Article
Multidisciplinary Sciences
Shih-Chiang Lo, Chao-Xuan You, Bo-Ren Chen, Ching-Chu Hsieh, Cheng-En Li, Che-Chi Shu
Summary: This study revealed that DNA in gene circuits plays a special role in resetting noise, allowing cells to switch between upstream TF and downstream products. By applying the stochastic simulation algorithm, researchers identified the parameter values that lead to this interesting phenomenon.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Zhuo Chen, Brenda Zarazua-Osorio, Priyanka Srivastava, Masaya Fujita, Oleg A. Igoshin
Summary: In this study, the researchers used mathematical modeling and experiments to show that a regulator called Spo0A controls cell differentiation in Bacillus subtilis. They also explained why biofilm formation and sporulation appear to be mutually exclusive on a single-cell level.
Article
Immunology
Dorota Iwaszkiewicz-Grzes, Magdalena Piotrowska, Mateusz Gliwinski, Zuzanna Urban-Wojciuk, Piotr Trzonkowski
Summary: The study revealed that insulin beta chain peptide 9-23 favored specific Tregs expression, while whole insulin activated both Tregs and Teffs. Tregs SPECB:9-23 showed the highest level of expression in crucial genes and lower methylation levels.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Wencheng Yin, Luis Mendoza, Jimena Monzon-Sandoval, Araxi O. Urrutia, Humberto Gutierrez
Summary: Transcriptomes self-organize into gene co-expression clusters where genes display coordinated expression patterns across samples. Highly co-expressed gene groups are enriched in common functions and processes. Widespread co-expression naturally emerges in regulatory networks and serves as a reliable indicator of active co-regulation in cellular contexts.
Article
Multidisciplinary Sciences
Renjie Wu, Bangyan Zhou, Wei Wang, Feng Li
Summary: This study categorizes the states of single eukaryotic genes, identifies 6 essential transcriptional events, and reveals how transcriptional bursting is modulated by various regulators. The results provide insights into transcriptional sensitivity, burst profiles, intrinsic transcriptional noise, and gene induction requirements.
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
Biotechnology & Applied Microbiology
Yongge Li, Fusong Ju, Zhiyuan Chen, Yiming Qu, Huanhuan Xia, Liang He, Lijun Wu, Jianwei Zhu, Bin Shao, Pan Deng
Summary: This study introduces a neural network model called CREaTor, which can simulate cis-regulatory patterns up to 2 Mb from target genes and predict specific cis-regulatory patterns in new cell types without prior knowledge of cCRE-gene interactions or additional training, using only RNA-seq and ChIP-seq data.
Article
Biochemical Research Methods
Alexander P. Wu, Jian Peng, Bonnie Berger, Hyunghoon Cho
Summary: ShareNet is a Bayesian framework that enhances the accuracy of cell type-specific gene regulatory networks by sharing information across related cell types. The method demonstrates significantly improved accuracy on three benchmark scRNA-seq datasets and reveals key changes in gene associations that support the complex rewiring of regulatory networks.
Article
Biotechnology & Applied Microbiology
Louis Graf, Younhee Shin, Ji Hyun Yang, Il Ki Hwang, Hwan Su Yoon
Summary: The study reveals clear spatial and temporal variation in the expression patterns and biological functions of genes in different tissues of brown algae.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Biology
Fernanda M. Bosada, Karel van Duijvenboden, Alexandra E. Giovou, Mathilde R. Rivaud, Jae-Sun Uhm, Arie O. Verkerk, Bastiaan J. Boukens, Vincent M. Christoffels, Kalyanam Shivkumar
Summary: Heart development and rhythm control are affected by the dosage of Tbx5. Increased expression of TBX5 is associated with atrial fibrillation (AF), while haploinsufficiency of TBX5 causes conduction disorders. In this study, two AF-associated genomic regions in the Tbx5 locus were deleted, leading to a modest increase in Tbx5 expression in the postnatal atria. This increase in Tbx5 expression resulted in changes in gene expression, ion transport, conduction, susceptibility to atrial arrhythmias, and action potential duration of atrial cardiomyocytes. The study also identified an AF-associated variant that affects the transcriptional activity of a region in Tbx5. Additionally, an interaction between Tbx5 and another AF gene, Prrx1, was discovered. This study highlights the importance of dosage-dependent transcription factors in cardiac gene regulation and disease susceptibility.
Article
Biology
Carol A. Edwards, William M. D. Watkinson, Stephanie B. Telerman, Lisa C. Hulsmann, Russell S. Hamilton, Anne C. Ferguson-Smith, Deborah Bourc'his
Summary: In mice and humans, imprinting genes play important roles in development, behavior, and post-natal adaptations. Failure to properly imprint genes in humans is associated with various disorders and diseases. Researchers have used RNA-seq technologies and hybrid mouse strains to identify novel imprinted genes, leading to an increase in reported genes with parental origin-specific expression bias. However, validation experiments show that many of these genes are not genuine imprinted genes and that the mouse strain has a greater influence on expression biases than parental origin.
Article
Biology
Lucy Ham, Marcel Jackson, Michael P. H. Stumpf
Summary: Single-cell expression profiling reveals extensive cell-to-cell variability at the transcriptomic and proteomic level, posing challenges in inferring dynamics and causes of variability. New mathematical models and experimental set-ups are proposed to distinguish intrinsic and extrinsic noise, providing insights into understanding the origins and effects of cell-to-cell variability.
Article
Multidisciplinary Sciences
Helen C. Schuster, Frank Hirth
Summary: Conserved cis-regulatory elements (CREs) control the expression networks of Engrailed-, Pax2-, and dachshund-related genes, directing the formation and function of midbrain circuits in arthropods and vertebrates. Analysis of 31 sequenced genomes from different animal clades reveals the presence of Pax2- and dachshund-related CRE-like sequences in anthozoan Cnidaria. The full complement, including Engrailed-related CRE-like sequences, is found in spiralians, ecdysozoans, and chordates with a brain, indicating a conserved core domain that distinguishes these genes from randomly assembled sequences.
Article
Mathematical & Computational Biology
Meiling Chen, Tianshou Zhou, Jiajun Zhang
Summary: The transcription of genes in single cells is discussed as a probabilistic process, with emphasis on the relationship between variance and mean expression. It is revealed that the sign of a key parameter beta in this relationship is entirely controlled by external regulation, rather than promoter structure, and is determined by the independence or correlation of regulators as stochastic variables. The findings suggest that external regulation governs the mean-noise relationship more so than promoter sequence.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Madalena Chaves, Luis C. Gomes-Pereira, Jeremie Roux
Summary: This study developed a modeling approach utilizing single-cell response data to identify regulatory reactions driving population heterogeneity in drug response, providing potential regulatory targets to curb cell dynamics of drug resistance.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Anne-Sophie L'Honneur, Herve Leh, Fanny Laurent-Tchenio, Uriel Hazan, Flore Rozenberg, Stephanie Bury-Mone
Article
Multidisciplinary Sciences
Alejandro Pina-Iturbe, Diego Ulloa-Allendes, Catalina Pardo-Roa, Irenice Coronado-Arrazola, Francisco J. Salazar-Echegarai, Bianca Sclavi, Pablo A. Gonzalez, Susan M. Bueno
SCIENTIFIC REPORTS
(2018)
Article
Microbiology
Wurihan, Gezi, Elisa Brambilla, Shuwen Wang, Hongwei Sun, Lifei Fan, Yixin Shi, Bianca Sclavi, Morigen
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Ecology
Bianca Sclavi, John Herrick
JOURNAL OF EVOLUTIONARY BIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Soumaya Najah, Corinne Saulnier, Jean-Luc Pernodet, Stephanie Bury-Mone
Article
Biochemistry & Molecular Biology
Malikmohamed Yousuf, Ilaria Iuliani, Reshma T. Veetil, Aswin Sai Narain Seshasayee, Bianca Sclavi, Marco Cosentino Lagomarsino
NUCLEIC ACIDS RESEARCH
(2020)
Article
Multidisciplinary Sciences
Estelle Crozat, Catherine Tardin, Maya Salhi, Philippe Rousseau, Armand Lablaine, Tommaso Bertoni, David Holcman, Bianca Sclavi, Pietro Cicuta, Francois Cornet
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Yang Si, Chloe Grazon, Gilles Clavier, Jutta Rieger, Yayang Tian, Jean-Frederic Audibert, Bianca Sclavi, Rachel Meallet-Renault
Article
Microbiology
Qing Zhang, Elisa Brambilla, Rui Li, Hualin Shi, Marco Cosentino Lagomarsino, Bianca Sclavi
Article
Multidisciplinary Sciences
Michal Wlodarski, Leonardo Mancini, Bianca Raciti, Bianca Sclavi, Marco Cosentino Lagomarsino, Pietro Cicuta
Article
Biochemistry & Molecular Biology
M. Cristofalo, C. A. Marrano, D. Salerno, R. Corti, V Cassina, A. Mammola, M. Gherardi, B. Sclavi, M. Cosentino Lagomarsino, F. Mantegazza
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2020)
Article
Multidisciplinary Sciences
Mia Panlilio, Jacopo Grilli, Giorgio Tallarico, Ilaria Iuliani, Bianca Sclavi, Pietro Cicuta, Marco Cosentino Lagomarsino
Summary: By studying the dynamic size-growth behavior of single cells during nutrient upshifts, it was found that the division rate changes quickly before the growth rate reaches a steady state, while adder correlations are robustly conserved. Proposed mechanisms involving replication-segregation or septum completions were falsified, and instead, an accumulation of a putative constitutively expressed P-sector divisor protein was shown to explain the behavior during the shift.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Virginia S. Lioy, Jean-Noel Lorenzi, Soumaya Najah, Thibault Poinsignon, Herve Leh, Corinne Saulnier, Bertrand Aigle, Sylvie Lautru, Annabelle Thibessard, Olivier Lespinet, Pierre Leblond, Yan Jaszczyszyn, Kevin Gorrichon, Nelle Varoquaux, Ivan Junier, Frederic Boccard, Jean-Luc Pernodet, Stephanie Bury-Mone
Summary: The linear chromosome structure of Streptomyces bacteria is linked to genetic compartmentalization, and the onset of metabolic differentiation involves rearrangement of chromosome architecture.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Audrey Vingadassalon, Florence Lorieux, Maud Juguet, Alba Noel, Luisa D. F. Santos, Laura Marin Fernandez, Jean-Luc Pernodet, Stephanie Bury-Mone, Sylvie Lautru
Summary: The production of specialized metabolites by Streptomyces bacteria is typically regulated temporally and involves global and pathway-specific mechanisms. The biosynthesis of congocidine, a pyrrolamide metabolite, in Streptomyces ambofaciens ATCC23877 is controlled by the transcriptional regulator Cgc1. This study reveals a new feed-forward induction mechanism in which congocidine induces its own biosynthesis by activating the transcription of cgc1.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biology
Shi Yu, Julian Sheats, Pietro Cicuta, Bianca Sclavi, Marco Cosentino Lagomarsino, Kevin D. Dorfman
COMMUNICATIONS BIOLOGY
(2018)
