Article
Immunology
Olivier Papapietro, Sergey Nejentsev
Summary: TOP2B plays a crucial role in transcription regulation and maintaining genome organization by unwinding DNA structures. Deficiency of TOP2B may lead to developmental defects in B-cell progenitors.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Cell Biology
Shi-Meng Guo, Yi-Ran Zhang, Bing-Xin Ma, Li-Quan Zhou, Ying Yin
Summary: In this study, the inhibition of DRP1 activity in mESCs led to an increase in cleavage embryo gene levels and a tendency towards a new expression profile similar to the 2C-like state. Additionally, the glycolysis/gluconeogenesis pathway and its related enzymes were downregulated in 2C-like cells. Furthermore, inhibiting DRP1 activity from the late zygote stage resulted in inhibited development of early embryos and inefficient silencing of cleavage embryo genes at the late 2C stage.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Karolina Jodkowska, Vera Pancaldi, Maria Rigau, Ricardo Almeida, Jose M. Fernandez-Justel, Osvaldo Grana-Castro, Sara Rodriguez-Acebes, Miriam Rubio-Camarillo, Enrique Carrillo-de Santa Pau, David Pisano, Fatima Al-Shahrour, Alfonso Valencia, Maria Gomez, Juan Mendez
Summary: In this study, the authors analyzed the activity of origins in mouse embryonic stem cells and examined their response to replicative stress. They found that stressed origins were also active in a small fraction of cells during normal S phase, and stress increased their activation frequency. The study also identified that origin efficiency is proportional to the proximity to transcriptional start sites and the number of contacts established between origin-containing chromatin fragments.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Edward J. Calabrese
Summary: This paper provides a thorough assessment of hormetic dose responses in embryonic stem cells, suggesting that this response may serve as a fundamental and highly conserved evolutionary strategy.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Article
Physics, Multidisciplinary
Xiakun Chu, Jin Wang
Summary: This study introduced a nonequilibrium model to investigate chromosome structural reorganizations in a simplified cell developmental system, predicting the roles of neural progenitor cells and identifying early bifurcations in stem cell differentiation and reprogramming pathways. The theoretical results are consistent with experimental evidence, facilitating future applications.
PHYSICAL REVIEW LETTERS
(2022)
Article
Developmental Biology
Bailey A. T. Weatherbee, Tongtong Cui, Magdalena Zernicka-Goetz
Summary: Early human post-implantation development is crucial and lack of precise control over these processes can result in pregnancy loss. Stem cells and stem cell-derived models serve as useful tools in investigating mechanisms underlying human embryogenesis.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Xiakun Chu, Jin Wang
Summary: This study integrates Hi-C data and polymer simulations to reveal differences in chromosome structure between normal and cancer cells, as well as the dynamic changes in chromosome structure during cancer initiation and progression. The research found that chromosomes in transient intermediate states during cancer formation exhibit significant similarity to stem cells. The study provides a molecular-scale picture of cancer formation from the perspective of chromosome structure.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Omer Habib, Gizem Habib, Gue-Ho Hwang, Sangsu Bae
Summary: Prime editing is a precise and versatile genome editing technique that can directly copy desired genetic modifications into target DNA sites. It has great potential for gene function analysis, disease modeling, and correction of pathogenic mutations. In this study, prime editing was successfully tested in human pluripotent stem cells (hPSCs) and compared with base editing. Whole-genome sequencing showed that prime editing does not lead to guide RNA-independent off-target mutations in the genome.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell Biology
Chika Ogura, Shoko Nishihara
Summary: This study demonstrated the important role of DS in maintaining the undifferentiated state of mESCs and influencing their differentiation direction and Wnt signaling pathway. Knockdown or overexpression experiments targeting the D4ST1 gene revealed the mechanism of DS in mESCs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Engineering, Biomedical
Kyeong-Mo Koo, Young-Hyun Go, Seong-Min Kim, Chang-Dae Kim, Jeong Tae Do, Tae-Hyung Kim, Hyuk-Jin Cha
Summary: This study presents an electrochemical method for the label-free and non-destructive detection of naive embryonic stem cells (ESCs) derived from mouse ESCs, based on differences in cellular metabolism. By blocking glycolysis and oxidative phosphorylation, it was found that mitochondrial energy generation is the origin of the strong electrochemical signals of naive ESCs. The developed sensing platform can also sensitively identify mouse PSCs derived from MEFs among other cell types.
Article
Cell Biology
Chen Gao, Xiaolan Qi, Xin Gao, Jin Li, Yumin Qin, Yunjun Yin, Fei Gao, Tao Feng, Sen Wu, Xuguang Du
Summary: Screening with a CRISPR library under stringent conditions revealed key regulators of pluripotency exit, including previously reported genes and 17 unreported genes. Zfp771 and Olfr769 were found to be potentially involved in pluripotency exit.
Article
Multidisciplinary Sciences
Dashiell J. Massey, Amnon Koren
Summary: This study uses high throughput sequencing of individual cells to reveal the variability in DNA replication initiation and progression. The results show that initiation sites are mainly concentrated in specific genomic regions, and the firing order is similar but not strictly deterministic across cells.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Yusen Ye, Shihua Zhang, Lin Gao, Yuqing Zhu, Jin Zhang
Summary: The exploration of single-cell 3D genome maps reveals that chromatin domains are physical structures presenting in single cells and their boundaries vary from cell to cell. However, the association between regulatory factor binding and the formation of chromatin domains in single cells has not been systematically analyzed. A hierarchical chromatin domain structure identification algorithm named HiCS is developed, which shows superior performance in accuracy and efficiency. The results suggest that multiple factors, including CTCF-cohesin complex, Polycomb, TrxG, pluripotent protein families, contribute to shaping chromatin domain boundaries in single embryonic stem cells. Different cooperation patterns of these factors drive genomic position categories with differential preferences forming boundaries. Retrotransposons are differentially distributed in these genomic position categories, suggesting their role in regulating cell functions.
Review
Biochemistry & Molecular Biology
Yahong Wu, Weiwei Zhang
Summary: Pluripotent stem cells, including ESCs and iPSCs, are crucial for studying early development and treating diseases, with ubiquitination playing a key role in pluripotency regulation, particularly through the actions of E3 ligases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Biomedical
Tingting Gao, Xiyuan Zhao, Jie Hao, Yao Tian, Huike Ma, Wenjing Liu, Bin An, Faguo Sun, Shasha Liu, Baojie Guo, Shuaishuai Niu, Zhongwen Li, Chenxin Wang, Yukai Wang, Guihai Feng, Liu Wang, Wei Li, Jun Wu, Meijin Guo, Qi Zhou, Qi Gu
Summary: In this study, a new microcarrier with hyaluronic acid (HA) as the core material was developed for scalable serum-free suspension culture of hESC-derived MSCs. The optimal microcarriers, with a coating collagen concentration of 100 μg/mL or concave-structured surface (cHAMCs), allowed for the expansion of IMRCs within six days with a high yield. The harvested cells showed high viability, immunomodulatory and regenerative therapeutic promise, as well as increased secretion of extracellular matrix (ECM).
MATERIALS TODAY BIO
(2023)
Article
Biochemistry & Molecular Biology
Izaskun Mallona, Ioana Mariuca Ilie, Ino Dominiek Karemaker, Stefan Butz, Massimiliano Manzo, Amedeo Caflisch, Tuncay Baubec
Summary: Studies reveal that DNMT3A and DNMT3B exhibit distinct preferences during de novo methylation, which are attributed to differences in their catalytic domains rather than genome recruitment. These preferences are also observed at non-CpG sites, providing new insights into the complex regulation of DNA methylation patterns.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Cell Biology
Rodrigo Villasenor, Tuncay Baubec
Summary: Nucleosomes are basic structures used to package genetic information, subject to diverse chemical modifications. These modifications serve as interaction hubs for nuclear proteins, ensuring correct deposition to the genome. The regulation of chromatin marks relies on coordinated activities of writer, eraser, and reader enzymes, often depending on complex multicomponent regulatory circuits.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Article
Evolutionary Biology
Jeannie Mounger, M. Teresa Boquete, Marc W. Schmid, Renan Granado, Marta H. Robertson, Sandy A. Voors, Kristen L. Langanke, Mariano Alvarez, Cornelis A. M. Wagemaker, Aaron W. Schrey, Gordon A. Fox, David B. Lewis, Catarina Fonseca Lira, Christina L. Richards
Summary: The study focused on genetic and epigenetic diversity in natural populations of Rhizophora mangle, revealing low genetic diversity but high epigenetic diversity. It also found that a significant portion of epigenetic differences among offspring can be explained by maternal family, suggesting that epigenetic variation could play an important role in adaptation to challenging environments in genetically depauperate populations of this foundation species.
EVOLUTION & DEVELOPMENT
(2021)
Article
Biochemistry & Molecular Biology
Bin Yang, Alicia C. Borgeaud, Marcela Buricova, Lorene Aeschbach, Oscar Rodriguez-Lima, Gustavo A. Ruiz Buendia, Cinzia Cinesi, Alysha S. Taylor, Tuncay Baubec, Vincent Dion
Summary: Studies show that HDAC5 and DNMT1 do not affect the instability of expanded CAG/CTG repeats, but the expanded repeats reduce the effectiveness of gene silencing mediated by HDAC5 and DNMT1.
HUMAN MOLECULAR GENETICS
(2022)
Article
Plant Sciences
Marc W. Schmid, Sofia J. van Moorsel, Terhi Hahl, Enrica De Luca, Gerlinde B. De Deyn, Cameron Wagg, Pascal A. Niklaus, Bernhard Schmid
Summary: The diversity and interactions between plant and soil microbial communities are complex, with plant community history and soil legacy significantly influencing soil microbial composition. Specific plant species compositions are associated with particular soil microbial taxa, impacting below-ground community composition in re-assembled plant communities.
JOURNAL OF ECOLOGY
(2021)
Article
Clinical Neurology
Clarissa D. Voegel, Sara L. Kroll, Marc W. Schmid, Ann-Kathrin Kexel, Markus R. Baumgartner, Thomas Kraemer, Tina M. Binz, Boris B. Quednow
Summary: The study found that hair cortisone levels were significantly higher in individuals with chronic cocaine use disorder, while OEA and PEA levels were significantly lower. Elevated cocaine hair concentration among cocaine users was associated with increased glucocorticoid and decreased OEA levels. Additionally, more self-reported cannabis use was correlated with lower eCB levels in hair.
INTERNATIONAL JOURNAL OF NEUROPSYCHOPHARMACOLOGY
(2022)
Article
Multidisciplinary Sciences
Cristiana Bersaglieri, Jelena Kresoja-Rakic, Shivani Gupta, Dominik Baer, Rostyslav Kuzyakiv, Martina Panatta, Raffaella Santoro
Summary: The authors developed a method to map nucleolar-associated domains using DNA methylation, and characterized these domains in mouse embryonic stem cells and neural progenitor cells. They found distinct chromatin states and changes in genome architecture during differentiation.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Jack Rhodes, Andra-Octavia Roman, Marta Bjornson, Benjamin Brandt, Paul Derbyshire, Michele Wyler, Marc W. Schmid, Frank L. H. Menke, Julia Santiago, Cyril Zipfel
Summary: This study reports on a previously uncharacterised family of plant signalling peptides, CTNIPs, and identifies the orphan receptor HSL3 as their receptor. The HSL3-CTNIP signalling module is conserved in most extant angiosperms. This discovery is important for understanding the diverse functions of plant signalling peptides and receptor-ligand co-evolution.
Article
Cell & Tissue Engineering
Madlen Muller, Moritz Schaefer, Tara Fah, Daniel Spies, Victoria Hermes, Richard Patryk Ngondo, Rodrigo Pena-Hernandez, Raffaella Santoro, Constance Ciaudo
Summary: In this study, we demonstrate that AGO1 and AGO2 have additional functions beyond the miRNA pathway in mouse embryonic stem cells. These proteins regulate a specific set of genes through modulation of chromatin states and gene expression. Interestingly, the pluripotency factor KLF4 plays a key role in this novel axis of gene regulation.
Article
Cell Biology
Thom M. Molenaar, Muddassir Malik, Joana Silva, Ning Qing Liu, Judith H. Haarhuis, Christina Ambrosi, Eliza Mari Kwesi-Maliepaard, Tibor van Welsem, Tuncay Baubec, William J. Faller, Fred van Leeuwen
Summary: Cell size is tightly regulated and changes in cell size are frequently observed in cancer. In this study, we found that SETD2, a lysine methyltransferase protein, plays a role in regulating cell size by negatively regulating global protein synthesis rates. Overexpression of the H3K36 demethylase KDM4A or the oncohistone H3.3K36M also led to an increase in cell size, suggesting the importance of H3K36 methylation in cell size regulation.
JOURNAL OF CELL SCIENCE
(2022)
Article
Genetics & Heredity
Stefan Butz, Nina Schmolka, Ino D. Karemaker, Rodrigo Villasenor, Isabel Schwarz, Silvia Domcke, Esther C. H. Uijttewaal, Julian Jude, Florian Lienert, Arnaud R. Krebs, Nathalie P. de Wagenaar, Xue Bao, Johannes Zuber, Ulrich Elling, Dirk Schuebeler, Tuncay Baubec
Summary: Genomic imprinting is regulated by DNA methylation of imprinting control regions (ICRs) with parental-specificity. The epigenetic states of ICRs, despite having an identical DNA sequence, are determined by genetic and epigenetic factors. Through iterative integration of ICRs and DNA sequences, this study identified the DNA sequence features required for maintaining the epigenetic states in embryonic stem cells. Additionally, ATF7IP and ZMYM2 were found to be important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
Article
Multidisciplinary Sciences
G. Veggiani, R. Villasenor, G. D. Martyn, J. Q. Tang, W. M. Krone, J. Gu, C. Chen, M. L. Waters, K. H. Pearce, T. Baubec, S. S. Sidhu
Summary: Engineered chromodomains are promising probes for histone methylation analysis, with enhanced affinity for methylated histone marks. They can be used for genome-wide binding analysis, live-cell imaging, and highly efficient gene silencing.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Ricardo S. Randall, Claire Jourdain, Anna Nowicka, Kateina Kaduchova, Michaela Kubova, Mohammad A. Ayoub, Veit Schubert, Christophe Tatout, Isabelle Colas, Kalyanikrishna, Sophie Desset, Sarah Mermet, Aurelia Boulaflous-Stevens, Ivona Kubalova, Terezie Mandakova, Stefan Heckmann, Martin A. Lysak, Martina Panatta, Raffaella Santoro, Daniel Schubert, Ales Pecinka, Devin Routh, Celia Baroux
Summary: This article provides a compendium of strategies for analyzing the spatial distribution of nuclear and chromosomal signals from three-dimensional image stacks obtained through fluorescence microscopy imaging. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and better explore the discovery potential of their images.
Article
Cell Biology
Cristiana Bersaglieri, Raffaella Santoro
Summary: The nucleolus is an important subcompartment in the nucleus responsible for ribosome biogenesis. Recent studies have shown that it also plays a role in organizing the chromosomes in the nucleus. These genomic domains, called nucleolar associated domains (NADs), are characterized by repressive chromatin states. However, accurate identification of NADs has been challenging due to the lack of a membrane.
CURRENT OPINION IN CELL BIOLOGY
(2023)
Article
Biology
Marcin Roganowicz, Dominik Bar, Cristiana Bersaglieri, Rossana Aprigliano, Raffaella Santoro
Summary: BAZ2A represses not only rRNA genes but also genes frequently silenced in metastatic prostate cancer through its RNA-binding TAM domain, which interacts with TOP2A and KDM1A. RNA-based interactions between BAZ2A and TOP2A/KDM1A play a critical role in gene regulation in prostate cancer and may have implications for risk stratification and treatment.
LIFE SCIENCE ALLIANCE
(2023)
