Abstract
Meiosis, an indispensable process in all sexually reproducing species, entails generating haploid gametes by splitting sets of chromosomes during a series of complex steps. The formation and repair of DSBs in chromosomes are the highlights of meiosis that help genetic recombination using adult chromosomes. The primary focus of the Neale lab is determining the mechanisms governing the breakage of double-stranded DNA bulges (DSBs) and repair thereof using the model yeast Saccharomyces cerevisiae (Fusco & Minelli, 2023). This work explores the effects of the changes in 3D structure on double-strand break (DSB) generation and repair, emphasizing the roles of DNA damage signalling pathways.
The main objective of this research is to discover how these pathways of DNA repair signalling, more precisely, the Tel1 kinase and Sae2 endonuclease, function in chromosomal architecture during meiosis. To reach this goal, the study will generate yeast strains with different mutations in critical genes that control DSB formation and repair (Tian et al., 2023). It will hereafter track how the meiosis goes through prophase I and do high-resolution Hi-C mapping to figure out any changes that occurred at the level of chromosome conformation (Vainshelbaum et al., 2022). Consequently, the study will also determine the molecular mechanisms involved in telomere maintenance and repair of DSBs via Tel1 and Sae2 in the chromosomal architecture.
The anticipated product of this research will be more knowledge concerning the mechanism of signalling DNA repair pathways in the formation of chromosome structure during meiosis. The study aims to identify specific alterations in chromosomal organization caused by the impairment of DSB formation and dives into how these proteins block these aberrant forms of chromatin. This may afford new perspectives into signalling systems of DNA repair and how they are related to genome stability and evolution in the broader sense.
In conclusion, this study provides a basis for the emerging knowledge on meiotic chromosome architecture and response to DNA damage. The outcomes could change all branches of biology, ranging from genetics and cells to evolutionary biology. This clarification of the molecular mechanisms of DSB formation and repair could be the source of helpful information on genetic recombination and genome stability, impacting human health and disease.
Introduction
Meiosis is a fundamental process in developing eukaryotes with a sexual reproduction system that creates genetic variability and evolution. As it happens, mitosis results in two identical daughter cells, while meiosis produces haploid gametes with distinct genetic combinations thanks to chromosome segregation and recombination (Svetec Miklenić and Svetec, 2021). Such a combination is pivotal for genetic diversity within the population, the species’ survivability, and adaptability.
Genetic recombination in meiosis is a process in which DSBs are formed and repaired within chromosomes. Embedding the Spo11 endonuclease, which initiates the breaks and is required to exchange genetic material between homologous chromosomes, is essential. Homologous recombination manages the restoration of the breaks, and the consequence of this is crossover, which is the exchange of chromosome segments between homologs. This mechanism allows the genetic data to be rearranged in the offspring, which leads to genetic diversity.
The architecture of meiotic chromosomes is one of the critical components in repairing as well as forming DSBs. During meiosis, chromosomes have a distinctive three-dimensional structure in which attached chromatin loops are arranged around a central proteinaceous axis. This architecture mechanism is essential for the proper orientation and pairing of homologous chromosomes of the proper DSBs repair through homologous recombination. Nonetheless, although the exact mechanisms by which chromosome organization is controlled during meiosis, particularly in response to double-stranded breaks, is still unclear, there is a clear need to research the subject further.
This project is intended to fill the information void and discover how the DNA repair signalling pathways affect the meiotic chromosome organization. In the introduction, we will highlight the role of the Tel1 kinase and Sae2 endonuclease in DSB repair and meiotic chromosome movement. We suggest that these pathways are involved in the function of chromosome restructuring in their response to the formation of the DSB, which leads to an efficient repair and correct separation of the chromosomes in meiosis.
By constructing yeast strains containing mutations in the genes responsible for all DSB formation and repair processes, we will be able to achieve the stated objectives. These aberrant strains will then be traced to the locus of meiotic progression and the changes in chromosome architecture using large-scale Hi-C mapping. The goal is to uncover the molecular mechanisms that control the shape and function of chromosomes during meiosis.
This information will provide valuable insights into genetic recombination and genome stability. It can be further associated with human health and disease and the role of gene recombination in cellular resistance to various disorders (Sanders et al., 2020). Ultimately, this investigation could be a turning point in revealing the details of the foundation of meiotic chromosome structure and genetic crossing-over. The study of DNA repair signalling pathways responsible for its organization into the chromosome structure will complement the knowledge of genome stability preservation mechanisms and phases of evolution.
Objectives
- To create yeast strains with single and multi-redundant mutations in SPO11, REC8, TEL1, and SAE2.
- Measure the progression of meiosis through prophase I of the meiotic sporulation by these genotypes from synchronized time courses.
- Fixing cell populations in particular sub-stages for the high-resolution Hi-C mapping of close-fitting mutations for chromosome DNA changes.
- In the first phase of computing, we have to compare the branch with the domain of increased interactions between mutants between the TCRs and MHC-I, which have interacted more than the wild-type cells.
- Link DSB genome-homeostasis disruption and DDR signalling with the difficulties in the architectural plan.
- Bridge the enzymatic activity of Tel1 and Sae2 with axial factors-driven strand separation.
Hypothesis
The central hypothesis of this experiment is focused on the molecular signalling pathways of DNA repair, such as the Tel1 kinase and Sae2 endonuclease, which are essential in adjusting the meiotic chromosome shape and activity in response to the formation of double-strand breaks (DSBs). The assumption is borrowed from research indicating a close connection between DNA repair signalling pathways and meiotic chromosome dynamics. Earlier studies have proved that cells lacking Tel1 and Sae2 cannot repair DSBs, showing abnormal chromosome structures in yeast. Furthermore, the research indicates that the SMC protein complex, including Rec8, participates in dictating meiotic chromosome organization and promotes DSB mapping.
Based on the comparison of Hi-C analyses of spo11-YF single mutants and also of spo11-YF cells with TEL1 point mutated cells, there is a likelihood that telomeres releasing aberrant protein aggregates that are not related to DSB formation may take place during impaired meiotic prophase in (Lambing et al., 2022). Among the catalytic poison spo11-YF (alone) and the spo11-YF mutant without the tel1 gene, tel1Δ spo11-YF strains manifested a terrific growth in the number of such domains and the mean domain size (Johnson et al., 2021). Such cells secrete superfluous recombination proteins if they hinder inducing DSBs, which is harmful (Kumar Yadav vs. Claeys Bouuaert, 2021). However, it is eventually capped by the activity of the Tel1 protein. It is postulated that, among candidate mechanisms, one of the ways to reduce recombination complex trapping during the pause initiation stage at a part of Spo11-DSBs in wild-type cells could be the disassembly of meiotic recombination complexes trapped in futile relationships.
Recent work found that conserved endonuclease Sae2 initiates Spo11-DSB cleavage, which causes an increased decrease after meiotic DSBs are formed. Based on the overview of Sun et al. (2019), Sae2-sponsored variability in structure possibly brings about the regression in DNA repair complexes’ activity. Then, it promotes more precise homologous search and inter-homologous recombination. The analysis will be based on Hi-C mapping with high-resolution of spo11-YF single mutants when compared with univalent tel1Δ and sae2Δ double mutants to see if Tel1 and Sae2 can prevent the formation of illegitimate recombinase condensation when there are scarce DSB substrates present.
Thus, abolishing these genes should increase abnormalities in the domain expansion if Tel1 and Sae2 limit the number of repair factors that can be isolated during phase separation without the breakage of DSB triggers (Rinaldi et al., 2023). Furthermore, it will produce reversed chromosomes with rec8Δ to ascertain whether the restrictions exerted by Tel1/Sae2 and central structure work together or independently for controlling aggregations in the event of modified DSB landscapes.
This theory is initially based on data showing distorted chromosome architecture in yeast strains with Tel1 and Sae2 mutations, demonstrating that these pathways regulate chromosome organization during meiosis. Moreover, the paths could be linked with other factors, including but not limited to the SMC protein complex, for proper chromosome segregation and DSB repair. In short, the hypothesis is that Tel1 and Sae2 are leading actors in regulating DSB repair and chromosomal architecture during meiosis and unravelling the molecular details involved is highly interesting.
Literature Review
Meiosis plays a crucial role in sexual reproduction, maintaining genetic diversity by creating haploid gametes differing in genetic makeup. The following procedure is a complex and similar coordinated series of events involving pairing the homologous chromosomes, recombination, and final division into the haploid gamete. The core of meiosis is the generation of double-strand breaks in chromosomes, which is of utmost importance for genetic recombination in homologous chromosomes (Rinaldi et al., 2023). Homologous recombination allows us to bridge these interruptions and exchange genetic material between parental chromosomes, the source of the diversity of genetics.
The architecture of meiotic chromosomes provides the basis for the DSB formation and repair. Within their three-dimensional organization, meiotic chromosomes are linked through chromatin loops to a central proteinaceous axis. This architecture enables proper chromosome segregation as well as the process of recombination. The structural maintenance of chromosomes (SMC) protein complex, which contains products such as Rec8, is essential for organizing meiotic chromosomes and mediating DSB repair. For example, in addition to Hop1, Red1, and the RMM complex proteins, other proteins are involved in the formation and repair of DSBs, and this outlines a complex web of proteins required for the proper chromosome architecture and its function during meiosis.
The DNA repair signalling pathways are essential in the DSB path and meiotic chromosome movements. For instance, the Tel1 kinase, which represents one of the highly conserved PIKK family subunits, is one of these pathways. Tel1 can phosphorylate the proteins associated with DNA repair, chromatin modification, and cell cycle checkpoint. Another critical performer in break processing is the Sae2 endonuclease that, as part of the initial processing of the DSB, ends to facilitate recombination. The research in yeast has revealed that a disruption of Tel1 and Sae2 results in the distortion of chromosome structures and delays DSB repair, indicating that these pathways are fundamental for meiotic chromosome organizing.
Although previous studies have added relevant information that has helped understand some of the critical aspects of DNA damage signalling involving the meiotic chromosome architecture, there are still some significant gaps in knowledge (Allison et al., 2023). An example would be that the precise mode of regulation by Tel1 and Sae2 of chromosome architecture during meiosis isn’t known yet. Besides, the mechanisms by which these pathways converge with other factors, such as the SMC protein complex, to affect nucleosome structure have yet to be well known.
This work aims to remedy the need for more knowledge regarding the functions of Tel1 and Sae2 in meiotic chromosome regulation. This experiment will be done by engineering different mutants of these essential genes like replication, transcription, and homologous recombination. High-resolution Chromosome Conformation Capture (Hi-C) mapping will analyze the structural chromosome changes during meiosis. Such mechanisms are very relevant for knowledge of meiosis and potentially human health. It has been shown that errors associated with chromosome missegregation during cell replication may lead to genetic disorders like Down syndrome.
Methods
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Construction of yeast strains with mutations in critical genes:
The constructing phase entails setting up mutation primers that are highly specific to the target genes and then working hard to locate the exact genomic sites. The process of mutation verification will continue where sequencing is done to detect the introduced mutations accurately. This meticulous method is necessary to sustain the accurate and monospecific nature of the mutant strains, which allows us to confidently claim that the mutations observed result from targeted genome modification (Lübberstedt et al., 2023). The mutant yeast cells will be selected using genetic markers, which are necessarily located with the mutated genes. This makes spotting and obtaining the yeast cells with the wanted mutations possible. Controls encompass wild-type yeast strains and those with mutations in unrelated genes, which will be used to verify that the observed effects are specific. These controls will be the critical criteria, thereby helping scientists separate between the mutations that resulted from the targeted mutations and the background genetic variability (Oz et al., 2022). Altogether, generating mutant yeast strains is a critical experimental method in this study, where it serves as a vehicle to explore the particular roles played by Tel1, Sae2, and other essential genes in dictating the evolution of meiotic chromosome architecture and repair. Genetically modifying such bacteria enables explorers of the molecular underpinnings of meiosis and DNA repair to get essential clues, pressing our knowledge to alleviate a genetic disorder.
We shall make a selection procedure where mutant strains shall be subjected to an accurate check to eliminate any possible contamination or undesired genetic changes. The controls of those strains are also subjected to the same selection process, which functions to validate the specificity of the observed effects. Therefore, mutant and control strains can be directly compared to each other. By such an approach, the primary roles of both Tel1 and Sae2, as well as other essential genes, in meiotic chromosome architecture and repair, will be explored, and the molecular mechanisms behind the procedures will be clarified (González-Arranz et al., 2021). The development of mutant yeast strains is a pivotal stage of this study, which results in a targeted examination of the effects of DNA repair signalling pathways on meiotic chromosome dynamics. Using standard genetic methods with suitable controls may allow the researchers to distinguish clearly between the effects of targeting specific mutations and the observed effects, thereby deepening our knowledge about meiosis and the genetic recombination process.
Creating yeast strains with mutations in vital genes, particularly Tel and Sae, is paramount to understanding their functions on meiotic chromosome architecture and repair. Conventional gene engineering methods, e.g., PCR-based mutagenesis and homologous recombination, will induce mutations into the yeast genome precisely. The accuracy of mutation integration is the main component of this process, which requires a thoughtful primer design and proper sequencing validation. Next, the mutant strains will be chosen depending on the presence of the genetic markers connected to the mutated genes, making sure that only yeast cells with the desired mutations survive the selection for further research. The controls using the wild-type yeast strains and strains with mutations in genes unrelated to the DNA repair and chromosome dynamics will parallel this selection process to validate the specificity of these observed effects (Ovejero et al., 2020). The specific nature of this careful selection process helps reduce contamination or unexpected genetic changes. It ensures that any observed effects are exclusive to the mutation under study. A comparative analysis of the mutant strains performing similarly to the control strain helps researchers understand how the particular mutations in Tel1, Sae2, and other essential genes impact the meiotic chromosome architecture and repair. This comparison is, therefore, imperative for grasping the more profound effects of these genes in meiosis. The engineering of mutant yeast strains will give an appropriate understanding of molecular processes controlling the dynamics of chromosome construction during meiosis and the place of pathways of signalling DNA repair in the interaction of the structure of chromosomes and their restoration.
Tracking of meiotic progression through prophase I:
Meiosis cell development is a delicate and regulated process ensuring the fruitful yield of sexual recombination in eukaryotes. The process results from a sequence of well-coordinated events that result in gametes (haploid cells) from a diploid cell in the culture. The development course is graded into several stages, and cellular and molecular alterations characterize every stage. It is essential to understand meiotic passages for diverse reasons. Besides, in meiosis, genetic diversity is produced by shuffling genetic substances of homologous chromosomes and promoting the exchange of genetic information by recombination (Ito et al., 2024). Genetic variability is a necessary process through which species adapt and evolve. Following this, the meiotic problem can also cause chromosomal abnormalities like aneuploidy, which may eventually cause developmental disorders and infertility. Consequently, the meiotic regulation study is significant for better comprehension of the genetic causes of these conditions and their possible treatments.
Time-lapse microscopy, a vital tool for investigating the meiotic progression, enables scientists to visualize the dynamic series of changes. This type of visualization allows researchers to witness critical stages such as condensation, pairing, synapsis and recombination, thus revealing the sequence of events and the coordination of the process. Through measuring the meiotic process, scientists can gain a more profound explanatory knowledge of molecular mechanisms during meiosis and the leading role of meiosis in genetic diversity and reproductive health.
While cells are in prophase I of meiosis, chromosomes execute several extremely complicated and strictly regulated processes that are important for accurately segregating chromosomes and generating genetic diversity. At this point, homologous chromosomes find each other and form pairs of sister chromatids. The process is significant because it achieves one copy of each chromosome for each gamete, with genetic information from both parents (González-Arranz et al., 2021). Additionally, synapsis, or the physical pairing of homologous chromosomes, co-occurs as the synaptonemal complex, which provides pairing and communication between the homologous chromosomes. This protein structure is the binding agent between the homologous chromosomes. In doing so, this mechanism guarantees the correct alignments of the homologous chromosomes and the success of their recombination.
This includes recombination, a process that occurs during the creation and repair of DSBs and is genetically diverse. DSBs are caused by the endonuclease Spo11, which is indispensable for homologous chromosome genetic recombination. Repairing the occurring breaks due to homologous recombination will ensure the exchange of genetic information between parental chromosomes, adding to the genetic diversity. It is essential to keep track of the generation and repair of DSBs to adequately comprehend processes maintaining proper chromosomal segregation and genetic diversity in meiosis.
Scientists employ fluorescent markers, which they use to label specific proteins involved in meiotic recombination and chromosome organization to follow the steps of meiosis and when it is completed. These markers permit the localization of these proteins and the exploration of their activities in live cell proteins employed under a microscope. This offers a snapshot that displays the function of these proteins in real-time, and this shows their role in the recombination and chromosome movement. (Lafontaine et al., 2021) It is worth noting that controls are essential for such a purpose. Controls are the wild-type yeast cells expressing the same fluorescent proteins tagged to the mutant cells. These control cells are a standard for normal meiosis, wherein they can be used to compare with the mutant cells with essential genes not working, such as Tel1 and Sae2. Comparing mutations of these genes with normal cells will allow scientists to discover how mutations influence meiosis progression, chromosome structure, and DSB repair.
Fluorescent tagging of proteins provides the opportunity for scientists to observe the nature of these proteins at a level that was previously unreached. For instance, the researchers can trace the DSBs formation and repair, the homologous chromosome pairing and synapsis, and the meiosis chromosome movement during meiosis (Niu et al., 2019). This method reveals deep insights into the molecular process of meiosis that is essential for understanding how mutations in these processes can lead to genetic diseases and infertility.
Employing fluorescent markers and controls is a versatile tool for meiosis research. It enables researchers to see intricate processes taking place instantly, leading to innovative ideas that reveal the secrets of how chromosome structure is organized and genetic information is exchanged. This knowledge is the key that opens up the black box of meiosis and shows how it works and why this process is so crucial for genetic diversity and reproductive health.
High-resolution Hi-C mapping of chromosome conformation changes
The high-resolution Hi-C mapping provides us with meaningful data that gives us many details on the chromosomes’ three-dimensional architecture. This methodology is built on chromatin conformation capture, a tool used to comprehend spatial locations of different genomic regions based on their physical interaction. The next-level interaction analysis is enabled by utilizing Hi-C, which can capture such associations at the whole genome level and with the finest resolution (Jia et al., 2023). The initial step is to fix the chromatin within the nuclei in their native positions to pick the spatial proximities of distant chromosomal regions close to each other due to folding and looping. The next step is crosslinking, then chromatin is digested, and the DNA fragments are ligated together. Then, these hybrid DNA particles (the representation of interactionally overlapped regions) are sequenced (Gong et al., 2022). The sequencing data is analyzed to determine the number of connections between different nodal points of the genome and the in-depth details of the genome’s spatial organization.
In Hi-C, high-resolution mapping has led to a breakthrough with its exploration of both intricate features and organization of chromatin folding, compartmentalization, and the formation of chromatin loops. This technology leads to discovering the nucleus’s proprieties, such as the ‘A’ and ‘B’ compartments, which correspond to active and inactive chromatin, respectively (Bylino et al., 2021). Furthermore, the study of Hi-C showed the arranging of chromatin in a hierarchy way into topologically associating domains (TADs), which are segments of DNA that seemingly interact with one another. In this work, Hi-C mapping accurate to the high resolution will play an essential role in the understanding of how the mutations in Tel1, Sae2 and other genes responsible for DNA repair and the chromosome dynamics affect the three-dimensional organization of the chromosomes in the meiosis process (Dozmorov et al., 2023). Through Hi-C mapping in the mutant yeast strains and comparing the results with controls, the researchers will get the most valuable information regarding how these mutations influence the formation of chromatin loops and the spatial arrangement of chromatin. This will open new horizons of the chromosome architecture at the level of meiosis.
Controls in this work are significant for obtaining a baseline comparison for determining the effect of mutations in Tel1, Sae2, and other genes after being silenced on the structure of chromosomes. The wild-type cell controls will be treated in the same manner as mutant cells by following the Hi-C mapping protocol. By aligning the Hi-C maps of mutant pictures to those of controls, researchers will learn how mutations affect the configuration of chromosomes during meiosis. Such a contrastive assessment is, as it is for differentiating between variations caused by mutations and naturally occurring variability in chromosome architecture.
Statistical analyses will lead to data interpretation by the Hi-C mapping method. The outcomes of these evaluations will be used to test the statistical significance of any differences detected between treatment groups. Using this approach to measure the likelihood that the same changes have occurred by chance, researchers can be guaranteed to say the changes resulted from the mutations in Tel1, Sae2, and other genes (Daiki Imanishi & Takahashi, 2023). Besides that, the replication of each experiment is included so the reliability and reproducibility of the results can be ensured. Replication stabilizes the process, making it more reliable and predictable. Consequently, this will ensure that the experimental results are replicated in multiple trials.
These methods integrate to determine the efficiency of how meiotic chromosome architecture is displayed and associated with DNA repair signalling pathways (Yu et al., 2022). The approach combines high-resolution Chi-C map control, statistical tests, and replicates to unravel the molecular mechanisms controlling chromosome movement in meiosis (Wu et al., 2021). Moreover, these techniques will investigate the hypothesis that Tel1 and Sae2 are critical in synchronizing chromosome structure and DNA double break repair. This study attempts to advance the comprehension of meiotic recombination and genetic diversity by elucidating such mechanisms.
This study is anticipated to reach several critical outcomes that will contribute considerably to the knowledge of the meiotic chromosome architecture and the DNA repair signalling pathways. Firstly, the analysis of meiotic progression in mutant strains of yeast that have a mutation in Tel1, Sae2, and another essential gene is expected to identify deviations in chromosome development and dynamics compared to wild-type controls (Lovell et al., 2021). With this result, it is right to assume that TEL1 and SAE2 are essential factors in regulating meiotic chromosome structure and DSB repair, harmonious with the research hypothesis.
Furthermore, the next-generation Hi-C technology, which allows us to see how mutations in Tel1, Sae2, and the other genes affect the chromosome structure organization during meiosis, is expected to provide details on this topic. Hi-C maps of mutant cells are expected to reveal the changes in chromatin interactions and loop formation, evidenced by disruptions in chromosome structure. The structural outcomes would name the roles of Tel1: Sae2 and other DNA repair signalling pathways in performing the meiotic process.
This is done by conducting the statistical tests of the Hi-C data and repeating the experiments that will contribute to the reliability and robustness of the results. For instance, if the outcomes continuously indicate meaningful differences among mutants and control cells, it would strongly suggest the hypothesis that Tel1 and Sae2 play some critical roles in controlling meiotic chromosome architecture (Huang & Zhou, 2020). In general, the results of this study are aimed at making us more aware of the molecular mechanisms of meiotic recombination and genetic diversity, which will be helpful in many fields, such as genetics, cell biology, and reproductive medicine.
Conclusion
In conclusion, this research study provides a detailed investigation of the role of DNA repair signalling pathways, especially Tel1 kinase and Sae2 endonuclease, in controlling the role of meiosis chromosome architecture. Meiosis is one of the central processes for genetic recombination and diversity, and the mechanisms that regulate chromosome dynamics during this process are also fundamental. The literature review shows evidence about the importance of meiosis, the role of chromosomes, and the loopholes in our knowledge. The idea is that Tel1 and Sae2 are critical regulators in establishing chromosome architecture during meiosis, and results will be obtained to either support or extend this hypothesis. A set of approaches, including genetically engineered yeast, time-lapse microscopy, and high-resolution Hi-C mapping, will reveal the mechanism of chromosome motion and DNA repair during meiosis. Having controls and doing statistical analysis guarantee the robustness and credibility of findings.
While these findings may not cure diseases, they can significantly expand our knowledge of meiotic chromosome organization and DNA repair mechanisms. Gene expression regulation has been scientifically proven to be an essential factor influencing genetic diversity, evolution, and human health. In summary, this study could be instrumental in uncovering the refined processes responsible for chromosome evolution during meiosis. By focusing on the research objectives and testing the hypothesis, this research can contribute to scientific knowledge and catch the broader interest of many disciplines.
References
Allison, R. M., Johnson, D. J., Neale, M. J., and Gray, S. (2023). Recombinase-independent chromosomal rearrangements between dispersed inverted repeats in Saccharomyces cerevisiae meiosis. Nucleic Acids Research, 51(18), 9703–9715. https://doi.org/10.1093/nar/gkad650
Bylino, O. V., Ibragimov, A. N., Pravednikova, A. E., and Shidlovskii, Y. V. (2021). Investigation of the Basic Steps in the Chromosome Conformation Capture Procedure. Frontiers in Genetics, 12. https://doi.org/10.3389/fgene.2021.733937
Daiki Imanishi, and Takahashi, S. (2023). RNA sequencing data analysis of the yeast Vanrija (Cryptococcus) humicola strain UJ1 grown on l- and d-aspartate. Data in Brief, 47, 109008–109008. https://doi.org/10.1016/j.dib.2023.109008
Dozmorov, M. G., Marshall, M. A., Rashid, N. S., Grible, J. M., Valentine, A., Olex, A. L., Murthy, K., Chakraborty, A., Reyna, J., Daniela Salgado Figueroa, Hinojosa-Gonzalez, L., Erika Da-Inn Lee, Baur, B. A., Roy, S., Ay, F., and J Chuck Harrell. (2023). Rewiring of the 3D genome during the acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft. Scientific Reports, 13(1). https://doi.org/10.1038/s41598-023-32568-7
Fusco, G., and Minelli, A. (2023). Understanding Reproduction. In Google Books. Cambridge University Press. https://books.google.com/books?hl=en&lr=&id=z2TOEAAAQBAJ&oi=fnd&pg=PR13&dq=Meiosis+is+a+cell+division+process+that+specializes+in+haploid+gamete+production+among+sexually+reproducing+organisms.&ots=M_Y-VhpiJX&sig=pBCoB3wLWTWWW8wV5ebcRCBCoUI
Gao, Y., Liu, C., Wu, T., Liu, R., Mao, W., Gan, X., Lu, X., Liu, Y., Wan, L., Xu, B., & Chen, M. (2022). Current status and perspectives of non-coding RNA and phase separation interactions. BioScience Trends, 16(5), 330–345. https://doi.org/10.5582/bst.2022.01304
Gartner, A., and Engebrecht, J. (2022). DNA repair, recombination, and damage signalling. Genetics, 220(2), iyab178. https://doi.org/10.1093/genetics/iyab178
Gong, T., Borgard, H., Zhang, Z., Chen, S., Gao, Z., and Deng, Y. (2022). Analysis and Performance Assessment of the Whole Genome Bisulfite Sequencing Data Workflow: Currently Available Tools and a Practical Guide to Advance DNA Methylation Studies. Small Methods, 6(3), 2101251. https://doi.org/10.1002/smtd.202101251
González-Arranz, S., Acosta, I., Carballo, J. A., Santos, B., and San-Segundo, P. A. (2021). The N-Terminal Region of the Polo Kinase Cdc5 Is Required for Downregulation of the Meiotic Recombination Checkpoint. Cells, 10(10), 2561. https://doi.org/10.3390/cells10102561
Hou, H., Kyriacou, E., Thadani, R., Klutstein, M., Chapman, J. H., and Cooper, J. P. (2021). Centromeres are dismantled by foundational meiotic proteins Spo11 and Rec8. Nature, 591(7851), 671–676. https://doi.org/10.1038/s41586-021-03279-8
Huang, R.-X., and Zhou, P.-K. (2020). DNA damage response signalling pathways and targets for radiotherapy sensitization in cancer. Signal Transduction and Targeted Therapy, 5(1), 1–27. https://doi.org/10.1038/s41392-020-0150-x
Ito, M., Fujita, Y., and Shinohara, A. (2024). Positive and negative regulators of RAD51/DMC1 in homologous recombination and DNA replication. DNA Repair, 134, 103613. https://doi.org/10.1016/j.dnarep.2023.103613
Ito, M., Furukohri, A., Matsuzaki, K., Fujita, Y., Toyoda, A., and Shinohara, A. (2023). FIGNL1 AAA+ ATPase remodels RAD51 and DMC1 filaments in pre-meiotic DNA replication and meiotic recombination. Nature Communications, 14(1), 6857. https://doi.org/10.1038/s41467-023-42576-w
Jammu, R. A. V. (2020). The AAA+ ATPase Pch2 and the HORMA protein Hop1 regulate meiotic prophase checkpoint function. https://doi.org/10.17185/duepublico/73479
Jia, G.-S., Zhang, W.-C., Liang, Y., Liu, X.-H., Rhind, N., Pidoux, A., Brysch-Herzberg, M., and Du, L.-L. (2023). A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus. G3 Genes|Genomes|Genetics. https://doi.org/10.1093/g3jThenal/jkad028
Johnson, D., Crawford, M., Cooper, T., Claeys Bouuaert, C., Keeney, S., Llorente, B., Garcia, V., and Neale, M. J. (2021). Concerted cutting by Spo11 illuminates meiotic DNA break mechanics. Nature, 594(7864), 572–576. https://doi.org/10.1038/s41586-021-03389-3
Jolanda van Leeuwen, Pons, C., Tan, G., Jason Zi Wang, Hou, J., Jochen Weile, Gebbia, M., Liang, W., Ermira Shuteriqi, Z, L., Lopes, M., Matej Ušaj, Lopes, S., Natascha van Lieshout, Myers, C. L., Roth, F. P., Aloy, P., Andrews, B., and Boone, C. (2020). Systematic analysis of bypass suppression of essential genes. Molecular Systems Biology, 16(9). https://doi.org/10.15252/msb.20209828
Lafontaine, D. L., Yang, L., Dekker, J., and Gibcus, J. H. (2021). Hi‐C 3.0: Improved Protocol for Genome‐Wide Chromosome Conformation Capture. Current Protocols, 1(7). https://doi.org/10.1002/cpz1.198
Lambing, C., Kuo, P., Kim, J., Osman, K., Amy Leanne Whitbread, Yang, J., Choi, K., Franklin, C. H., and Henderson, I. R. (2022). Differentiated function and localization of SPO11-1 and PRD3 on the chromosome axis during meiotic DSB formation in Arabidopsis thaliana. 18(7), e1010298–e1010298. https://doi.org/10.1371/jThenal.pgen.1010298
Lovell, J. T., Bentley, N. B., Bhattarai, G., Jenkins, J. W., Sreedasyam, A., Alarcon, Y., Bock, C., Boston, L. B., Carlson, J., Cervantes, K., Clermont, K., Duke, S., Krom, N., Kubenka, K., Mamidi, S., Mattison, C. P., Monteros, M. J., Pisani, C., Plott, C., and Rajasekar, S. (2021). The chromosome-scale genomes and a pan-genome annotation to accelerate pecan tree breeding. Nature Communications, 12(1), 4125. https://doi.org/10.1038/s41467-021-24328-w
Lu, R., Zhang, H., Jiang, Y.-N., Wang, Z.-Q., Sun, L., and Zhou, Z.-W. (2021). Post-Translational Modification of MRE11: Its Implication in DDR and Diseases. Genes, 12(8), 1158. https://doi.org/10.3390/genes12081158
Lübberstedt, T., Bhattacharyya, M., and Suza, W. (2023). Markers and Sequencing. Iastate.pressbooks.pub. https://iastate.pressbooks.pub/molecularplantbreeding/chapter/markers-and-sequencing/
Niu, L., Shen, W., Huang, Y., He, N., Zhang, Y., Sun, J., Wan, J., Jiang, D., Yang, M., Tse, Y. C., Li, L., and Hou, C. (2019). Amplification-free library preparation with SAFE Hi-C uses ligation products for deep sequencing to improve traditional Hi-C analysis. Communications Biology, 2(1), 1–8. https://doi.org/10.1038/s42003-019-0519-y
Ovejero, S., Bueno, A., and Sacristán, M. P. (2020). Working on Genomic Stability: From the S-Phase to Mitosis. Genes, 11(2), 225. https://doi.org/10.3390/genes11020225
Oz, T., Mengoli, V., Rojas, J., Jonak, K., Braun, M., Ievgeniia Zagoriy, and Wolfgang Zachariae. (2022). The Spo13/Meikin pathway confines the onset of gamete differentiation to meiosis II in yeast. The EMBO JThenal, 41(4). https://doi.org/10.15252/embj.2021109446
Patel, L., Kang, R., Rosenberg, S. C., Qiu, Y., Raviram, R., Chee, S., Hu, R., Ren, B., Cole, F., and Corbett, K. D. (2019). Dynamic reorganization of the genome shapes the recombination landscape in the meiotic prophase. Nature Structural and Molecular Biology, 26(3), 164–174. https://doi.org/10.1038/s41594-019-0187-0
Rimbault, C., Kashyap Maruthi, Christelle Breillat, Genuer, C., Crespillo, S., Puente‐Muñoz, V., Chamma, I., Gauthereau, I., Antoine, S., Thibaut, C., Tai, Dartigues, B., Dolors Grillo-Bosch, Stéphane Claverol, Poujol, C., Choquet, D., Mackereth, C. D., and Matthieu Sainlos. (2019). Engineering selective competitors for the discrimination of highly conserved protein-protein interaction modules. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-12528-4
Rinaldi, C., Paolo Pizzul, Casari, E., Mangiagalli, M., Tisi, R., and Maria Pia Longhese. (2023). The Ku complex promotes DNA end-bridging, and this function is antagonized by Tel1/ATM kinase. Nucleic Acids Research, 51(4), 1783–1802. https://doi.org/10.1093/nar/gkad062
Rocha, J. J., Satish Arcot Jayaram, Stevens, T. J., Muschalik, N., Shah, R. D., Sahar Emran, Robles, C., Freeman, M., and Munro, S. (2023). Functional economics: Systematic screening of conserved genes of unknown function. PLOS Biology, 21(8), e3002222–e3002222. https://doi.org/10.1371/jThenal.pbio.3002222
Sanders, J. T., Freeman, T. F., Xu, Y., Golloshi, R., Stallard, M. A., Hill, A. M., San Martin, R., Balajee, A. S., and McCord, R. P. (2020). Radiation-induced DNA damage and repair effects on 3D genome organization. Nature Communications, 11(1), 6178. https://doi.org/10.1038/s41467-020-20047-w
Silva, G. L. A. da. (2022, September 14). Characterization of the role of the ATR kinase homolog in L. major response to replication stress. Www.teses.usp.br. https://www.teses.usp.br/teses/disponiveis/17/17136/tde-01122022-121302/en.php
Smith, M. J., Bryant, E. E., Joseph, F. J., and Rothstein, R. (2019). DNA damage triggers increased mobility of chromosomes in G1-phase cells. Molecular Biology of the Cell, 30(21), 2620–2625. https://doi.org/10.1091/mbc.e19-08-0469
Sun, Y., McCorvie, T. J., Yates, L. A., and Zhang, X. (2019). Structural basis of homologous recombination. Cellular and Molecular Life Sciences, 77(1), 3–18. https://doi.org/10.1007/s00018-019-03365-1
Svetec Miklenić, M., and Svetec, I. K. (2021). Palindromes in DNA—A Risk for Genome Stability and Implications in Cancer. International Journal of Molecular Sciences, 22(6), 2840. https://doi.org/10.3390/ijms22062840
Tian, Y., Liu, L., Gao, J., and Wang, R. (2023). Homologous chromosome pairing: The linchpin of accurate segregation in meiosis. JThenal of Cellular Physiology, 239(1), 3–19. https://doi.org/10.1002/jcp.31166
Tisi, R., Vertemara, J., Zampella, G., and Longhese, M. P. (2020). Functional and structural insights into the MRX/MRN complex are key in recognizing and repairing DNA double-strand breaks. Computational and Structural Biotechnology JThenal, 18, 1137–1152. https://doi.org/10.1016/j.csb j.2020.05.013
Vainshelbaum, N. M., Salmina, K., Gerashchenko, B. I., Lazovska, M., Zayakin, P., Cragg, M. S., Pjanova, D., and Erenpreisa, J. (2022). Role of the Circadian Clock “Death-Loop” in the DNA Damage Response Underpinning Cancer Treatment Resistance. Cells, 11(5), 880. https://doi.org/10.3390/cells11050880
Vikash Kumar Yadav, and Corentin Claeys Bouuaert. (2021). Mechanism and Control of Meiotic DNA Double-Strand Break Formation in S. cerevisiae. Frontiers in Cell and Developmental Biology, 9. https://doi.org/10.3389/fcell.2021.642737
Wu, H., Wang, X., Chu, M., Li, D., Cheng, L., and Zhou, K. (2021). HCMB: A stable and efficient algorithm for normalizing highly sparse Hi-C contact data. Computational and Structural Biotechnology JThenal, 19, 2637–2645. https://doi.org/10.1016/j.csbj.2021.04.064
Yadav, V. K., and Claeys Bouuaert, C. (2021). Mechanism and Control of Meiotic DNA Double-Strand Break Formation in S. cerevisiae. Frontiers in Cell and Developmental Biology, 9. https://doi.org/10.3389/fcell.2021.642737
Yoneyama, S., Shirai, N., Ando, N., Azuma, T., Tsuda, M., and Matsumoto, T. (2020). Identifying an SNP and developing a PCR-based allele-specific marker of the sporulation-deficient (sporeless) trait of the Tamogitake 108Y2D mutant using next-generation sequencing. Breeding Science, 70(5), 530–539. https://doi.org/10.1270/jsbbs.20039
You, Q., Anthony Youzhi Cheng, Gu, X., Harada, B. T., Yu, M., Wu, T., Ren, B., Ouyang, Z., and He, C. (2020). Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution. Nature Biotechnology, 39(2), 225–235. https://doi.org/10.1038/s41587-020-0643-8
Yu, H., Ness, S., Li, Chung-I., Bai, Y., Mao, P., and Guo, Y. (2022). Surveying mutation density patterns around specific genomic features. Genome Research, 32(10), 1930–1940. https://doi.org/10.1101/gr.276770.122
Zhang, N., Mendieta-Esteban, J., Magli, A., Lilja, K. C., Perlingeiro, R. C. R., Marti-Renom, M. A., Tsirigos, A., and Dynlacht, B. D. (2020). Muscle progenitor specification and myogenic differentiation are associated with changes in chromatin topology. Nature Communications, 11(1), 6222. https://doi.org/10.1038/s41467-020-19999-w
Zuo, W., Chen, G., Gao, Z., Li, S., Chen, Y., Huang, C., Chen, J., Chen, Z., Lei, M., and Bian, Q. (2021). Stage-resolved Hi-C analyses reveal meiotic chromosome organizational features influencing homolog alignment. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-26033-0
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