Article
Genetics & Heredity
Vicente A. Yepez, Mirjana Gusic, Robert Kopajtich, Christian Mertes, Nicholas H. Smith, Charlotte L. Alston, Rui Ban, Skadi Beblo, Riccardo Berutti, Holger Blessing, Elzbieta Ciara, Felix Distelmaier, Peter Freisinger, Johannes Haeberle, Susan J. Hayflick, Maja Hempel, Yulia S. Itkis, Yoshihito Kishita, Thomas Klopstock, Tatiana D. Krylova, Costanza Lamperti, Dominic Lenz, Christine Makowski, Signe Mosegaard, Michaela F. Mueller, Gerard Munoz-Pujol, Agnieszka Nadel, Akira Ohtake, Yasushi Okazaki, Elena Procopio, Thomas Schwarzmayr, Joel Smet, Christian Staufner, Sarah L. Stenton, Tim M. Strom, Caterina Terrile, Frederic Tort, Rudy Van Coster, Arnaud Vanlander, Matias Wagner, Manting Xu, Fang Fang, Daniele Ghezzi, Johannes A. Mayr, Dorota Piekutowska-Abramczuk, Antonia Ribes, Agnes Roetig, Robert W. Taylor, Saskia B. Wortmann, Kei Murayama, Thomas Meitinger, Julien Gagneur, Holger Prokisch
Summary: The lack of functional evidence hampers variant interpretation, but further sequencing of transcriptomes can help probe gene expression defects. A streamlined experimental and computational process involving RNA-seq analysis of skin fibroblasts led to the establishment of genetic diagnoses for 16% of WES-inconclusive cases, with detection of aberrant gene expression playing a major role in diagnosis, especially in identifying splice-disrupting variants.
Article
Biochemistry & Molecular Biology
Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Bjoern Gruening, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, Maciej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bhiman, Josie Everatt, Daniel G. Amoako, James Emmanuel San, Jennifer Giandhari, Alex Sigal, Carolyn Williamson, Nei-yuan Hsiao, Anne von Gottberg, Arne De Klerk, Robert W. Shafer, David L. Robertson, Robert J. Wilkinson, B. Trevor Sewell, Richard Lessells, Anton Nekrutenko, Allison J. Greaney, Tyler N. Starr, Jesse D. Bloom, Ben Murrell, Eduan Wilkinson, Ravindra K. Gupta, Tulio de Oliveira, Sergei L. Kosakovsky Pond
Summary: This study found 13 rare mutations among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene, which may impact important regions and functions of the S-gene. The mutations were predicted to decrease the fitness of the virus they occurred in prior to the emergence of Omicron. The study also suggests that the mutations in each cluster interact cooperatively to alter the function of Spike. Understanding how these complex and highly adaptive mutation constellations were assembled in the Omicron S-gene, and why they went undetected in the early stages, is crucial.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Genetics & Heredity
Laralynne Przybyla, Luke A. Gilbert
Summary: The latest approaches in CRISPR-based functional genomics screens provide a scalable and multiplexable way to characterize genes and gene regulatory elements encoded by the human genome. These tools promise to reveal mechanisms of gene function and regulation, as well as enable exploration of how genes work together to modulate complex phenotypes.
NATURE REVIEWS GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Xiujie Liu, Bin Hu, Chengcai Chu
Summary: Nitrogen is essential for crop yields, but excessive application can lead to increased production costs and environmental problems. Understanding the molecular mechanisms of nitrogen use efficiency (NUE) and breeding crops with higher NUE is crucial. NUE is determined by nitrogen uptake, transport, assimilation, and remobilization, involving key enzymes like NR, NiR, GS, and GOGAT.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Genetics & Heredity
Zhen Zhang, Zi-Xian Wang, Yan-Xing Chen, Hao-Xiang Wu, Ling Yin, Qi Zhao, Hui-Yan Luo, Zhao-Lei Zeng, Miao-Zhen Qiu, Rui-Hua Xu
Summary: By analyzing single-cell RNA sequencing data from ICI-treated patients, it was found that cancer stemness may be associated with resistance to ICI treatment. The developed novel stemness signature (Stem.Sig) showed improved predictive performance for ICI response across multiple cancers, potentially serving as a competitive tool for patient selection in immunotherapy.
Review
Genetics & Heredity
Kirsten Seale, Steve Horvath, Andrew Teschendorff, Nir Eynon, Sarah Voisin
Summary: This article reviews the changes in DNA methylation during aging and the statistical tools used to quantify them. It also explores the evidence linking DNA methylation to aging phenotypes and strategies for extending healthspan and lifespan. Finally, it discusses theories on the mechanistic causes of epigenetic aging.
NATURE REVIEWS GENETICS
(2022)
Review
Genetics & Heredity
James P. B. Lloyd, Ryan Lister
Summary: The authors review the intra-individual and inter-individual plant epigenome variation during development and in response to environmental changes, stress included. They also discuss the functions of epigenome plasticity and editing technologies that will drive future research. Advancements in technologies for reading and writing epigenomic patterns are enabling a more detailed characterization and functional interrogation of plant epigenome variation.
NATURE REVIEWS GENETICS
(2022)
Review
Genetics & Heredity
Mark S. Hibbins, Matthew W. Hahn
Summary: Phylogenomics has revealed the frequent occurrence of introgression across different species, and the development of methods for detecting and characterizing introgression from whole-genome sequencing data has played a crucial role in these discoveries. These methods range from simple tests to model-based approaches and utilize data across species to infer and characterize introgression. This article provides a detailed overview of the different signals of introgression in the genome and how current methods are designed to detect them. It discusses the strengths and limitations of these approaches, identifies areas for future development, and highlights the signals of introgression and the power of each method to detect them. The article concludes with a discussion on the challenges in inferring introgression and potential solutions.
Review
Genetics & Heredity
Ethan Bier
Summary: This Review discusses the impact of CRISPR-based gene-drive systems on controlling populations such as insect vectors of disease. It summarizes progress in designing full-drive elements, updating genetic elements, and mitigating strategies, while emphasizing the importance of ethical and social considerations in advancing these technologies towards field implementation.
NATURE REVIEWS GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Aine O'Toole, Oliver G. Pybus, Michael E. Abram, Elizabeth J. Kelly, Andrew Rambaut
Summary: The study investigates how SARS-CoV-2 Pango lineages can be reliably designated using spike-only nucleotide sequences. While many lineages can be identified clearly with spike-only sequences, some sequences are shared among multiple lineages. The concept of lineage-sets is introduced to represent the range of Pango lineages consistent with observed mutations in spike sequences, providing a foundation for software tools to assign newly-generated sequences to lineage sets.
Article
Genetics & Heredity
Charles J. Underwood, Kitty Vijverberg, Diana Rigola, Shunsuke Okamoto, Carla Oplaat, Rik H. M. Op den Camp, Tatyana Radoeva, Stephen E. Schauer, Joke Fierens, Kim Jansen, Sandra Mansveld, Marco Busscher, Wei Xiong, Erwin Datema, Koen Nijbroek, Evert-Jan Blom, Ross Bicknell, Andrew Catanach, Sylvia Erasmuson, Christopher Winefield, Arjen J. van Tunen, Marcel Prins, M. Eric Schranz, Peter J. van Dijk
Summary: The PAR gene in dandelion triggers embryo development without fertilization, a rare phenomenon in flowering plants. This gene is inserted with a MITE transposon in the promoter region, and its expression is able to induce embryogenesis in the absence of fertilization.
Article
Genetics & Heredity
Jennifer E. Huffman, Guillaume Butler-Laporte, Atlas Khan, Erola Pairo-Castineira, Theodore G. Drivas, Gina M. Peloso, Tomoko Nakanishi, Andrea Ganna, Anurag Verma, J. Kenneth Baillie, Krzysztof Kiryluk, J. Brent Richards, Hugo Zeberg
Summary: The OAS1/2/3 cluster has been identified as a risk locus for severe COVID-19 among individuals of European ancestry, with a protective haplotype derived from Neanderthals. The splice variant of OAS1 is found in individuals of African ancestry independently, and it is likely responsible for the association with COVID-19 severity.
Review
Biochemistry & Molecular Biology
Uttpal Anand, Abhijit Dey, Arvind K. Singh Chandel, Rupa Sanyal, Amarnath Mishra, Devendra Kumar Pandey, Valentina De Falco, Arun Upadhyay, Ramesh Kandimalla, Anupama Chaudhary, Jaspreet Kaur Dhanjal, Saikat Dewanjee, Jayalakshmi Vallamkondu, Jose M. Perez de la Lastra
Summary: Cancer is a deadly disease characterized by uncontrolled cell proliferation and the formation of aggressive malignancies. In recent years, advances in molecular understanding have led to the development of new therapeutic approaches such as targeted drug therapy and immunotherapy. Despite the potential of these treatments, chemotherapy remains a commonly used option due to its effectiveness in advanced-stage malignancies. This report reviews the current advancements in chemotherapy and discusses the emerging role of targeted therapies in improving clinical outcomes for cancer patients.
Article
Agronomy
Dinesh Kumar Saini, Puja Srivast, Neeraj Pal, P. K. Gupta
Summary: In this study, meta-analysis was conducted using 2852 major QTLs out of 8998 known QTLs in wheat for yield and related traits. A total of 141 meta-QTLs were identified, including breeder's MQTLs and ortho-MQTLs. Additionally, 1202 candidate genes and 50 homologues of genes from other cereals for yield were identified. The findings of this study have important implications for wheat breeding and future research in cereals.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Huijuan Zhou, Kejun He, Jun Chen, Xianyang Zhang
Summary: Differential abundance analysis is a crucial statistical analysis in microbiome data. The compositional nature of microbiome sequencing data poses challenges in controlling false positives. In this study, the authors propose LinDA, a simple yet flexible and scalable approach that addresses the compositional effects by fitting linear regression models on centered log-ratio transformed data and correcting the bias caused by compositional effects. They demonstrate the effectiveness of LinDA through simulations and real examples, and highlight its asymptotic FDR control and extensions to mixed-effect models for correlated microbiome data.
Review
Biochemistry & Molecular Biology
Zhejun Ji, Guang-Hui Liu, Jing Qu
Summary: This article reviews the role of mitochondrial sirtuins (SIRT3, SIRT4, and SIRT5) in metabolic regulation, aging, and aging-related diseases. By understanding how sirtuins regulate metabolic processes and their functional differences in canonical pathways and signaling networks, a deeper understanding of the mechanisms underlying the delay or acceleration of biological aging can be achieved.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Review
Genetics & Heredity
Pavana Lakshmi Vaddavalli, Bjoern Schumacher
Summary: The TP53 gene is the most frequently mutated gene in human cancers, and p53 plays a crucial role in responding to DNA damage. Dysfunctional p53 leads to continued proliferation of cells with damaged genome, promoting malignant transformation. Recent research has shed light on the complexity of p53 regulation in the DNA damage response, as well as its systemic effects influenced by non-cell-autonomous signaling mechanisms. There have also been advancements in therapeutic targeting of p53.
TRENDS IN GENETICS
(2022)
Article
Genetics & Heredity
Hao Chi, Puyu Jiang, Ke Xu, Yue Zhao, Bingyu Song, Gaoge Peng, Bingsheng He, Xin Liu, Zhijia Xia, Gang Tian
Summary: This study constructed a prognostic model for HNSCC using anoikis-related genes (ANRGs) and found differential immune status and drug sensitivity between high-risk and low-risk groups. In addition, through DCA analysis, the researchers demonstrated the potential clinical benefit of the model in the clinical practice.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Esther Danenberg, Helen Bardwell, Vito R. T. Zanotelli, Elena Provenzano, Suet-Feung Chin, Oscar M. Rueda, Andrew Green, Emad Rakha, Samuel Aparicio, Ian O. Ellis, Bernd Bodenmiller, Carlos Caldas, H. Raza Ali
Summary: Imaging mass cytometry profiling of 693 breast tumors revealed 10 recurrent tumor microenvironment spatial structures, associated with genomic profiles and outcomes. These multicellular structures within the TME, varying in vascular content, stromal activation, and leukocyte composition, could improve patient stratification and link spatial organization to local TME function.
Review
Cell Biology
Karen M. Ridge, John E. Eriksson, Milos Pekny, Robert D. Goldman
Summary: This review discusses the essential functions of vimentin intermediate filaments (IFs) revealed from studies of Vim(-/-) mice and cells derived from them. It has been found that Vim(-/-) mice and their organs, tissues, and cells exhibit various phenotypes, frequently reflecting altered responses in tissue recovery. Cell-based experiments have confirmed the critical role of vimentin IFs in regulating cell mechanics.
GENES & DEVELOPMENT
(2022)
