Article
Biochemistry & Molecular Biology
Muhammad Azhar, Caoling Xu, Xue Jiang, Wenqing Li, Yuzhu Cao, Xiaoli Zhu, Xuemei Xing, Limin Wu, Jiaqi Zou, Lan Meng, Yu Cheng, Wenjie Han, Jianqiang Bao
Summary: This study reveals the crucial role of Prmt1 in the establishment and maintenance of spermatogonia, and its regulation of transcriptional homeostasis. The enrichment of Prmt1-deposited H4R3me2a mark in mouse spermatogonia has a significant impact on the transcriptomic landscape and alternative splicing pattern.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Rui Yan, Xin Cheng, Chan Gu, Yanhong Xu, Xin Long, Jinglei Zhai, Fengyuan Sun, Jingjing Qian, Yarui Du, Hongmei Wang, Fan Guo
Summary: This study characterizes the presence of DNA 5-hydroxymethylcytosine (5hmC) in mouse early embryos and germ cells and explores its relationship with DNA methylation reprogramming. It was found that 5hmC is most strongly correlated with DNA demethylation and is targeted to specific de novo methylated sites. The generation of 5hmC is also dependent on DNA replication, especially in the female pronucleus. Aberrant nuclear localization of Dnmt1/Uhrf1 in mouse zygotes due to maternal deficiency of Nlrp14 led to defects in DNA replication-coupled passive demethylation and impaired 5hmC deposition.
Article
Developmental Biology
Brandon S. Carpenter, Teresa W. Lee, Caroline F. Plott, Juan D. Rodriguez, Jovan S. Brockett, Dexter A. Myrick, David J. Katz
Summary: The study demonstrates that in Caenorhabditis elegans, MES-4 protects key germline genes by preventing reprogramming, thus avoiding developmental delays.
Article
Multidisciplinary Sciences
Mirunalini Ravichandran, Dominik Rafalski, Claudia I. Davies, Oscar Ortega-Recalde, Xinsheng Nan, Cassandra R. Glanfield, Annika Kotter, Katarzyna Misztal, Andrew H. Wang, Marek Wojciechowski, Michal Razew, Issam M. Mayyas, Olga Kardailsky, Uwe Schwartz, Krzysztof Zembrzycki, Ian M. Morison, Mark Helm, Dieter Weichenhan, Renata Z. Jurkowska, Felix Krueger, Christoph Plass, Martin Zacharias, Matthias Bochtler, Timothy A. Hore, Tomasz P. Jurkowski
Summary: TET enzymes catalyze the oxidation of 5-methylcytosine bases in DNA and have a strong preference for CGs embedded within transcription factor-binding sites. This preference is determined by intrasubstrate interactions and the flanking CG sequence. The study of TET sequence preferences is physiologically relevant and helps explain the process of DNA demethylation. The most and least favorable TET motifs represent DNA sites bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), shedding light on the function of TET in transcriptional responses and pluripotency support.
Article
Biochemistry & Molecular Biology
Tom Mattimoe, Bernhard Payer
Summary: This article provides an overview of the complex dynamics of X-chromosome dosage control in female mammals and explores its potential role in normal germline competency.
BIOCHEMICAL JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Shengbo He, Xiaoqi Feng
Summary: DNA methylation plays crucial regulatory roles in the development of animals and plants. Recent studies using whole-genome sequencing, cell isolation techniques, and bioinformatics tools have revealed the dynamic changes of DNA methylation during plant germline development, and discovered functional methylation reprogramming events.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Cell Biology
Yingying Meng, Guliang Wang, Hongjuan He, Kin H. Lau, Allison Hurt, Brianna J. Bixler, Andrea Parham, Seung-Gi Jin, Xingzhi Xu, Karen M. Vasquez, Gerd P. Pfeifer, Piroska E. Szabo
Summary: A biological process that erases Z-DNA specifically in germ cells of the mouse male foetus has been discovered, which is mediated by a previously uncharacterized zinc finger protein, ZBTB43. This process prevents DNA double-strand breaks and promotes de novo DNA methylation, ensuring genomic and epigenomic integrity.
NATURE CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Filipe Borges, Mark T. A. Donoghue, Chantal LeBlanc, Emily E. Wear, Milos Tanurdzic, Benjamin Berube, Ashley Brooks, William F. Thompson, Linda Hanley-Bowdoin, Robert A. Martienssen
Summary: The research found that symmetric mCG and mCHG are selectively retained in actively dividing cells during the plant cell cycle, while mCHH is depleted. Spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation pathway. Loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.
Article
Biochemistry & Molecular Biology
Jose Maria Costa-Junior, Sandra Mara Ferreira, Mirian Ayumi Kurauti, Diana L. Bernstein, Elena G. Ruano, Vasumathi Kameswaran, Jonathan Schug, Ricardo Freitas-Dias, Claudio C. Zoppi, Antonio C. Boschero, Camila A. M. de Oliveira, Gustavo J. Santos, Everardo M. Carneiro, Klaus H. Kaestner
Summary: Paternal exercise has a positive impact on the metabolic health of offspring, which can be achieved through transgenerational inheritance. The study showed that paternal exercise improves glucose tolerance and insulin sensitivity in the offspring, and this effect may be achieved by influencing the epigenetic mechanisms of transgenerational inheritance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Bo-Wen Zhou, Qing-Qin Wu, David H. Mauki, Xuan Wang, Shu-Run Zhang, Ting-Ting Yin, Fang-Liang Chen, Chao Li, Yan-Hu Liu, Guo-Dong Wang, Ya-Ping Zhang
Summary: This study identified 11 germline gene fusions (GGFs) in canine transmissible venereal tumor (CTVT) using multi-omics data, indicating their higher genetic susceptibility. Additionally, a complex gene fusion mechanism and the downregulation of GGFs during tumor regression phase associated with DNA methylation level were illustrated. These findings provide a comprehensive landscape of gene fusions (GFs) in CTVT and offer valuable genetic resources for exploring potential genetic mechanisms underlying cancer development in both dogs and humans.
Article
Biochemistry & Molecular Biology
Changliang Hou, Xinyan Zhao, Geng G. Tian, Ji Wu
Summary: This study reveals the role of Stella in regulating FGSC proliferation and differentiation, provides insights into the mechanisms of DNA methylation and chromatin structure regulation, and sheds light on FGSC development.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Review
Cell Biology
Zhuo Chen, Rama Natarajan
Summary: Inherent and acquired abnormalities in gene regulation due to genetics and epigenetics underlie many diseases including diabetes. Epigenetic changes are associated with complications of diabetes, and these changes persist even after restoration of normal blood sugar levels, known as metabolic memory. Epigenetic modifications provide a therapeutic opportunity to ameliorate cellular dysfunction and reverse metabolic memory.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2022)
Article
Cell Biology
Rui Gao, Shiyang Zeng, Dongxu Yang, Xiaocui Li, Wenqiang Liu, Yawei Gao, Dandan Bai, Linfeng Zhang, Chuan Chen, Yunzhe Kang, Beiying Wang, Wei Hong, Mingzhu Wang, Jiqing Yin, Hong Wang, Qiaolin Deng, Shaorong Gao, Yong Zhang, Jiayu Chen
Summary: Histone modifications play critical roles in regulating gene expression during early embryo development. This study provides the first genome-wide profiles of three key histone modifications in human primordial germ cells, revealing the positive correlation between H3K4me3 and gene expression, as well as the important roles of H3K27me3 in regulating specific promoters and X chromosome reactivation. The repressive marks of H3K9me3 and H3K27me3 jointly regulate demethylation-resistant regions in hPGCs.
Article
Cell & Tissue Engineering
Mutsumi Kobayashi, Misato Kobayashi, Junko Odajima, Keiko Shioda, Young Sun Hwang, Kotaro Sasaki, Pranam Chatterjee, Christian Kramme, Richie E. Kohman, George M. Church, Amanda R. Loehr, Robert S. Weiss, Harald Juppner, Joanna J. Gell, Ching C. Lau, Toshi Shioda
Summary: In this study, long-term culture human primordial germ cell-like cells (LTC-hPGCLCs) were successfully established, which can proliferate rapidly in a serum-free and feeder-free condition and maintain the characteristics of primordial germ cells. LTC-hPGCLCs can differentiate into different cell types in appropriate culture conditions.
Article
Cell Biology
Naoko Irie, Sun-Min Lee, Valentina Lorenzi, Haiqi Xu, Jinfeng Chen, Masato Inoue, Toshihiro Kobayashi, Carmen Sancho-Serra, Elena Drousioti, Sabine Dietmann, Roser Vento-Tormo, Chun-Xiao Song, M. Azim Surani
Summary: The commitment of germline during early human development is crucial for the subsequent gametogenesis. A study on PGC-like cells derived from human embryonic stem cells reveals that the induction of DMRT1 and SOX17 promotes epigenetic resetting and the expression of DNA methylation-sensitive genes, indicating the initiation of the germline commitment programme.
NATURE CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Oscar Ortega-Recalde, Robert C. Day, Neil J. Gemmell, Timothy A. Hore
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Erica Todd, Oscar Ortega-Recalde, Hui Liu, Melissa S. Lamm, Kim M. Rutherford, Hugh Cross, Michael A. Black, Olga Kardailsky, Jennifer A. Marshall Graves, Timothy A. Hore, John R. Godwin, Neil J. Gemmell
Article
Agriculture, Dairy & Animal Science
Oscar Ortega-Recalde, Alexander Goikoetxea, Timothy A. Hore, Erica V. Todd, Neil J. Gemmell
ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 8, 2020
(2020)
Article
Biochemistry & Molecular Biology
Issam M. Mayyas, Robert J. Weeks, Robert C. Day, Helena E. Magrath, Karina M. O'Connor, Olga Kardailsky, Timothy A. Hore, Mark B. Hampton, Ian M. Morison
Summary: Although the mechanism of DNA demethylating drugs has been well understood, the direct impact of these drugs on methylation of DNA complementary strands has not been formally demonstrated. Using hairpin-bisulphite sequencing, the study showed complete loss of methylation on daughter strands and heterogeneous methylation patterns in synchronized Jurkat cells following treatment with the DNMT1 inhibitor decitabine.
Article
Biology
Victoria J. Sugrue, Joseph Alan Zoller, Pritika Narayan, Ake T. Lu, Oscar J. Ortega-Recalde, Matthew J. Grant, C. Simon Bawden, Skye R. Rudiger, Amin Haghani, Donna M. Bond, Reuben R. Hore, Michael Garratt, Karen E. Sears, Nan Wang, Xiangdong William Yang, Russell G. Snell, Timothy A. Hore, Steve Horvath
Summary: Research reveals that castrated male sheep age at a slower rate than intact males, partly due to the removal of androgens. Specific CpG dinucleotides sensitive to androgens show differences in methylation between intact males and castrated males/females, suggesting a potential mechanism for male-accelerated aging in divergent mammalian species.
Article
Pharmacology & Pharmacy
Daniel Felipe Silgado-Guzman, Mariana Angulo-Aguado, Adrien Morel, Maria Jose Nino-Orrego, Daniel-Armando Ruiz-Torres, Nora Constanza Contreras Bravo, Carlos Martin Restrepo, Oscar Ortega-Recalde, Dora Janeth Fonseca-Mendoza
Summary: This study investigated the genetic variability of drug-related genes in a Colombian population using whole-exome sequencing. The findings suggest that rare genetic variants play a significant role in interindividual variability in drug response. Additionally, the genetic frequencies in the Colombian population differed from other Latin-American populations.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Medicine, General & Internal
Mariana Angulo-Aguado, David Corredor-Orlandelli, Juan Camilo Carrillo-Martinez, Monica Gonzalez-Cornejo, Eliana Pineda-Mateus, Carolina Rojas, Paula Triana-Fonseca, Nora Constanza Contreras Bravo, Adrien Morel, Katherine Parra Abaunza, Carlos M. Restrepo, Dora Janeth Fonseca-Mendoza, Oscar Ortega-Recalde
Summary: This study evaluated the association of non-genetic factors and three polymorphisms with COVID-19 severity and long-term symptoms. Age, sex, hypertension, and type 2 diabetes mellitus were found to be significantly associated with disease severity. The polymorphism LZTFL1 rs11385942 was identified as a potential biomarker for COVID-19 severity. Long-term symptoms were also found to be associated with disease severity.
FRONTIERS IN MEDICINE
(2022)
Article
Biology
Alexandria Ragsdale, Oscar Ortega-Recalde, Ludovic Dutoit, Anne A. Besson, Jolyn H. Z. Chia, Tania King, Shinichi Nakagawa, Anthony Hickey, Neil J. Gemmell, Timothy Hore, Sheri L. Johnson
Summary: This study investigates the cross-generational acclimation to hypoxia using zebrafish as a model. The results show that short-term paternal exposure to hypoxia can enhance the offspring's tolerance to acute hypoxia. The study also reveals upregulation of hemoglobin expression in the offspring of hypoxia-exposed males, suggesting the maintenance of an epigenetic memory of past hypoxia exposure. The findings imply that the environmentally induced information can be transferred to subsequent generations, enabling them to cope with hypoxic conditions.
Article
Infectious Diseases
Betsy E. Castro, Rafael Rios, Lina P. Carvajal, Monica L. Vargas, Monica P. Cala, Lizeth Leon, Blake Hanson, An Q. Dinh, Oscar Ortega-Recalde, Carlos Seas, Jose M. Munita, Cesar A. Arias, Sandra Rincon, Jinnethe Reyes, Lorena Diaz
Summary: This study characterized the biomolecular profile of clinical hVISA and found that the mechanism of hVISA involves major changes in regulatory systems, expression of virulence factors, and reduction in glycolysis via TCA cycle.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Multidisciplinary Sciences
Mirunalini Ravichandran, Dominik Rafalski, Claudia I. Davies, Oscar Ortega-Recalde, Xinsheng Nan, Cassandra R. Glanfield, Annika Kotter, Katarzyna Misztal, Andrew H. Wang, Marek Wojciechowski, Michal Razew, Issam M. Mayyas, Olga Kardailsky, Uwe Schwartz, Krzysztof Zembrzycki, Ian M. Morison, Mark Helm, Dieter Weichenhan, Renata Z. Jurkowska, Felix Krueger, Christoph Plass, Martin Zacharias, Matthias Bochtler, Timothy A. Hore, Tomasz P. Jurkowski
Summary: TET enzymes catalyze the oxidation of 5-methylcytosine bases in DNA and have a strong preference for CGs embedded within transcription factor-binding sites. This preference is determined by intrasubstrate interactions and the flanking CG sequence. The study of TET sequence preferences is physiologically relevant and helps explain the process of DNA demethylation. The most and least favorable TET motifs represent DNA sites bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), shedding light on the function of TET in transcriptional responses and pluripotency support.
Article
Pharmacology & Pharmacy
Juan Fernando Parada-Marquez, Nicolas David Maldonado-Rodriguez, Paula Triana-Fonseca, Nora Constanza Contreras-Bravo, Carlos Alberto Calderon-Ospina, Carlos M. M. Restrepo, Adrien Morel, Oscar Javier Ortega-Recalde, Daniel Felipe Silgado-Guzman, Mariana Angulo-Aguado, Dora Janeth Fonseca-Mendoza
Summary: This study describes the rare and common variants found in genes related to the metabolism of analgesic and anesthetic drugs in the Colombian population. The results identified 148 molecular variants potentially related to the therapeutic response to commonly used anesthesia drugs. The allelic frequency comparison showed that the Colombian population has a unique pharmacogenomic profile for anesthesia drugs.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Biochemical Research Methods
Karen Marcela Jimenez, Dora Janeth Fonseca-Mendoza, Adrien Morel, Oscar Ortega-Recalde, Nora Constanza Contreras Bravo, Camilo Andres Velandia-Piedrahita, Adriana Steevens, Luisa Daniela Caldas, Juan Pablo Ribon, Martha Sanchez, Carlos Martin Restrepo, Rodrigo Cabrera
Summary: RT-PCR tests have become the gold standard for detecting the SARS-CoV-2 virus. This study presents an alternative implementation using widely available and low-cost equipment and reagents, which shows comparable sensitivity and specificity to automated detection methods. This method has the potential to be adopted by diagnostic laboratories worldwide.
METHODS AND PROTOCOLS
(2022)
Article
Peripheral Vascular Disease
David Corredor-Orlandelli, Santiago Sambracos-Parrado, Santiago Mantilla-Garcia, Josue Tovar-Tirado, Valentina Vega-Ramirez, Santiago David Mendoza-Ayus, Laura Catalina Pena, Maria Fernanda Leal, Juliana Rodriguez-Carrillo, Juanita Leon-Torres, Juan Mauricio Pardo-Oviedo, Katherine Parra Abaunza, Nora Contreras Contreras Bravo, Oscar Ortega-Recalde, Dora Janeth Fonseca Mendoza
Summary: The study investigated the association of PON1 p.Q192R with CAD and clopidogrel response in the Colombian population, finding a positive association between the 192R allele and decreased susceptibility to CAD, but no association with HPR.
VASCULAR HEALTH AND RISK MANAGEMENT
(2021)
