Article
Anatomy & Morphology
Marc Fernandez-Guerrero, Sofia Zdral, Alejandro Castilla-Ibeas, Lucille Lopez-Delisle, Denis Duboule, Marian A. Ros
Summary: This study analyzed the transcriptomes of distal limb mesenchymal progenitors and ectodermal cells, revealing specific transcriptional signatures for different developmental stages. Genes with previously unnoticed roles in limb development were identified, along with signaling pathways enriched between different layers.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Hongbo Pang, Qiang Chen, Yueying Li, Ze Wang, Longkun Wu, Qingwen Yang, Xiaoming Zheng
Summary: By comparatively analyzing the transcriptomes of the two rice subspecies, indica and japonica, it was found that they have significantly different gene expression profiles, and identified some differentially expressed genes that may be responsible for their reproductive isolation and phenotypic differences.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Shalu Jhanwar, Jonas Malkmus, Jens Stolte, Olga Romashkina, Aimee Zuniga, Rolf Zeller
Summary: This study compared mouse and chicken limb bud development to investigate the impact of genome evolution on gene regulatory interactions, revealing the importance of spatio-temporal regulation of gene expression in embryonic development. The authors identified shared and species-specific epigenomic and genomic variations, and observed synchrony in chromatin accessibility and gene expression dynamics in mouse forelimb buds, while uncovering species-specific regulatory heterochrony in chicken wing buds. Mapping of transcription factor binding sites and construction of target gene networks revealed both conserved and species-specific interactions, providing a molecular framework for comparative Evo-Devo studies.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Sora Yonezawa, Hidemasa Bono
Summary: This study conducted a meta-analysis to explore the expression of heat stress-related genes in humans and mice, identifying common upregulated and downregulated genes and conducting further functional analysis. These findings are important for addressing climate change and technological advancements.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Svetlana Markman, Mor Zada, Eyal David, Amir Giladi, Ido Amit, Elazar Zelzer
Summary: Through single-cell RNA sequencing of developing mouse forelimb, we identify three progenitor states: naive, proximal, and autopodial, with Msx1 as a marker for naive progenitors. Lineage tracing confirms the role of naive progenitors and locates them at the outer margin of the limb along the anterior-posterior axis. Sequential pulse-chase experiments show that the progressive transition of Msx1+ naive progenitors into proximal and autopodial progenitors coincides with their differentiation into Sox9+ chondroprogenitors, occurring along all the forming skeletal segments. Hence, the skeleton forms progressively in a complex pattern.
DEVELOPMENTAL CELL
(2023)
Article
Plant Sciences
Alex Rajewski, Dinusha C. Maheepala, Jessica Le, Amy Litt
Summary: By comparing the fruit development and gene expression patterns of multiple species, we found that the expression of core fruit development genes is somewhat conserved. These genes play important roles in cell division, cell wall synthesis, and developmental patterning. In addition, we identified accessory genes with conserved expression patterns within different fruit types, highlighting the significant differences between these phenotypic classes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Miguel Ramirez, Yuliya Badayeva, Joanna Yeung, Joshua Wu, Ayasha Abdalla-Wyse, Erin Yang, Brett Trost, Stephen W. Scherer, Daniel Goldowitz
Summary: This study identified active enhancers in the mouse cerebellum during embryonic and postnatal stages, revealing dynamic gene expression regulation during cerebellar development. The enhancers were enriched for neural transcription factor binding sites and showed cell-type specific expression regulation.
Article
Immunology
Keah Higgins, Lauren N. Woodie, Haley Hallowell, Michael W. Greene, Elizabeth Hiltbold Schwartz
Summary: Obesity has been rapidly increasing in the United States over the past two decades, with serious impacts on public health. There has been a deeper understanding in recent years of the role of intestinal microbiota in obesity, especially regarding bacterial constituents.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Endocrinology & Metabolism
Jing Zhao, Ke Yao, Hua Yu, Ling Zhang, Yuyan Xu, Lang Chen, Zhen Sun, Yuqing Zhu, Cheng Zhang, Yuli Qian, Shuyan Ji, Hongru Pan, Min Zhang, Jie Chen, Cristina Correia, Taylor Weiskittel, Da-Wei Lin, Yuzheng Zhao, Sriram Chandrasekaran, Xudong Fu, Dan Zhang, Heng-Yu Fan, Wei Xie, Hu Li, Zeping Hu, Jin Zhang
Summary: This study reveals the dynamic metabolic remodelling during early mouse embryo development, with two-cell embryos favoring reductive metabolism and blastocysts showing a more oxidative state. There is a reciprocal relationship between alpha-KG and l-2-HG, with different levels in two-cell embryos and blastocysts. The data demonstrate interconnected metabolic, transcriptional, and epigenetic network remodelling, highlighting key metabolites for epigenetic reprogramming.
Article
Immunology
Shilpi Chandra, Gabriel Ascui, Thomas Riffelmacher, Ashu Chawla, Ciro Ramirez-Suastegui, Viankail C. Castelan, Gregory Seumois, Hayley Simon, Mallory P. Murray, Goo-Young Seo, Ashmitaa L. R. Premlal, Benjamin Schmiedel, Greet Verstichel, Yingcong Li, Chia-Hao Lin, Jason Greenbaum, John Lamberti, Raghav Murthy, John Nigro, Hilde Cheroutre, Christian H. Ottensmeier, Stephen M. Hedrick, Li-Fan Lu, Pandurangan Vijayanand, Mitchell Kronenberg
Summary: This study characterized the different populations of MAIT cells in mice and humans using single-cell RNA sequencing and other analyses. The study found that MAIT cells in different organs and tissues exhibit different transcriptomes and metabolic states. The study also identified environmental influences on MAIT cell subsets and function.
SCIENCE IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Hidemasa Bono
Summary: This study applied a meta-analysis approach to evaluate insect oxidative transcriptomes using publicly available data, finding many genes downregulated under oxidative stress and related to organ system process and adherens junction organization. Analysis of Drosophila melanogaster and Caenorhabditis elegans RNA-seq data demonstrated the importance of research methods in deciphering conserved networks in oxidative stress response.
Article
Multidisciplinary Sciences
Trisha A. Macrae, Miguel Ramalho-Santos
Summary: The study reveals a regulatory axis between the deubiquitinase Usp9x and PRC2 that is critical for self-renewal of mouse embryonic stem cells. Different levels of Usp9x lead to distinct chromatin and transcriptional patterns in ES cells, reminiscent of different developmental stages. Deletion of Usp9x in post-implantation embryos results in derepression of genes and morphological abnormalities, suggesting a crucial role of Usp9x-PRC2 axis in development.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Feng Chen, Zizhang Li, Xiaoyu Zhang, Peng Wu, Wenjing Yang, Junnan Yang, Xiaoshu Chen, Jian-Rong Yang
Summary: A cell lineage tree describes the accumulation of gene expression differences between cells during clonal expansion, but how functional homeostasis is maintained in the face of continuous accumulation of transcriptomic heterogeneity remains unknown. To answer this question, we experimentally determined the single-cell transcriptomes and lineage relationships, and our analyses revealed the constrained accumulation of transcriptomic heterogeneity among cells, providing novel insights into the functional homeostasis of cell populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Marco Vicari, Reza Mirzazadeh, Anna Nilsson, Reza Shariatgorji, Patrik Bjaerterot, Ludvig Larsson, Hower Lee, Mats Nilsson, Julia Foyer, Markus Ekvall, Paulo Czarnewski, Xiaoqun Zhang, Per Svenningsson, Lukas Kaell, Per E. Andren, Joakim Lundeberg
Summary: We present a method that combines histology, mass spectrometry imaging, and spatial transcriptomics to measure mRNA transcripts and low-molecular-weight metabolites simultaneously across tissue regions. The potential of this method is demonstrated using mouse and human brain samples in the context of dopamine and Parkinson's disease.
NATURE BIOTECHNOLOGY
(2023)
Article
Biology
Markus Frederik Schliffka, Anna Francesca Tortorelli, Ozge Ozguc, Ludmilla de Plater, Oliver Polzer, Diane Pelzer, Jean-Leon Maitre
Summary: Studies have shown that actomyosin contractility plays a crucial role in driving mammalian embryo development, and even in cases of failed cell division, morphogenesis and fate specification can still take place in the embryo.
Article
Anatomy & Morphology
Leonardo Beccari, Gabriel Jaquier, Lucille Lopez-Delisle, Eddie Rodriguez-Carballo, Benedicte Mascrez, Sandra Gitto, Joost Woltering, Denis Duboule
Summary: HOXA13 and HOXD13 transcription factors cooperatively activate Dbx2 gene expression by binding to mammalian specific regulatory sequences in the Dbx2 neighborhood during digit development. Enhancers near Dbx2 can overcome TAD boundaries in order to co-regulate a set of genes located in distinct chromatin domains.
DEVELOPMENTAL DYNAMICS
(2021)
Article
Multidisciplinary Sciences
Benjamin D. Weger, Cedric Gobet, Fabrice P. A. David, Florian Atger, Eva Martin, Nicholas E. Phillips, Aline Charpagne, Meltem Weger, Felix Naef, Frederic Gachon
Summary: The study investigated the roles of the circadian clock and feeding rhythms in regulating rhythmic gene expression in the liver, highlighting their importance and differential contributions. Both feeding patterns and the circadian clock influence gene expression rhythms, with distinct amplitudes. By analyzing multiple core clock regulators, the research revealed their varying impacts on liver gene expression regulation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Jerome Mermet, Jake Yeung, Felix Naef
Summary: The study reveals that both clock-controlled and clock-independent chromatin topology play a role in regulating the rhythmic physiology of the liver in mice. Dynamic and static DNA contacts contribute to the circadian transcription of liver physiology.
Article
Biochemistry & Molecular Biology
Nicholas E. Phillips, Alice Hugues, Jake Yeung, Eric Durandau, Damien Nicolas, Felix Naef
Summary: Research on single-cell mRNA dynamics of core clock genes in mouse fibroblasts using single-molecule fluorescence technology revealed significant variability between cells. A probabilistic model was developed to account for transcriptional bursting, circadian time, and cell-to-cell heterogeneity, with clock time contributing only a small fraction to mRNA number variability between cells.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Editorial Material
Multidisciplinary Sciences
Katharine C. Abruzzi, Cedric Gobet, Felix Naef, Michael Rosbash
Summary: The study by Ray et al. claimed the presence of temperature-compensated free-running mRNA oscillations in Bmal1(-/-) liver slices and skin fibroblasts. However, upon reanalysis, fewer reproducible mRNA oscillations were found in this genotype, along with errors and potentially inappropriate analyses.
Article
Anatomy & Morphology
Marc Fernandez-Guerrero, Sofia Zdral, Alejandro Castilla-Ibeas, Lucille Lopez-Delisle, Denis Duboule, Marian A. Ros
Summary: This study analyzed the transcriptomes of distal limb mesenchymal progenitors and ectodermal cells, revealing specific transcriptional signatures for different developmental stages. Genes with previously unnoticed roles in limb development were identified, along with signaling pathways enriched between different layers.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Christopher Chase Bolt, Lucille Lopez-Delisle, Benedicte Mascrez, Denis Duboule
Summary: This study explores the link between rearrangements in the HoxD cluster and mesomelic dysplasia in both humans and mice, providing a mechanistic framework to understand the molecular origins of this condition associated with 2q31. By engineering a 1 Mb inversion including the HoxD gene cluster, the authors demonstrate the role of ectopic HOXD13 in inducing mesomelic dysplasia and show that this bone anomaly can be rescued by a secondary Hoxd13 null mutation. Single-cell expression analysis and evaluation of HOXD13 binding sites suggest that the phenotype primarily arises through genes controlled by HOXD13 in distal limb cells.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Andrea Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodriguez-Carballo
Summary: This study investigates the function of boundaries in regulating gene expression during development, particularly focusing on the ability of certain boundary sequences to act independently of their genomic context. The researchers found that a boundary sequence from the HoxD gene cluster can split a topological domain and affect gene expression levels, even when introduced into a different genomic context. This suggests that topological boundaries can function autonomously, providing important insights into gene regulation processes in mammalian genomes.
Article
Cell Biology
Ana Rita Amandio, Leonardo Beccari, Lucille Lopez-Delisle, Benedicte Mascrez, Jozsef Zakany, Sandra Gitto, Denis Duboule
Summary: Understanding the diverse functions of CTCF sites within the Hox gene clusters is crucial for the formation of TAD borders and maintaining gene expression, showing significant evolutionary conservation.
GENES & DEVELOPMENT
(2021)
Article
Developmental Biology
Aurelie Hintermann, Isabel Guerreiro, Lucille Lopez-Delisle, Christopher Chase Bolt, Sandra Gitto, Denis Duboule, Leonardo Beccari
Summary: Modifications in gene regulation are important for the evolution of organisms. This study focuses on cis-regulatory elements (CREs), which interact with target genes through higher-order chromatin structures. The researchers analyzed the regulation of Hoxd genes in murine vibrissae and chicken feather primordia, and compared it with the regulation in the elongation of the posterior trunk. They found that different subsets of Hoxd genes were regulated by lineage-specific enhancers in the two structures, while the regulation in the embryonic trunk relied on conserved CREs. These non-coding sequences in the trunk have functionally diverged between species, but transcriptional robustness is maintained.
Article
Multidisciplinary Sciences
Christopher Chase Bolt, Lucille Lopez-Delisle, Aurelie Hintermann, Benedicte Mascrez, Antonella Rauseo, Guillaume Andrey, Denis Duboule
Summary: The study demonstrates that a strong enhancer sequence can be regulated by the chromatin environment provided by a nearby topologically associated domain (TAD). Furthermore, the results indicate that the functioning of enhancer elements is subordinated to the host chromatin context.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Clemence S. Hurni, Benjamin Weger, Cedric S. Gobet, Felix Naef
Summary: This study analyzed the temporal regulation of RNA synthesis, splicing, nuclear export, and degradation in eukaryotes, specifically focusing on the circadian cycle. The researchers found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs.
Article
Multidisciplinary Sciences
Lorenzo Talamanca, Cedric Gobet, Felix Naef
Summary: The study revealed that the circadian clock regulates human physiology, but the specific gene expression rhythms and their dependence on age and sex in humans were not well-defined. By combining data from the GTEx project and an algorithm, the researchers identified mRNA rhythms in 46 tissues and found that they varied in breadth and were affected by sex and age. The overall gene expression rhythms were more sustained in females, while rhythmic programs generally dampened with age.
Article
Genetics & Heredity
Hocine Rekaik, Lucille Lopez-Delisle, Aurelie Hintermann, Benedicte Mascrez, Celia Bochaton, Alexandre Mayran, Denis Duboule
Summary: In mouse pseudo-embryos in vitro, the temporal activation of Hox genes starts from the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Afterwards, posterior CTCF sites act as transient insulators, regulating the timed transcription of more posterior genes. This temporal activation contributes to the proper identities of structures along the rostrocaudal axis.
Article
Endocrinology & Metabolism
Colas Droin, Jakob El Kholtei, Keren Bahar Halpern, Clemence Hurni, Milena Rozenberg, Sapir Muvkadi, Shalev Itzkovitz, Felix Naef
Summary: This study reveals the interplay between gene regulation in space and time in the liver using single-cell RNA-seq, showing that many genes exhibit both zonation and rhythmic expression, covering key hepatic functions as well as other processes such as protein chaperones. Additionally, the expression of Wnt target genes is shown to be rhythmic and localized, potentially influenced by rhythmically expressed Wnt ligands from non-parenchymal cells near the central vein.
