA end resection, the first step of HR. However, residual DNA end resection still occurs in Nbs1 knockout (KO) spermatocytes for unknown reasons. Here, we show that DNA end resection is completely abolished in Mre11 KO spermatocytes. In addition, Mre11 KO, but not Nbs1 KO, undifferentiated spermatogonia are rapidly exhausted due to DSB accumulation, proliferation defects, and elevated apoptosis. Cellular studies reveal that a small amount of MRE11 retained in the nucleus of Nbs1 KO cells likely underlies the differences between Mre11 and Nbs1 KO cells. Taken together, our study not only demonstrates an irreplaceable role of the MRE11 in DNA end resection at SPO11-linked DSBs but also unveils a unique function of MRE11 in maintaining the long-term viability of undifferentiated spermatogonia.
PubMed: 38894566
DOI: 10.1111/cpr.13685 -
PLoS Genetics Jun 2024Very little is known about the process of meiosis in the apicomplexan parasite Cryptosporidium despite the essentiality of sex in its life cycle. Most cell lines only...
Very little is known about the process of meiosis in the apicomplexan parasite Cryptosporidium despite the essentiality of sex in its life cycle. Most cell lines only support asexual growth of Cryptosporidium parvum (C. parvum), but stem cell derived intestinal epithelial cells grown under air-liquid interface (ALI) conditions support the sexual cycle. To examine chromosomal dynamics during meiosis in C. parvum, we generated two transgenic lines of parasites that were fluorescently tagged with mCherry or GFP on chromosomes 1 or 5, respectively. Infection of ALI cultures or Ifngr1-/- mice with mCherry and GFP parasites resulted in cross-fertilization and the formation of "yellow" oocysts, which contain 4 haploid sporozoites that are the product of meiosis. Recombinant oocysts from the F1 generation were purified and used to infect HCT-8 cultures, and phenotypes of the progeny were observed by microscopy. All possible phenotypes predicted by independent segregation were represented equally (~25%) in the population, indicating that C. parvum chromosomes exhibit a Mendelian inheritance pattern. The most common pattern observed from the outgrowth of single oocysts included all possible parental and recombinant phenotypes derived from a single meiotic event, suggesting a high rate of crossover. To estimate the frequency of crossover, additional loci on chromosomes 1 and 5 were tagged and used to monitor intrachromosomal crosses in Ifngr1-/- mice. Both chromosomes showed a high frequency of crossover compared to other apicomplexans with map distances (i.e., 1% recombination) of 3-12 kb. Overall, a high recombination rate may explain many unique characteristics observed in Cryptosporidium spp. such as high rates of speciation, wide variation in host range, and rapid evolution of host-specific virulence factors.
Topics: Animals; Cryptosporidium parvum; Mice; Oocysts; Recombination, Genetic; Cryptosporidiosis; Meiosis; Humans; Receptors, Interferon; Interferon gamma Receptor; Chromosome Segregation; Sporozoites; Mice, Knockout; Phenotype
PubMed: 38885280
DOI: 10.1371/journal.pgen.1011162 -
Genetics Jun 202453BP1 plays a crucial role in regulating DNA damage repair pathway choice and checkpoint signaling in somatic cells; however, its role in meiosis has remained enigmatic....
53BP1 plays a crucial role in regulating DNA damage repair pathway choice and checkpoint signaling in somatic cells; however, its role in meiosis has remained enigmatic. In this study, we demonstrate that the Caenorhabditis elegans ortholog of 53BP1, HSR-9, associates with chromatin in both proliferating and meiotic germ cells. Notably, HSR-9 is enriched on the X chromosome pair in pachytene oogenic germ cells. HSR-9 is also present at kinetochores during both mitotic and meiotic divisions but does not appear to be essential for monitoring microtubule-kinetochore attachments or tension. Using cytological markers of different steps in recombinational repair, we found that HSR-9 influences the processing of a subset of meiotic double strand breaks into COSA-1-marked crossovers. Additionally, HSR-9 plays a role in meiotic X chromosome segregation under conditions where X chromosomes fail to pair, synapse, and recombine. Together, these results highlight that chromatin-associated HSR-9 has both conserved and unique functions in the regulation of meiotic chromosome behavior.
PubMed: 38884610
DOI: 10.1093/genetics/iyae102 -
DNA Repair Jun 2024FANCM is a multifunctional DNA repair enzyme that acts as a sensor and coordinator of replication stress responses, especially interstrand crosslink (ICL) repair... (Review)
Review
FANCM is a multifunctional DNA repair enzyme that acts as a sensor and coordinator of replication stress responses, especially interstrand crosslink (ICL) repair mediated by the Fanconi anaemia (FA) pathway. Its specialised ability to bind and remodel branched DNA structures enables diverse genome maintenance activities. Through ATP-powered "branchpoint translocation", FANCM can promote fork reversal, facilitate replication traverse of ICLs, resolve deleterious R-loop structures, and restrain recombination. These remodelling functions also support a role as sensor of perturbed replication, eliciting checkpoint signalling and recruitment of downstream repair factors like the Fanconi anaemia FANCI:FANCD2 complex. Accordingly, FANCM deficiency causes chromosome fragility and cancer susceptibility. Other recent advances link FANCM to roles in gene editing efficiency and meiotic recombination, along with emerging synthetic lethal relationships, and targeting opportunities in ALT-positive cancers. Here we review key properties of FANCM's biochemical activities, with a particular focus on branchpoint translocation as a distinguishing characteristic.
PubMed: 38878565
DOI: 10.1016/j.dnarep.2024.103701 -
Journal of Molecular Biology Jun 2024Meiotic recombination plays a pivotal role in genetic evolution. Genetic variation induced by recombination is a crucial factor in generating biodiversity and a driving...
Meiotic recombination plays a pivotal role in genetic evolution. Genetic variation induced by recombination is a crucial factor in generating biodiversity and a driving force for evolution. At present, the development of recombination hotspot prediction methods has encountered challenges related to insufficient feature extraction and limited generalization capabilities. This paper focused on the research of recombination hotspot prediction methods. We explored deep learning-based recombination hotspot prediction and scrutinized the shortcomings of prevalent models in addressing the challenge of recombination hotspot prediction. To addressing these deficiencies, an automated machine learning approach was utilized to construct recombination hotspot prediction model. The model combined sequence information with physicochemical properties by employing TF-IDF-Kmer and DNA composition components to acquire more effective feature data. Experimental results validate the effectiveness of the feature extraction method and automated machine learning technology used in this study. The final model was validated on three distinct datasets and yielded accuracy rates of 97.14%, 79.71%, and 98.73%, surpassing the current leading models by 2%, 2.56%, and 4%, respectively. In addition, we incorporated tools such as SHAP and AutoGluon to analyze the interpretability of black-box models, delved into the impact of individual features on the results, and investigated the reasons behind misclassification of samples. Finally, an application of recombination hotspot prediction was established to facilitate easy access to necessary information and tools for researchers. The research outcomes of this paper underscore the enormous potential of automated machine learning methods in gene sequence prediction.
PubMed: 38871176
DOI: 10.1016/j.jmb.2024.168653