Review
Cell Biology
Erin Bonnell, Emeline Pasquier, Raymund J. Wellinger
Summary: Telomeres, crucial for maintaining genomic stability, pose challenges for replication due to their repetitive nature and the formation of secondary structures, leading to replication fork stalling. Multiple mechanisms are involved in overcoming these obstacles to ensure efficient telomeric DNA duplication and preserve genome integrity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Simona Giunta, Solene Herve, Ryan R. White, Therese Wilhelm, Marie Dumont, Andrea Scelfo, Riccardo Gamba, Cheng Kit Wong, Giulia Rancati, Agata Smogorzewska, Hironori Funabiki, Daniele Fachinetti
Summary: The study demonstrates the importance of the centromere-specific histone H3 variant CENP-A in safeguarding DNA replication of alpha-satellite repeats to prevent structural aneuploidy during S phase, providing insights into how specialized centromeric chromatin maintains the integrity of transcribed noncoding repetitive DNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Celine Duc, Christophe Thiriet
Summary: The review focuses on the remodeling of chromatin during DNA replication in the S-phase, including the eviction of nucleosomes and the assembly of newly synthesized histones. The recycling of parental histones and the nuclear import of histones are also discussed in relation to epigenetic inheritance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Savannah J. Hoyt, Jessica M. Storer, Gabrielle A. Hartley, Patrick G. S. Grady, Ariel Gershman, Leonardo G. de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J. Core, Jennifer L. Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F. A. Smit, Aaron F. Straight, Mitchell R. Vollger, Travis J. Wheeler, Michael C. Schatz, Evan E. Eichler, Adam M. Phillippy, Winston Timp, Karen H. Miga, Rachel J. O'Neill
Summary: Mobile elements and repetitive genomic regions play a crucial role in lineage-specific genomic innovation and can uniquely identify individual genomes. This study presents a novel approach to de novo repeat discovery and annotation of the T2T-CHM13 human reference genome, expanding our understanding of the diversity, distribution, and evolution of repetitive regions in the human genome.
Article
Multidisciplinary Sciences
Abdelhalim Boukaba, Jian Liu, Carl Ward, Qiongfang Wu, Alexei Arnaoutov, Jierong Liang, Elena M. Pugacheva, Mary Dasso, Victor Lobanenkov, Miguel Esteban, Alexander V. Strunnikov
Summary: Many tumors express meiotic genes that can cause chromosome instability. The abnormal expression of meiotic cohesins is associated with chromosome missegregation, DNA damage, and altered gene expression. Additionally, meiotic cohesins localize to the same sites as BORIS/CTCFL, rather than the CTCF sites associated with somatic cohesins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Aleksandra Bliznina, Aki Masunaga, Michael J. Mansfield, Yongkai Tan, Andrew W. Liu, Charlotte West, Tanmay Rustagi, Hsiao-Chiao Chien, Saurabh Kumar, Julien Pichon, Charles Plessy, Nicholas M. Luscombe
Summary: This study presents a chromosome-scale genome assembly of the larvacean Oikopleura dioica using a hybrid approach of multiple sequencing technologies and chromosome conformation information. The assembly revealed complete autosomes as well as proposed sex chromosomes, allowing for cross-genome comparisons and studies of chromosomal evolution in this lineage.
Article
Biochemistry & Molecular Biology
Chih-Yi Gabriela Lin, Anna Christina Naeger, Thomas Lunardi, Aleksandra Vancevska, Gerald Lossaint, Joachim Lingner
Summary: Telomere shortening can lead to diseases and aging, often due to the lack of telomerase in cells. By developing a new isolation protocol, specific proteins associated with telomere replication can be purified, revealing their importance for maintaining telomere stability. This study provides a valuable resource for understanding the dynamic changes of the telomeric proteome during replication.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Calla B. Shubin, Rini Mayangsari, Ariel D. Swett, Carol W. Greider
Summary: In budding yeast, Rif1 negatively regulates telomere length through a region with HEAT repeats that mediate telomere length regulation, separate from its proposed DNA binding function. Conserved amino acids from position 436 to 577 play a crucial role in telomere length regulation.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Constanze Pentzold, Miriam Kokal, Stefan Pentzold, Anja Weise
Summary: Chromosomal fragile sites, positioned in the interphase nucleus with anchoring points at the nuclear lamina, exhibit fragility in mitosis but actually start in interphase, influencing genomic integrity and sustaining cellular diversity.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Editorial Material
Cell Biology
Pawel Kordowitzki
Summary: Research has shown that the pool of oocytes in females starts to decline before birth, and as women age, characteristics such as chromosomal abnormalities, decreased mitochondrial function, and telomere shortening become more common. This may contribute to higher rates of miscarriage and chromosomal non-disjunction in older women who choose to delay pregnancy.
Editorial Material
Biochemistry & Molecular Biology
Zhiming Li, Zhiguo Zhang
Summary: Histone chaperones play important roles in the biogenesis, transportation, and deposition of histones, affecting processes such as DNA replication, transcription, and epigenetic inheritance. In this study, Carraro et al. uncover an interconnected chaperone network and discover a surprising function of the histone chaperone DAXX in de novo deposition of H3.3K9me3.
Article
Biochemistry & Molecular Biology
Laura Tovini, Sarah C. Johnson, Molly A. Guscott, Alexander M. Andersen, Diana Carolina Johanna Spierings, Rene Wardenaar, Floris Foijer, Sarah E. McClelland
Summary: Cancer cells exhibit persistent chromosomal instability, with different tumor types showing characteristic subsets of aneuploidies. Researchers used dCas9 as a carrier to recruit the kinetochore-nucleating domain of CENP-T protein to ectopically assemble kinetochores near specific genomic loci, resulting in increased chromosome instability and partial aneuploidies of target chromosomes in various cell types. The study also analyzed potential endogenous repeats that could support ectopic kinetochore formation.
Review
Biochemistry & Molecular Biology
Baraah Al Ahmad Nachar, Filippo Rosselli
Summary: DNA replication is a crucial process that requires the coordinated action of multiple proteins to permit, initiate, and progress replication forks. However, there are obstacles that can impede replication fork progression. Cells have developed various mechanisms to protect DNA replication and ensure its completion before entering mitosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Mikko Rautiainen, Sergey Nurk, Brian P. Walenz, Glennis A. Logsdon, David Porubsky, Arang Rhie, Evan E. Eichler, Adam M. Phillippy, Sergey Koren
Summary: The Telomere-to-Telomere consortium has achieved the first complete sequence of a human genome. They used a combination of long Nanopore sequencing reads and high-resolution assembly graph to resolve repeat sequences and automate the process in their Verkko pipeline. The result is a phased, diploid assembly with many chromosomes assembled from end to end. This advance is crucial for constructing comprehensive pangenome databases and chromosome-scale comparative genomics.
NATURE BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Lingzhan Xue, Yu Gao, Meiying Wu, Tian Tian, Haiping Fan, Yongji Huang, Zhen Huang, Dapeng Li, Luohao Xu
Summary: The study on the haplotype-resolved genome assembly of zig-zag eel sheds light on the evolution of sex chromosomes and recombination suppression mechanisms, revealing a similar sex-linked region on the X and Y chromosomes and identifying a potential sex-determining gene in the SLR.
Review
Plant Sciences
Rekha Agrawal, Fajkus Jiri, Jitendra K. Thakur
Summary: The Mediator complex, which conveys regulatory information from transcription factors to RNA polymerase II, consists of four modules including a kinase module. The kinase module, composed of MED12, MED13, CycC, and CDK8, is able to significantly alter the structure and function of the complex, playing a crucial role in transcription regulation.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Klara Konecna, Pavla Polanska Sovakova, Karin Antekova, Jiri Fajkus, Miloslava Fojtova
Summary: The study found that exposure to the hypomethylation drug zebularine resulted in shorter telomeres in Arabidopsis plants, with progressive changes across generations, high inter-individual variability, and diverse responses among different ecotypes. Shortening of telomeres corresponded to the transcriptional activation of transposable elements (TEs), indicating a correlated response to zebularine treatment. Changes in telomere lengths and TE transcript levels were not always associated with cytosine hypomethylation, suggesting an independent regulatory mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Petr Fajkus, Vratislav Peska, Jiri Fajkus, Eva Sykorova
Summary: This study examined the presence and functional status of TERT variants in allotetraploid Nicotiana species of diverse evolutionary ages, as well as in other diploid and polyploid plant species. Results showed various patterns of retention or loss of parental TERT variants and divergence in their functions, with all identified TERT variants confirmed to be expressed. Synteny analyses revealed the conservation and translocation of TERT genes in representative plant genomes, with translocation becoming fixed in target loci in various diploid and polyploid species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Ivana Goffova, Jiri Fajkus
Summary: Genes encoding ribosomal RNA (rDNA) are crucial for cell survival and are sensitive to factors causing genomic instability. Their repetitive nature makes them susceptible to inappropriate recombination events, leading to unstable rDNA copy numbers. The review summarizes the structure and organization of rDNA, its role in sensing genome changes, and its relationship to aging, as well as recent findings on factors involved in chromatin assembly and DNA repair for maintaining rDNA stability in plant models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Martin Lycka, Vratislav Peska, Martin Demko, Ioannis Spyroglou, Agata Kilar, Jiri Fajkus, Miloslava Fojtova
Summary: This study introduces a new online toolset called WALTER for the rapid, reproducible, and user-friendly analysis of telomere length data and statistical evaluation, representing a major upgrade in TRF scan image processing.
BMC BIOINFORMATICS
(2021)
Article
Plant Sciences
Thomas Eekhout, Martina Dvorackova, Jose Antonio Pedroza Garcia, Martina Nespor Dadejova, Pooneh Kalhorzadeh, Hilde Van den Daele, Ilse Vercauteren, Jiri Fajkus, Lieven De Veylder
Summary: The inactivation of FAS1 gene results in the activation of ATM and SOG1-mediated G2/M arrest, rendering ATR and WEE1 redundant as checkpoint regulators. Knocking out SOG1 in fast plants restores replication stress sensitivity.
Article
Plant Sciences
Rekha Agrawal, Mohan Sharma, Nidhi Dwivedi, Sourobh Maji, Pallabi Thakur, Alim Junaid, Jiri Fajkus, Ashverya Laxmi, Jitendra K. Thakur
Summary: This study reveals the role of the Mediator complex as an integrator of jasmonate (JA) and auxin signaling pathways during thermomorphogenesis in Arabidopsis. Warm temperature induces the expression of JA signaling genes and promotes the accumulation of the JA signaling receptor COI1 and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9. The Mediator complex, specifically the mediator subunit MED17, occupies the promoters of thermosensory genes and facilitates enrichment of H3K4me3, which is dependent on the bHLH transcription factor PIF4.
Review
Plant Sciences
Fatemeh Aflaki, Ruben Gutzat, Iva Mozgova
Summary: Plants possess exceptional plasticity in development and the ability to reprogram cell identities during regeneration. Only a subset of cells with regeneration potential can reach pluripotency, and transcriptional reprogramming during this process involves the transient release and restoration of chromatin repression.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Petr Fajkus, Matej Adamik, Andrew D. L. Nelson, Agata M. Kilar, Michal Franek, Michal Bubenik, Radmila Capkova Frydrychova, Alena Votavova, Eva Sykorova, Jiri Fajkus, Vratislav Peska
Summary: Unlike the catalytic subunit of telomerase, the RNA subunit (TR) shows significant differences in size, sequence and biogenesis across eukaryotes. Previous views assumed a common origin of TRs transcribed with RNA polymerase II in Opisthokonta and Trypanosomida, and TRs transcribed with RNA polymerase III in TSAR and Archaeplastida. However, new findings from studying Hymenoptera TRs challenge this assumption and suggest an evolutionary switch in TR type and biogenesis that is associated with the divergence of Arthropods.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Klara Prikrylova Konecna, Agata Kilar, Petra Kovacikova, Jiri Fajkus, Eva Sykorova, Miloslava Fojtova
Summary: This study investigates the interaction between ARM and telomerase and explores the cellular functions of ARM. The results show that ARM is involved in crucial cellular processes and has a dominant effect. Additionally, ARM is implicated in circadian rhythms and responses to drugs and stimuli.
Article
Engineering, Environmental
Martin Lycka, Milos Bartak, Ondrej Helia, Stanislav Kopriva, Dana Moravcova, Josef Hajek, Lukas Fojt, Richard Cmelik, Jiri Fajkus, Miloslava Fojtova
Summary: Hydroponic experiments were conducted to investigate the effects of prolonged sulfate limitation and Cd exposure on Arabidopsis thaliana and Nicotiana tabacum. Both species showed adverse effects on morphology, photosynthetic and biochemical parameters, and nutritional status under low sulfate treatments and Cd stress. The responses to low sulfate supply, Cd exposure, or a combination of both factors were species-specific, and Cd exposure had opposing effects on the levels of certain elements in the roots.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Plant Sciences
Eva Dvorak Tomastikova, Fen Yang, Kristina Mlynarova, Said Hafidh, Sarka Schorova, Alzbeta Kusova, Marketa Pernisova, Tereza Prerovska, Bozena Klodova, David Honys, Jiri Fajkus, Ales Pecinka, Petra Prochazkova Schrumpfova
Summary: RUVBL1 and RUVBL2 are crucial for the proper development of male and female gametophytes in Arabidopsis. Mutations in these genes result in abnormal embryo sac structure and nuclear numbers. The expression of these proteins is observed in pollen grains, embryo sac, and tapetum cells, playing important roles in reproductive development.
Article
Plant Sciences
Michal Zavodnik, Petr Fajkus, Michal Franek, David Kopecky, Sonia Garcia, Steven Dodsworth, Andres Orejuela, Agata Kilar, Jiri Ptacek, Martin Matl, Anna Hyskova, Jiri Fajkus, Vratislav Peska
Summary: Telomerase, telomeric DNA, and associated proteins form a complex and conserved mechanism that maintains genome integrity by protecting chromosome ends. Evolutionary changes in telomere maintenance have given rise to species with unusual telomeric DNA sequences and telomerase components. Telomerase RNA (TR) plays a central role in telomere maintenance, and mutations in TR can disrupt telomere DNA synthesis and recognition by telomere proteins. Through bioinformatic and experimental analyses, this study investigates the evolutionary changes in TR that underlie telomere transitions in plants, and identifies telomere transitions corresponding to TR paralogs with diverse template regions.
Article
Cell Biology
Gianluca Teano, Lorenzo Concia, Lea Wolff, Leopold Carron, Ivona Biocanin, Katerina Adamusova, Miloslava Fojtova, Michael Bourge, Amira Kramdi, Vincent Colot, Ueli Grossniklaus, Chris Bowler, Celia Baroux, Alessandra Carbone, Aline Probst, Petra Prochazkova Schrumpfova, Jiri Fajkus, Simon Amiard, Stefan Grob, Clara Bourbousse, Fredy Barneche
Summary: A study in Arabidopsis reveals the role of linker histone H1 in nucleosome organization and its functional interactions with chromatin factors. It shows that H1 contributes to chromatin condensation and H3K27me3 deposition at Polycomb Repressive Complex 2 (PRC2) target genes, while selectively preventing H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins. This study provides insights into the mechanistic framework of how H1 safeguards nucleus architecture.
Review
Genetics & Heredity
Mallika Vijayanathan, Maria Guadalupe Trejo-Arellano, Iva Mozgova
Summary: Polycomb Repressive Complex 2 (PRC2) is an important complex in eukaryotes that regulates gene transcription through histone modification. PRC2 shows both common and divergent features among different eukaryotes, which is crucial for understanding its evolution.
