Article
Biology
Caroline Belser, Franc-Christophe Baurens, Benjamin Noel, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hribova, Jaroslav Dolezel, Arnaud Lemainque, Patrick Wincker, Angelique D'Hont, Jean-Marc Aury
Summary: A chromosome-scale assembly of a banana genome (Musa acuminata) was reported using Oxford Nanopore long-reads, with five out of the eleven chromosomes entirely reconstructed in a single contig from telomere to telomere, revealing the content of complex regions like centromeres or clusters of paralogous genes for the first time.
COMMUNICATIONS BIOLOGY
(2021)
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)
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.
Article
Multidisciplinary Sciences
Chia-Yu Guh, Hong-Jhih Shen, Liv WeiChien Chen, Pei-Chen Chiu, I-Hsin Liao, Chen-Chia Lo, Yunfei Chen, Yu-Hung Hsieh, Ting-Chia Chang, Chien-Ping Yen, Yi-Yun Chen, Tom Wei-Wu Chen, Liuh-Yow Chen, Ching-Shyi Wu, Jean-Marc Egly, Hsueh-Ping Catherine Chu
Summary: This study investigates the role of Telomeric Repeat-Containing RNA (TERRA) in the Alternative Lengthening of Telomeres (ALT) mechanism. The depletion of TERRA has been shown to reduce ALT-associated PML bodies, telomere clustering, and telomere lengthening. TERRA interacts with DNA repair proteins, particularly the endonuclease XPF, to activate the DNA damage response (DDR) and induce break-induced telomere synthesis and lengthening. These findings reveal the mechanisms underlying the initiation and maintenance of ALT.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Maria Sol Jacome Burbano, Jerome D. Robin, Serge Bauwens, Marjorie Martin, Emma Donati, Lucia Martinez, Peipei Lin, Sabrina Sacconi, Frederique Magdinier, Eric Gilson
Summary: TRF2 and FOXO3a play important roles in regulating skeletal muscle aging. Loss of TRF2 leads to oxidative stress, which triggers FOXO3a binding to telomeres and protects against ATM activation.
COMMUNICATIONS BIOLOGY
(2023)
Article
Genetics & Heredity
Yichen Tao, Chengpeng He, Deng Lin, Zhenglong Gu, Weilin Pu
Summary: This study identifies and explores the impacts of mitochondrial pseudogenes (NUMTs) in human reference genomes. Using the human pan-mitogenome, the authors discovered additional NUMTs and previously un-assembled NUMTs in the reference genome. They also found mtDNA-like short segments in the nuclear genome, which should be avoided in certain detection methods. Furthermore, the study concludes that NUMTs have minimal impact on bulk ATAC-seq.
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
Oncology
Adar Yaacov, Oriya Vardi, Britny Blumenfeld, Avraham Greenberg, Dashiell J. Massey, Amnon Koren, Sheera Adar, Itamar Simon, Shai Rosenberg
Summary: This study systematically analyzed the mutational landscape of tumors and identified the association between mutational processes and replication timing. A novel method was developed to improve understanding of the etiology of mutational signatures.
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.
Review
Biochemistry & Molecular Biology
Eugene Shakirov, Julian J-L Chen, Dorothy E. Shippen
Summary: This review summarizes the recent advances in plant telomere biology and compares it to telomere and telomerase research in other eukaryotic lineages. Despite the divergence between plants and animals over a billion years ago, the knowledge gained from plants has continued to contribute to the understanding of telomere biology and its implications for human health, aging, and stress responses. Studies of plant telomeres have revealed unexpected divergence in telomere sequence and architecture, and have provided new insights into the evolution and core components of telomerase across major eukaryotic kingdoms. Additionally, the cataloging of natural variation in plants like Arabidopsis thaliana and maize has provided valuable information on the genetic networks governing telomere length and its interactions with environmental factors and plant physiology.
Article
Biology
Alexander N. Malyavko, Olga A. Petrova, Maria Zvereva, Vladimir Polshakov, Olga A. Dontsova
Summary: This study reports the functional characterization of the Rif1 homologue from the methylotrophic thermotolerant budding yeast Hansenula polymorpha DL-1. The study reveals that Rif1 in H. polymorpha suppresses telomerase-dependent telomere elongation through direct DNA binding and association with the Ku heterodimer. It is also found that Rif1 binds Stn1 and promotes its accumulation at telomeres in H. polymorpha.
Article
Biochemistry & Molecular Biology
Samantha L. Sholes, Kayarash Karimian, Ariel Gershman, Thomas J. Kelly, Winston Timp, Carol W. Greider
Summary: We developed a method to tag and measure telomere length in yeast using nanopore sequencing. We observed stable chromosome-specific telomere lengths and examined the role of RIF1 and TEL1 in telomere length regulation. The study suggests the influence of Y ' elements on telomere length regulation and provides insights into possible new biological mechanisms.
Article
Multidisciplinary Sciences
Daniel J. Giguere, Alexander T. Bahcheli, Samuel S. Slattery, Rushali R. Patel, Tyler S. Browne, Martin Flatley, Bogumil J. Karas, David R. Edgell, Gregory B. Gloor
Summary: Phaeodactylum tricornutum, a marine diatom, has a new telomere-to-telomere genome assembly generated using Oxford Nanopore long reads. The study identified 25 nuclear chromosomes and corrected assembly errors, providing new insights for genetic engineering and synthetic biology applications.
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
Cell Biology
Jonathan Barroso-Gonzalez, Laura Garcia-Exposito, Pablo Galaviz, Michelle Lee Lynskey, Joshua A. M. Allen, SongMy Hoang, Simon C. Watkins, Hilda A. Pickett, Roderick J. O'Sullivan
Summary: Alternative lengthening of telomeres (ALT) is a telomere-elongation mechanism observed in 15% of cancer subtypes. Disruption of the MutSa DNA mismatch repair complex leads to striking telomere hyperextension in ALT cells. MutSa is specifically recruited to telomeres in ALT cells by associating with the PCNA subunit of the replisome, counteracting the role of BLM helicase in stabilizing hyper-extended telomeres and maintaining the survival of MutSa-deficient ALT cancer cells.
Article
Hematology
Marwan Kwok, Ceri Oldreive, Andy C. Rawstron, Anshita Goel, Grigorios Papatzikas, Rhiannon E. Jones, Samantha Drennan, Angelo Agathanggelou, Archana Sharma-Oates, Paul Evans, Edward Smith, Surita Dalal, Jingwen Mao, Robert Hollows, Naheema Gordon, Mayumi Hamada, Nicholas J. Davies, Helen Parry, Andrew D. Beggs, Talha Munir, Paul Moreton, Shankara Paneesha, Guy Pratt, A. Malcolm R. Taylor, Francesco Forconi, Duncan M. Baird, Jean-Baptiste Cazier, Paul Moss, Peter Hillmen, Tatjana Stankovic
Editorial Material
Cell Biology
Lea Harrington, Duncan M. Baird
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2020)
Review
Genetics & Heredity
Kez Cleal, Duncan M. Baird
TRENDS IN GENETICS
(2020)
Article
Immunology
Giovanni Galletti, Gabriele De Simone, Emilia M. C. Mazza, Simone Puccio, Claudia Mezzanotte, Timothy M. Bi, Alexey N. Davydov, Maria Metsger, Eloise Scamardella, Giorgia Alvisi, Federica De Paoli, Veronica Zanon, Alice Scarpa, Barbara Camisa, Federico S. Colombo, Achille Anselmo, Clelia Peano, Sara Polletti, Domenico Mavilio, Luca Gattinoni, Shannon K. Boi, Benjamin A. Youngblood, Rhiannon E. Jones, Duncan M. Baird, Emma Gostick, Sian Llewellyn-Lacey, Kristin Ladell, David A. Price, Dmitriy M. Chudakov, Evan W. Newell, Monica Casucci, Enrico Lugli
Article
Biochemistry & Molecular Biology
Meera Adishesh, Rafah Alnafakh, Duncan M. Baird, Rhiannon E. Jones, Shannon Simon, Lucy Button, Areege M. Kamal, John Kirwan, S. Bridget DeCruze, Josephine Drury, Gabriele Saretzki, Dharani K. Hapangama
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Cell Biology
Raya Ahmed, Kelly L. Miners, Julio Lahoz-Beneytez, Rhiannon E. Jones, Laureline Roger, Christina Baboonian, Yan Zhang, Eddie C. Y. Wang, Marc K. Hellerstein, Joseph M. McCune, Duncan M. Baird, David A. Price, Derek C. Macallan, Becca Asquith, Kristin Ladell
Article
Genetics & Heredity
Kevin Norris, Amanda J. Walne, Mark J. Ponsford, Kez Cleal, Julia W. Grimstead, Alicia Ellison, Jenna Alnajar, Inderjeet Dokal, Tom Vulliamy, Duncan M. Baird
Summary: Telomere biology disorders are complex clinical conditions caused by mutations in genes related to telomere maintenance. High-throughput STELA (HT-STELA) has been shown to accurately measure telomere lengths in unaffected individuals and mutation carriers, providing important diagnostic and prognostic information for telomeropathies.
Article
Biochemistry & Molecular Biology
Isabel Garcia-Martin, Richard J. A. Penketh, Samantha M. Garay, Rhiannon E. Jones, Julia W. Grimstead, Duncan M. Baird, Rosalind M. John
Summary: The study found that prenatal depression symptoms were negatively associated with telomere length in female placenta, indicating accelerated aging. There was no significant association between maternal depression symptoms and telomere length in male placenta, nor was there an association with anxiety symptoms for either sex.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Letter
Oncology
Andrea G. S. Pepper, Antonella Zucchetto, Kevin Norris, Erika Tissino, Jerry Polesel, Zarni Soe, David Allsup, Anna Hockaday, Pei Loo Ow, Peter Hillmen, Andrew Rawstron, Daniel Catovsky, Pietro Bulian, Riccardo Bomben, Duncan M. Baird, Christopher D. Fegan, Valter Gattei, Chris Pepper
Article
Multidisciplinary Sciences
Greg H. P. Ngo, Julia W. Grimstead, Duncan M. Baird
Summary: DNA-RNA hybrid structures have been found near DNA double-strand breaks within transcriptional active regions of the genome, affecting the repair of these breaks. R loops, containing DNA-RNA hybrids and displaced ssDNA, can form at sub-telomeric DSBs independently of DNA resection and are induced alongside two-stranded DNA-RNA hybrids that form on ssDNA generated by DNA resection. UPF1, an RNA/DNA helicase, is identified as a crucial factor driving the formation of R loops and DNA-RNA hybrids to stimulate DNA repair processes.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Kez Cleal, Duncan M. Baird
Summary: Structural variation (SV) is important in genome evolution and disease, and Dysgu is a tool that accurately detects SVs using paired-end or long-read sequencing, with high sensitivity and fast running speed.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Helene E. B. Geiller, Adam Harvey, Rhiannon E. Jones, Julia W. Grimstead, Kez Cleal, Eric A. Hendrickson, Duncan M. Baird
Summary: Telomerase activity is the main telomere maintenance mechanism in human cancers, but 15% of cancers use a recombination-based mechanism called ALT. Loss of ATRX gene and telomere dysfunction during crisis can initiate the ALT pathway and confer replicative immortality to cells.
Article
Biochemistry & Molecular Biology
Kate Liddiard, Alys N. Aston-Evans, Kez Cleal, Eric A. Hendrickson, Duncan M. Baird
Summary: DNA polymerase theta (POLQ) is a key enzyme involved in the repair of DNA double-strand breaks. Research has shown that cells lacking POLQ are resistant to growth deceleration during telomere-driven crisis, and exhibit longer telomeres and increased genetic heterogeneity.
Article
Biochemistry & Molecular Biology
Kate Liddiard, Julia W. Grimstead, Kez Cleal, Anna Evans, Duncan M. Baird
Summary: Investigating telomere-driven crisis in human fibroblast lines revealed genomic rearrangements and transcriptome developments during the transition from dynamic proliferation into replicative crisis, suggesting changes in DNA repair capacity and telomere fusion patterns may be associated with crisis progression.
Article
Multidisciplinary Sciences
Els Mansell, Nahid Zareian, Camille Malouf, Chrysa Kapeni, Natalie Brown, Christophe Badie, Duncan Baird, Jon Lane, Katrin Ottersbach, Allison Blair, C. Patrick Case
SCIENTIFIC REPORTS
(2019)
