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.
Editorial Material
Biochemical Research Methods
Yafei Mao, Guojie Zhang
Summary: The release of the first telomere-to-telomere human genome sequence is a significant milestone in human genomics research, offering potential insights for evolutionary genomics. This article describes the advances of this new genome assembly and discusses the challenges of applying this sequencing strategy to various extant species.
Review
Biochemistry & Molecular Biology
Junko Kanoh
Summary: Eukaryotes have linear chromosomes with telomeres at both ends, which consist of simple tandem repeat DNA sequences and telomere-binding proteins. This review focuses on the subtelomeric chromatin and DNA structures in the fission yeast Schizosaccharomyces pombe. The subtelomeres form distinct chromatin structures, including the shelterin complex, heterochromatin, and knob, which play roles in gene expression regulation and preventing invasion of condensed chromatin structures. Recombination reactions within or near subtelomeric sequences enable chromosome circularization and survival in telomere shortening. The variable DNA structures of subtelomeres contribute to biological diversity and evolution.
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
Marco Corbo, Joana Damas, Madeline G. Bursell, Harris A. Lewin
Summary: This study used high throughput chromatin conformation capture (Hi-C) to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families. The results showed that chromatin conformation is conserved during carnivore evolution and can be accurately identified through Hi-C contact maps analysis. The study also discovered significant differences in chromatin conformation for the X chromosome and the red fox genome.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Mostafa Rahnama, Baohua Wang, Jane Dostart, Olga Novikova, Daniel Yackzan, Andrew Yackzan, Haley Bruss, Maray Baker, Haven Jacob, Xiaofei Zhang, April Lamb, Alex Stewart, Melanie Heist, Joey Hoover, Patrick Calie, Li Chen, Jinze Liu, Mark L. L. Farman
Summary: Telomeres play a crucial role in solving the end-replication problem, protecting chromosomes, and shaping genome architecture in the blast fungus Pyricularia. Telomere instability in some strains is caused by novel retrotransposons, leading to frequent break-induced rearrangements, while even telomeres lacking insertions exhibit poor preservation and frequent polymorphism. Chromosomal responses to failed telomere maintenance suggest that compromised telomere function may be driving the polymorphism in Pyricularia, including potential adaptive advantages from Adaptive Telomere Failure.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Gaorui Gong, Yang Xiong, Shijun Xiao, Xi-Yin Li, Peipei Huang, Qian Liao, Qingqing Han, Qiaohong Lin, Cheng Dan, Li Zhou, Fan Ren, Qi Zhou, Jian-Fang Gui, Jie Mei
Summary: We assembled highly homomorphic Y and X chromosomes in yellow catfish and discovered that the Y chromosome is at an early stage of differentiation with no clear evidence of evolutionary strata and recombination suppression. The accumulation of sex-antagonistic mutations and repetitive elements in the sex-determining region suggests their role in recombination suppression between young X and Y chromosomes. Additionally, we found distinct chromatin organizations and nuclear spatial organization in the YY supermales and XX females, indicating chromatin remodeling after sex reversal.
NATIONAL SCIENCE REVIEW
(2023)
Article
Genetics & Heredity
Karen H. Miga, Evan E. Eichler
Summary: Advances in long-read sequencing and assembly allow labs to generate phased genomes that are more accurate and contiguous than the original human reference genome. Complete genome assemblies will become standard in human genetics, even in clinical settings, due to advancements in technology and computational processing.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Microbiology
Mathieu Quenu, Artemis D. Treindl, Kate Lee, Daigo Takemoto, Torsten Thuenen, Samad Ashrafi, David Winter, Austen R. D. Ganley, Adrian Leuchtmann, Carolyn A. Young, Murray P. Cox
Summary: Genome rearrangements are common in filamentous fungi, but little is known about their evolution. In this study, we compared 15 complete genomes of the filamentous fungus genus Epichloe and found that the distinction between gene-rich and repeat-rich regions observed in isolated species is widespread across the Epichloe genus. Despite having the same number of nuclear chromosomes, the genomes of Epichloe species show low synteny and substantial rearrangement of gene content. These rearrangements are lineage-dependent and occur over short evolutionary distances with long periods of structural stability.
Article
Microbiology
Samuel S. Porter, Jennifer C. Liddle, Kristen Browne, Diana Pastrana, Benjamin A. Garcia, Christopher B. Buck, Matthew D. Weitzman, Alison A. McBride
Summary: Papillomaviruses package their genomes with host histones into virions, with specific histone modifications being acquired late in infection that benefit viral replication and gene expression. The viral minichromosome is enriched in posttranslational modifications associated with active chromatin, potentially aiding in evasion of detection and promoting early infection stages.
Review
Biochemistry & Molecular Biology
Sandra Nitsch, Lara Zorro Shahidian, Robert Schneider
Summary: Post-translational modifications of histone proteins can alter chromatin architecture and gene expression. Cellular metabolites can affect histone acylations, linking cell metabolism with chromatin structure and cellular adaptation. However, technical challenges currently hinder a full understanding of the impact of these modifications on chromatin dynamics.
Article
Multidisciplinary Sciences
Kenneth Wu, Namrita Dhillon, Kelvin Du, Rohinton T. Kamakaka
Summary: Gene silencing in budding yeast is maintained by unacetylated nucleosomes and requires 50% to 75% acetylation for activation. The Sir4 gene is a key component in maintaining gene silencing, with even a two-fold reduction in acetyltransferases potentially leading to transcriptional silence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Lucia Lopez-Gil, Amparo Pascual-Ahuir, Markus Proft
Summary: This scientific review highlights the central importance of genomic instability in the aging process and explores the cellular and molecular changes associated with aging, as well as the genetic and epigenetic alterations that contribute to genomic instability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Foyez Shams, Darryl D'Souza, Tariq Ezaz
Summary: In a study conducted on a representative sample of 94 boars from a commercial nucleus herd in Australia, it was found that 6.38% of the samples had novel chromosome rearrangements associated with hypoprolificacy. These rearrangements, including a previously detected translocation between chromosomes 3 and 16, were identified through standard and molecular cytogenetic analyses. Further research and routine monitoring will be essential to prevent the propagation of reciprocal translocations in the Australian pig population.
Article
Cell Biology
Paul B. Talbert, Steven Henikoff
Summary: Eukaryotic nucleosomes are organized by histones, with common histones deposited during S-phase and histone variants available throughout the cell cycle. Variants alter nucleosome structure and function, playing specialized roles in DNA repair, chromosome segregation, and transcriptional regulation.
JOURNAL OF CELL SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Ivaylo Nikolov, Angela Taddei
Article
Cell Biology
Nathanael Hoze, Myriam Ruault, Carlo Amoruso, Angela Taddei, David Holcman
MOLECULAR BIOLOGY OF THE CELL
(2013)
Article
Biochemistry & Molecular Biology
Antoine Hocher, Myriam Ruault, Petra Kaferle, Marc Descrimes, Mickael Garnier, Antonin Morillon, Angela Taddei
Review
Cell Biology
Judith Mine-Hattab, Angela Taddei
CURRENT OPINION IN CELL BIOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Myriam Ruault, Vittore F. Scolari, Luciana Lazar-Stefanita, Antoine Hocher, Isabelle Loiodice, Romain Koszul, Angela Taddei
Summary: The study reveals that in budding yeast, telomere clustering is functionally linked to heterochromatin formation, with Sir3 directly promoting long-range contacts between distant regions. Additionally, Sir3 is shown to promote rDNA compaction independently of its known partners, suggesting it acts as a molecular bridge stabilizing long-range interactions.
Article
Biology
Judith Mine-Hattab, Mathias Heltberg, Marie Villemeur, Chloe Guedj, Thierry Mora, Aleksandra M. Walczak, Maxime Dahan, Angela Taddei
Summary: In response to double strand breaks, repair proteins accumulate at damaged sites, forming membrane-less sub-compartments or foci. Rad52 molecules freely diffuse within repair foci while Rfa1 molecules bind to ssDNA, suggesting the existence of a liquid droplet structure around damaged DNA.
Article
Biochemistry & Molecular Biology
Ophelie Lautier, Arianna Penzo, Jerome O. Rouviere, Guillaume Chevreux, Louis Collet, Isabelle Loiodice, Angela Taddei, Frederic Devaux, Martine A. Collart, Benoit Palancade
Summary: The research reveals that the formation of the nuclear pore complex involves co-translational events in the cytoplasm and nucleus. Different NPC subunits establish binary interactions during translation. Localized translation ensures the proper delivery of proteins to the pore and the nucleus.
Article
Biology
Mathias L. Heltberg, Judith Mine-Hattab, Angela Taddei, Aleksandra M. Walczak, Thierry Mora
Summary: A theoretical framework is proposed to differentiate between different mechanisms of protein foci formation, with experimental validation. The multiple binding site model is rejected for a specific protein in favor of a liquid-liquid phase separation model. These results have implications for future experiments and suggest varying biological roles for liquid droplet and binding site foci.
Article
Cell Biology
Isabelle Loiodice, Mickael Garnier, Ivaylo Nikolov, Angela Taddei
Summary: Silent chromatin in eukaryotic cells is mainly located at the nuclear periphery, and the establishment of silencing is a stepwise process occurring over several cell cycles. Studying a budding yeast model, researchers have identified mechanisms and protein recruitment relationships during the process of establishing silencing at an ectopic locus.
Correction
Biochemistry & Molecular Biology
Siyu Liu, Judith Mine-Hattab, Marie Villemeur, Raphael Guerois, Henrik Dahl Pinholt, Leonid A. Mirny, Angela Taddei
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Siyu Liu, Judith Mine-Hattab, Marie Villemeur, Raphael Guerois, Henrik Dahl Pinholt, Leonid A. Mirny, Angela Taddei
Summary: Homologous recombination (HR) is a major pathway for DNA double-strand break repair. Rad51-single-stranded DNA nucleoprotein filaments (NPFs) play a crucial role in the homology search process. In this study, the authors develop and characterize a functional tagged version of Rad51, allowing for dynamic, in vivo studies of NPF formation. They observe that the NPFs exhibit flexibility and adopt various shapes in vivo, shedding new light on the function of Rad54 and Srs2. The formation of extended filaments and their compaction-extension dynamics provide an efficient search strategy for homologous sequences.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Amandine Batte, Clementine Brocas, Helene Bordelet, Antoine Hocher, Myriam Ruault, Adouda Adjiri, Angela Taddei, Karine Dubrana
Article
Biotechnology & Applied Microbiology
Micol Guidi, Myriam Ruault, Martial Marbouty, Isabelle Loiodice, Axel Cournac, Cyrille Billaudeau, Antoine Hocher, Julien Mozziconacci, Romain Koszul, Angela Taddei
Meeting Abstract
Biochemistry & Molecular Biology
A. Batte, C. Brocas, A. Hocher, M. Ruault, A. Taddei, K. Dubrana