Review
Plant Sciences
Lars Munck, Asmund Rinnan, Bekzod Khakimov, Birthe Moller Jespersen, Soren Balling Engelsen
Summary: The study demonstrates how pleiotropy can be observed as covarying global molecular patterns in a barley mutant seed model, defining each endosperm. Global coherence was found as a covariate coordinator within and between local genotype specific fingerprints.
TRENDS IN PLANT SCIENCE
(2021)
Article
Gastroenterology & Hepatology
Ming Ren Toh, Evelyn Yi Ting Wong, Sunny Hei Wong, Alvin Wei Tian Ng, Lit-Hsin Loo, Pierce Kah-Hoe Chow, Joanne Ngeow
Summary: Hepatocellular carcinoma (HCC) is a leading global cancer, primarily occurring in genetically susceptible individuals with liver cirrhosis and exposure to risk factors. Temporal and geographical variations exist in HCC, with a shift from viral to nonviral causes and a higher burden in regions with a high sociodemographic index. Hepatitis viruses are the predominant causes of HCC in Asia and Africa, while genetic conditions contributing to HCC risk are less recognized outside North America and Europe. This review evaluates the epidemiology, risk factors, and genetics of HCC, including monogenic diseases, single-nucleotide polymorphisms, gut microbiome, and somatic mutations.
Article
Cell Biology
Yixuan Cen, Yifeng Fang, Yan Ren, Shiyuan Hong, Weiguo Lu, Junfen Xu
Summary: This study explored the characteristics of extrachromosomal circular DNAs (eccDNAs) in high grade serous ovarian cancer (HGSOC) and identified DNMT1(circle10302690-10302961) as the most significantly down-regulated eccDNA in metastatic tumors of HGSOC. The lower expression of DNMT1(circle10302690-10302961) was associated with worse prognosis of HGSOC.
CELL DEATH & DISEASE
(2022)
Article
Multidisciplinary Sciences
Yuki Horisawa-Takada, Chisato Kodera, Kazumasa Takemoto, Akihiko Sakashita, Kenichi Horisawa, Ryo Maeda, Ryuki Shimada, Shingo Usuki, Sayoko Fujimura, Naoki Tani, Kumi Matsuura, Tomohiko Akiyama, Atsushi Suzuki, Hitoshi Niwa, Makoto Tachibana, Takashi Ohba, Hidetaka Katabuchi, Satoshi H. Namekawa, Kimi Araki, Kei-Ichiro Ishiguro
Summary: The study identified a protein complex composed of ZFP541 and KCTD19 as key transcriptional regulators in mouse meiotic prophase progression. This complex promotes the completion of meiotic prophase and triggers the reconstruction of transcriptional network and chromatin organization. ZFP541 binds to and suppresses genes associated with transcriptional regulation and covalent chromatin modification to ensure proper meiotic progression.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Lounis Yakhou, Anaelle Azogui, Nikhil Gupta, Julien Richard Albert, Fumihito Miura, Laure Ferry, Kosuke Yamaguchi, Sarah Battault, Pierre Therizols, Frederic Bonhomme, Elouan Bethuel, Arpita Sarkar, Maxim V. C. Greenberg, Paola B. Arimondo, Gael Cristofari, Olivier Kirsh, Takashi Ito, Pierre-Antoine Defossez
Summary: Epigenetic mechanisms play crucial roles in establishing and maintaining cellular identities in mammals. They regulate the expression of genes, transposable elements, and chromatin structures, and are essential for mammalian development. Bivalent promoters are particularly important during differentiation and development. BEND3 has been identified as a regulator of bivalent promoters, and its absence leads to genome-wide DNA methylation gains and reduced DNA hydroxymethylation, suggesting its direct and indirect roles in chromatin regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Editorial Material
Multidisciplinary Sciences
Benjamin Plackett
Summary: Sickle-cell disease is prevalent in the Middle East, with 2.6% of the population in some areas affected by this genetic disorder. Adlette Inati, a specialist in clinical haematology at the Lebanese American University, and president of a foundation supporting sickle-cell disease patients in Lebanon, discusses the potential benefits of genetic screening in this region.
Review
Chemistry, Multidisciplinary
Tamiko Nozaki, Motomu Kanai
Summary: Research focuses on developing abiotic chemical catalysts to intervene in complex chemical networks of life, aiming to mend dysregulated networks in diseases and advance catalysis science. Epigenetics, at the intersection of chemistry, biology, and medicine, serves as a suitable field for this idea. Chemical catalyst systems have been developed for endogenous histone modifications in living cells, showing potential applications in epigenetic tools and cancer therapy.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Sumeet K. Singh, Andres Reyna, Xiaowen Xie, Haibin Mao, Meihuan Ji, Ning Zheng, Peter L. Hsu, Champak Chatterjee
Summary: An efficient chemical synthesis method was used to generate site-specifically sumoylated histone H4, resulting in the production of uniformly modified mononucleosomes. These modified mononucleosomes were then used as substrates in biochemical assays with histone H2B-specific ubiquitin ligases Rad6 and Bre1, revealing the strong inhibition of H2B ubiquitylation by SUMO. This novel negative biochemical crosstalk between SUMO and ubiquitin was also confirmed to exist in human cells.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biology
H. Nayanga Thirmanne, Feinan Wu, Derek H. Janssens, Jherek Swanger, Ahmed Diab, Heather M. Feldman, Robert A. Amezquita, Raphael Gottardo, Patrick J. Paddison, Steven Henikoff, Bruce E. Clurman
Summary: The study investigated the effects of misregulated Fbw7 substrates on colorectal cancer cells using RNA-Seq and high-resolution mapping techniques. The findings revealed widespread transcriptional changes and altered transcription factor occupancy caused by Fbw7 mutations. Additionally, Fbw7 loss was associated with increased expression of MHC Class II genes such as CIITA.
Article
Agriculture, Dairy & Animal Science
L. C. Hardie, I. W. Haagen, B. J. Heins, C. D. Dechow
Summary: The study aimed to characterize the genetics of health traits in US organic dairy cows and determine the presence of genotype by environment interaction. Data from 16 USDA certified organic dairy farms were used, showing positive genetic correlations among most health traits.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Biochemical Research Methods
Yanyu Li, Xuecang Li, Yongsan Yang, Meng Li, Fengcui Qian, Zhidong Tang, Jianmei Zhao, Jian Zhang, Xuefeng Bai, Yong Jiang, Jianyuan Zhou, Yuexin Zhang, Liwei Zhou, Jianjun Xie, Enmin Li, Qiuyu Wang, Chunquan Li
Summary: TRlnc is a comprehensive database for human regulatory information of lncRNAs, providing detailed genetic and epigenetic annotation within transcriptional regulatory regions of lncRNAs, which aims at helping users gain in-depth insights into the transcriptional regulatory mechanisms of lncRNAs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Hematology
Marta Kulis, Jose Ignacio Martin-Subero
Summary: Chronic lymphocytic leukaemia (CLL) is characterized by both driver genetic alterations and extensive epigenetic changes. Epigenomic studies have revealed the DNA methylome, chromatin accessibility, histone modifications, and 3D genome architecture of CLL. The DNA methylome contains information about the cellular origin and proliferative history of CLL cells, which are independent prognostic factors. Integrative analyses of chromatin marks have identified novel regulatory elements and altered transcription factor networks in CLL. Additionally, CLL cells display disease-specific patterns of 3D genome interactions. Single-cell analyses are becoming increasingly important in CLL research.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Review
Biochemistry & Molecular Biology
John D. Bagert, Tom W. Muir
Summary: The field of epigenetics has rapidly expanded in the past two decades, revealing the complexity of genetic information storage and access in eukaryotes, with chemistry playing an increasingly important role. Molecular precision afforded by chemical tools is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Article
Multidisciplinary Sciences
Yodai Takei, Jina Yun, Shiwei Zheng, Noah Ollikainen, Nico Pierson, Jonathan White, Sheel Shah, Julian Thomassie, Shengbao Suo, Chee-Huat Linus Eng, Mitchell Guttman, Guo-Cheng Yuan, Long Cai
Summary: This study utilized DNA seqFISH+ technology to image 3,660 chromosomal loci in single mouse embryonic stem cells, along with observing 17 chromatin marks and subnuclear structures by sequential immunofluorescence and the expression profile of 70 RNAs. The results suggest that many loci are consistently associated with immunofluorescence marks and form "fixed points" in nuclear organizations in single cells, while highly expressed genes appear to be pre-positioned to active nuclear zones. The research also uncovered distinct mouse ES cell subpopulations with characteristic combinatorial chromatin states.
Article
Public, Environmental & Occupational Health
Daniel F. Morse, Sahil Sandhu, Kate Mulligan, Stephanie Tierney, Marie Polley, Bogdan Chiva Giurca, Sian Slade, Sonia Dias, Kamal R. Mahtani, Leanne Wells, Huali Wang, Bo Zhao, Cristiano Emanuel Marta De Figueiredo, Jan Joost Meijs, Hae Kweun Nam, Kheng Hock Lee, Carolyn Wallace, Megan Elliott, Juan Manuel Mendive, David Robinson, Miia Palo, Wolfram Herrmann, Rasmus Ostergaard Nielsen, Kerryn Husk
Summary: Social prescribing is an approach that aims to improve health and well-being by connecting individuals to non-clinical services and supports. It can empower individuals to manage their own health and well-being and promote collaboration across sectors to move beyond the traditional biomedical model of health. This paper explores the conceptualization and implementation of social prescribing in 17 countries and provides insights for tailoring models to local needs.
Article
Immunology
Camilla Luiza-Batista, Flore Nardella, Sabine Thiberge, Malika Serra-Hassoun, Marcelo U. Ferreira, Artur Scherf, Sylvie Garcia
Summary: The new Flow-FISH method combines RNA detection and cell staining techniques to accurately quantify different stages of malaria parasites, suitable for gene expression studies and analysis of liver-stage sporozoites.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Materials Science, Multidisciplinary
Matthew D. Ward, Jessica Wade, Xingyuan Shi, Jenny Nelson, Alasdair J. Campbell, Matthew J. Fuchter
Summary: A simple bilayer organic photodiode with high sensitivity to circularly polarized light has been developed, demonstrating fast switching speeds, large dynamic range, and high photocurrent dissymmetry.
ADVANCED OPTICAL MATERIALS
(2022)
Correction
Nanoscience & Nanotechnology
Li Wan, Jessica Wade, Xingyuan Shi, Shengda Xu, Matthew J. Fuchter, Alasdair J. Campbell
ACS APPLIED MATERIALS & INTERFACES
(2022)
Correction
Chemistry, Multidisciplinary
Li Wan, Jessica Wade, Francesco Salerno, Oriol Arteaga, Beth Laidlaw, Xuhua Wang, Thomas Penfold, Matthew J. Fuchter, Alasdair J. Campbell
Article
Cell Biology
Christopher Swale, Valeria Bellini, Matthew W. Bowler, Nardella Flore, Marie-Pierre Brenier-Pinchart, Dominique Cannella, Lucid Belmudes, Caroline Mas, Yohann Coute, Fabrice Laurent, Artur Scherf, Alexandre Bougdour, Mohamed-Ali Hakimi
Summary: The Apicomplexa, a phylum of single-celled protozoa, cause severe parasitic diseases in humans and animals. Current therapeutics are limited by their efficacy and resistance. In this study, altiratinib, originally developed for glioblastoma, is identified as a potential drug candidate with broad spectrum activity against apicomplexans. Altiratinib specifically targets the TgPRP4K of T. gondii and inhibits the development of intracellular parasites. The molecular basis of the inhibitory mechanism and species selectivity is further elucidated.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Camilla Luiza-Batista, Sabine Thiberge, Malika Serra-Hassoun, Flore Nardella, Aurelie Claes, Vanessa C. Nicolete, Pierre-Henri Commere, Liliana Mancio-Silva, Marcelo U. Ferreira, Artur Scherf, Sylvie Garcia
Summary: This study presents a new humanized mice model that supports human erythropoiesis and allows the multiplication and transmission of P. vivax parasites. It provides a unique tool for investigating the biology of intraerythrocytic P. vivax.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Alejandra Gonzalez, Magdalena Odaybat, My Le, Jake L. Greenfield, Andrew J. P. White, Xiang Li, Matthew J. Fuchter, Grace G. D. Han
Summary: This study reports on the reversible photoswitching behavior and energy storage capacity of Azobispyrazole derivatives with small terminal substituents. The findings reveal the unprecedentedly large effective light penetration depths and crystal-to-liquid phase transitions in condensed phases. The study also explores the impact of heteroarene design and substituents on the switching and energy storage properties.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Review
Microbiology
Eliana Real, Flore Nardella, Artur Scherf, Liliana Mancio-Silva
Summary: A survival strategy commonly observed in protozoan parasites is the sequential expression of clonally variant-surface antigens to avoid elimination by the host's immune response. In malaria-causing Plasmodium falciparum, the expression of these variant genes is not limited to intraerythrocytic developmental stages, but also plays a crucial role in transmission and preerythrocytic stages.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Optics
Li Wan, Yizhou Liu, Matthew J. Fuchter, Binghai Yan
Summary: Researchers have discovered that the handedness of circularly polarized light in OLEDs can be switched by reversing the current flow. This direction-dependent emission greatly increases the polarization rate and addresses the issue of symmetry loss in CP-OLEDs. The anomalous CP emission is attributed to the topological electronic property known as orbital-momentum locking in chiral materials.
Article
Biology
Gretchen M. Diffendall, Anna Barcons-Simon, Sebastian Baumgarten, Florent Dingli, Damarys Loew, Artur Scherf
Summary: RUF6 ncRNA interacts with RNA Pol II to sustain var gene expression, and Pf-DDX5 helicase resolves G-quadruplex secondary structures in var genes to facilitate transcriptional activation and progression.
LIFE SCIENCE ALLIANCE
(2023)
Article
Chemistry, Medicinal
Louis Minion, Jessica Wade, Juan Manuel Moreno-Naranjo, Sean Ryan, Giuliano Siligardi, Matthew J. Fuchter
Summary: We synthesized a fluorene-bithiophene co-polymer with chiral side chains and studied its chiroptical properties using synchotronradiation circular dichroism. Thin films of the polymer showed an intense circular dichroism of opposite handedness compared to similar polyfluorenes with the same enantiomeric chiral side chains. Comparing the polymer with a chiral side chain fluorene homopolymer, significant differences in thin film morphology were observed. Evidence of polymer chain bending in cPFT2 was uncovered through photoluminescence spectroscopy and theoretical calculations, providing an explanation for the observed inverted optical activity.
Article
Chemistry, Physical
Wenda Shi, Qiang Zhuang, Rui Zhou, Xueyan Hou, Xiaoming Zhao, Jie Kong, Matthew J. Fuchter
Summary: The use of chiral fullerenes as electron transport layers in perovskite solar cells has shown improved performance and operational stability.
ADVANCED ENERGY MATERIALS
(2023)
Editorial Material
Nanoscience & Nanotechnology
Jeanne Crassous, Matthew J. Fuchter, Danna E. Freedman, Nicholas A. Kotov, Jooho Moon, Matthew C. Beard, Sascha Feldmann
Summary: Solution-processable semiconductors based on small molecules, polymers or halide perovskites combine sustainable manufacturing with exceptional optoelectronic properties that can be chemically tailored to achieve flexible and highly efficient optoelectronic and photonic devices. A new exciting research direction is the study of the influence of chirality on light-matter interactions in these soft materials and its exploitation for the simultaneous control of charge, spin and light. In this Viewpoint, researchers working on different types of chiral semiconductors discuss the most interesting directions in this rapidly expanding field.
NATURE REVIEWS MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Kieran Griffiths, Jake L. Greenfield, Nathan R. Halcovitch, Matthew J. Fuchter, John M. Griffin
Summary: Arylazopyrazole-loaded metal-organic frameworks were synthesized and their contraction and expansion properties were studied. The shape and pendant groups of the guest molecules influenced the framework contraction, and the framework expanded under light illumination. Confinement within the framework extended the thermal stability of the isomer.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Biochemistry & Molecular Biology
Catarina Rosa, Parul Singh, Patty Chen, Ameya Sinha, Aurelie Claes, Peter R. Preiser, Peter C. Dedon, Sebastian Baumgarten, Artur Scherf, Jessica M. Bryant
Summary: The complex life cycle of the malaria parasite Plasmodium falciparum is driven by specific transcriptional programs, but the mechanisms behind gene activation or silencing at specific times are unclear. In this study, researchers investigated the role of the cohesin subunit SMC3 in P. falciparum. They found that knockdown of SMC3 during the early stages of the parasite's life cycle resulted in the upregulation of certain genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq analyses revealed that SMC3 binding at the promoter regions of these genes correlated with gene repression and chromatin accessibility during the parasite life cycle.