Article
Agriculture, Dairy & Animal Science
Artem Lisachov, Alexander Rumyantsev, Dmitry Prokopov, Malcolm Ferguson-Smith, Vladimir Trifonov
Summary: In this study, we describe the satellite DNA families found in two snake species from different families. Contrary to common belief, we found high conservation of these satellites in terms of nucleotide sequences and chromosomal localizations. Satellite DNA sequences make up a large portion of animal genomes, and they are typically located in heterochromatin clusters near centromeres or telomeres. The function of these clusters is to maintain chromosome and nuclear structure, and regulate chromosome behavior during cell division. Understanding satellite DNA diversity is important for studying sex chromosome evolution, hybridization, and speciation. Through our research, we identified four satellite DNA families in two snake species and determined their chromosomal localization. We found that one family is localized in the centromeres of both species, while the others form clusters on specific chromosomes or subsets of chromosomes. Our results demonstrate the high conservation of satellite DNA in snakes and support the library model of satellite DNA evolution.
Article
Cell Biology
Hazel Mangan, Brian McStay
Summary: The distribution of ribosomal gene arrays from multiple chromosomal nucleolar organizers within human nucleoli is not fully understood. By genetically manipulating individual NORs, customized functional ribosomes can be efficiently produced. Ribosome biogenesis is shown to occur within constrained territories, tethered to individual NORs inside the nucleolus.
GENES & DEVELOPMENT
(2021)
Review
Cell Biology
Monika Cechova, Karen H. Miga
Summary: This review focuses on the biology of satellite DNA on human X and Y chromosomes and its impact on sex chromosome aneuploidies. The findings provide insights into the prevalence and consequences of these aneuploidies.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yi-Tzu Kuo, Amanda Souza Camara, Veit Schubert, Pavel Neumann, Jiri Macas, Michael Melzer, Jianyong Chen, Jorg Fuchs, Simone Abel, Evelyn Klocke, Bruno Huettel, Axel Himmelbach, Dmitri Demidov, Frank Dunemann, Martin Mascher, Takayoshi Ishii, Andre Marques, Andreas Houben
Summary: This study reveals the holocentric characteristics of the lilioid plant Chionographis japonica, showing that its centromeres consist of evenly spaced units and differ from other known holocentric species. The study also finds that C. japonica forms clustered centromeres similar to monocentric species, but the large-scale chromatin arrangement is different. The formation of holocentromeres from interphase centromere clusters was simulated using polymer simulations.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Giuliana Giannuzzi, Glennis A. Logsdon, Nicolas Chatron, Danny E. Miller, Julie Reversat, Katherine M. Munson, Kendra Hoekzema, Marie-Noelle Bonnet-Dupeyron, Pierre-Antoine Rollat-Farnier, Carl A. Baker, Damien Sanlaville, Evan E. Eichler, Caroline Schluth-Bolard, Alexandre Reymond
Summary: This study identified a rare new class of structural variation, named alpha satellite insertion, which sheds light on the dynamics of alpha satellite DNA and suggests the possibility that alpha satellite arrays can relocate near vestigial centromeric sites.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Cell Biology
Kousik Sundararajan, Aaron F. Straight
Summary: Eukaryotes segregate their chromosomes during mitosis and meiosis by attaching them to the microtubules of the spindle using centromeres, with CENP-A playing a crucial role in centromere organization. Understanding and correcting errors in CENP-A organization is important for proper chromosome segregation during cell division.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Camila do Nascimento Moreira, Adauto Lima Cardoso, Mirela Pelizaro Valeri, Karen Ventura, Malcolm Andrew Ferguson-Smith, Yatiyo Yonenaga-Yassuda, Marta Svartman, Cesar Martins
Summary: Repetitive DNA, including SatDNA and transposable elements, is a common and significant component of eukaryotic genomes. This study focuses on Holochilus nanus and other species of Oryzomyini to examine the composition and role of repetitive DNA in chromosomal diversification. Through bioinformatic, cytogenetic, and molecular techniques, the study reveals the presence of Long Terminal Repeats, Short Interspersed Nuclear Elements, and Long Interspersed Nuclear Elements in the genome of HNA.
MOLECULAR GENETICS AND GENOMICS
(2023)
Article
Plant Sciences
Pavel Neumann, Ludmila Oliveira, Jana Cizkova, Tae-Soo Jang, Sonja Klemme, Petr Novak, Katarzyna Stelmach, Andrea Koblizkova, Jaroslav Dolezel, Jiri Macas
Summary: The parasitic genus Cuscuta stands out for its unique centromere organization and genome size variations among plants. Monocentric Cuscuta species show a remarkable 102-fold variation in genome sizes, while holocentric species have more moderate sizes. The transition to holocentric chromosomes in Cuscuta is associated with changes in epigenetic marks, chromosome number, and repetitive DNA sequence composition.
Article
Biochemistry & Molecular Biology
Marlena Cichocka, Anna Karlik, Patrycja Plewka, Kishor Gawade, Agata Stepien, Patrycja Swiergiel, Ankur Gadgil, Katarzyna Dorota Raczynska
Summary: hnRNP UL1 plays multiple important roles in the cell nucleus, including involvement in DNA double-strand break repair, stimulation of ribosomal DNA gene transcription, and interaction with various related proteins.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Francesca M. M. Piras, Eleonora Cappelletti, Wasma A. A. Abdelgadir, Giulio Salamon, Simone Vignati, Marco Santagostino, Lorenzo Sola, Solomon G. G. Nergadze, Elena Giulotto
Summary: In mammals, centromeres are determined by CENP-A and satellite DNA. We found a satellite-free centromere on chromosome 11 (ECA11) in horses and similar cases in other Equus species. These satellite-free centromeres arose through centromere repositioning and/or chromosomal fusion after inactivation of the ancestral centromere, while maintaining blocks of satellite sequences in many cases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Francesca M. Piras, Eleonora Cappelletti, Marco Santagostino, Solomon G. Nergadze, Elena Giulotto, Elena Raimondi
Summary: The centromere is a crucial locus for proper chromosome segregation. Although its function is conserved and epigenetically regulated, centromeric DNA sequences are composed of rapidly evolving satellite DNA. The recent discovery of functional satellite-free centromeres in certain animal and plant species has provided new insights into the epigenetic nature of centromeres and their evolutionary requirements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
Glennis A. Logsdon, Evan E. Eichler
Summary: The complete sequence of a human genome has provided a comprehensive view of satellite DNA organization associated with heterochromatin. The understanding of human centromeric DNA's genetic architecture and epigenetic properties has advanced as a result. Preliminary studies of human and nonhuman ape centromeres reveal complex mutational changes organized around evolutionary layers, providing new insights into centromeric function and its implications for human biology and health.
Article
Biochemistry & Molecular Biology
Rodrigo E. Caceres-Gutierrez, Marco A. Andonegui, Diego A. Oliva-Rico, Rodrigo Gonzalez-Barrios, Fernando Luna, Cristian Arriaga-Canon, Alejandro Lopez-Saavedra, Diddier Prada, Clementina Castro, Laurent Parmentier, Jose Diaz-Chavez, Yair Alfaro-Mora, Erick Navarro-Delgado, Eunice Fabian-Morales, Bao Tran, Jyoti Shetty, Yongmei Zhao, Nicolas Alcaraz, Carlos De la Rosa, Jose L. Reyes, Sabrine Hedouin, Florent Hube, Claire Francastel, Luis A. Herrera
Summary: The study reveals that proteasome inhibition leads to upregulation of repetitive RNAs, particularly affecting alpha-Satellite RNAs in cancer cells. The results show fluctuation of alpha-Satellite RNAs along the cell cycle and their interaction with members of the cohesin ring, suggesting a role in mitotic progression regulation.
Article
Environmental Sciences
Jianlin Lou, Shoukai Yu, Lingfang Feng, Xinnian Guo, Meng Wang, Alan T. Branco, Tao Li, Bernardo Lemos
Summary: Exposure to hexavalent chromium induces instability in the rDNA of human cells, leading to rapid amplification and contraction of the array. Environmental exposure and drinking habits, but not age, influence the natural variation in rDNA copy number in human populations exposed to Cr (VI).
ENVIRONMENT INTERNATIONAL
(2021)
Article
Cell Biology
Kezia Catharina Oxe, Dorthe Helena Larsen
Summary: Treacle/TCOF1 is an adaptor protein associated with nucleolar chromatin, playing important roles in promoting ribosome biogenesis and maintaining genome stability. Its involvement in cancer raises questions about its role in cancer development. On one hand, overexpression of Treacle may confer growth advantages to cancer cells, while on the other hand, its function as a gatekeeper in nucleolar DNA damage response may lead to mutations impairing its function.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Kuo-Ming Lee, Chi-Jene Chen, Shin-Ru Shih
TRENDS IN MICROBIOLOGY
(2017)
Article
Immunology
Kuo-Ming Lee, Yu-Nong Gong, Tzu-Hsuan Hsieh, Andrew Woodman, Nynke H. Dekker, Craig E. Cameron, Shin-Ru Shih
EMERGING MICROBES & INFECTIONS
(2018)
Article
Multidisciplinary Sciences
Chih-Chan Lee, Jiunn-Chang Lin, Wei-Lun Hwang, Ying-Ju Kuo, Hung-Kai Chen, Shyh-Kuan Tai, Chun-Chi Lin, Muh-Hwa Yang
NATURE COMMUNICATIONS
(2018)
Article
Virology
Andrew Woodman, Kuo-Ming Lee, Richard Janissen, Yu-Nong Gong, Nynke H. Dekker, Shin-Ru Shih, Craig E. Cameron
JOURNAL OF VIROLOGY
(2019)
Article
Biochemical Research Methods
Kuo-Ming Lee, Yu-Nong Gong, Shin-Ru Shih
Article
Biochemistry & Molecular Biology
Kuo-Ming Lee, Chih-Ching Wu, Shang-En Wu, Ya-Han Lin, Li-Ting Wang, Chun-Ru Chang, Peng-Nien Huang, Shin-Ru Shih, Rei-Lin Kuo
Article
Cell Biology
Yoyo Chih-Yun Yu, Tony Z. K. Hui, Tzu-Hao Kao, Hung-Fu Liao, Chih-Yi Yang, Chia-Chun Hou, Hsin-Ting Hsieh, Jen-Yun Chang, Yi-Tzang Tsai, Marina Pinskaya, Kai-Chien Yang, Yet-Ran Chen, Antonin Morillon, Mong-Hsun Tsai, Shau-Ping Lin
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2020)
Article
Microbiology
Chung-Guei Huang, Kuo-Ming Lee, Mei-Jen Hsiao, Shu-Li Yang, Peng-Nien Huang, Yu-Nong Gong, Tzu-Hsuan Hsieh, Po-Wei Huang, Ya-Jhu Lin, Yi-Chun Liu, Kuo-Chien Tsao, Shin-Ru Shih
JOURNAL OF CLINICAL MICROBIOLOGY
(2020)
Article
Cell Biology
Chih-Yi Yang, Rita Jui-Hsien Lu, Ming-Kang Lee, Felix Shih-Hsian Hsiao, Ya-Ping Yen, Chun-Chun Cheng, Pu-Sheng Hsu, Yi-Tzang Tsai, Shih-Kuo Chen, I-Hsuan Liu, Pao-Yang Chen, Shau-Ping Lin
Summary: MSCs lacking DNMT3L exhibit reduced colony forming ability and impaired osteogenesis in vitro, with differentially regulated genes associated with bone morphology-related phenotypes. The observed defects are hypothesized to result from pre-deposited epigenetic signatures from DNMT3L-expressing progenitors, rather than a direct effect of missing DNMT3L in MSCs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Sheng-Yu Huang, Yu-An Kung, Peng-Nien Huang, Sheng-Yun Chang, Yu-Nong Gong, Yi-Ju Han, Huan-Jung Chiang, Kuan-Ting Liu, Kuo-Ming Lee, Chia-Yu Chang, Chia-Ching Chang, Chung-Guei Huang, Shin-Ru Shih
Summary: The study reveals that SARS-CoV-2 remains stable and infectious after refrigeration or freezing, with stability and infectivity depending on the spike variant. The S-G614 variant shows higher stability and better binding ability with the ACE2 receptor, contributing to its rapid spread and infectivity. Further precautions should be taken when handling food stored in cold conditions.
Article
Cell Biology
Mu-Hui Wang, Chia-Lang Hsu, Cheng-Han Wu, Ling-Ling Chiou, Yi-Tzang Tsai, Hsuan-Shu Lee, Shau-Ping Lin
Summary: The study found that nerve-mediated repressive epigenetic modulator HDAC1 expression regulates gene expression at different time points during axolotl limb regeneration, affecting the regeneration process. HDAC1 activity is required to inhibit the premature elevation of genes related to tissue development, differentiation, and morphogenesis. WNT pathway-associated genes are also prematurely activated under HDAC1 inhibition.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Microbiology
Yu-An Kung, Kuo-Ming Lee, Huan-Jung Chiang, Sheng-Yu Huang, Chung-Jung Wu, Shin-Ru Shih
Summary: This review discusses the molecular mechanisms of SARS-CoV-2 and related coronaviruses, with a focus on host factors or pathways identified through genome-wide CRISPR screening that can be targeted for the development of effective antiviral agents.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2022)
Article
Immunology
Guan-Hong Wu, Kuo-Ming Lee, Chia-Yu Kao, Shin-Ru Shih
Summary: The role of the internal ribosome entry site (IRES) in determining the neurovirulence of enteroviruses EV-A71 and CV-A16 was characterized using an oral inoculation model. Replacing EV-A71 IRES with CV-A16 abolished neuropathological phenotypes, indicating that IRES determines the neurotropic potential of these viruses. Tissue-specific replication can be reflected in cell-based characterization.
MICROBES AND INFECTION
(2023)
Review
Cell Biology
Pu-Sheng Hsu, Shu-Han Yu, Yi-Tzang Tsai, Jen-Yun Chang, Li-Kuang Tsai, Chih-Hung Ye, Ning-Yu Song, Lih-Chiao Yau, Shau-Ping Lin
Summary: TEs are a major portion of genomic sequences in plants and animals, and can disrupt coding genes and regulatory sequences to cause disease. Host cells have evolved mechanisms to mitigate this disruption, and TE associated sequences can attract epigenetic modifiers to induce alterations. Additionally, endogenous TEs play physiological roles in gene regulation and modulating the host cell transcriptome, and advances in sequencing technologies have enabled the study of TEs despite their repetitive nature.
JOURNAL OF BIOMEDICAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Tzu-Wei Chuang, Chia-Chen Lu, Chun-Hao Su, Pei-Yu Wu, Sarasvathi Easwvaran, Chi-Chieh Lee, Hung-Che Kuo, Kuan-Yang Hung, Kuo-Ming Lee, Ching-Yen Tsai, Woan-Yuh Tarn