Article
Biotechnology & Applied Microbiology
Zhenyang Liao, Fei Dong, Juan Liu, Lele Xu, Amy Marshall-Colon, Ray Ming
Summary: This research analyzed the developmental stages of papaya pistil and identified differentially expressed genes related to pistil development and sex differentiation. Transcription factor and hormone-related genes were revealed based on functional and regulatory network analysis. These findings provide new insights into the molecular mechanism of pistil development and sex differentiation in papaya.
Article
Biochemistry & Molecular Biology
Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti, Robert J. Schmitz
Summary: By analyzing single-cell genomics data from six maize organs, researchers identified cis-regulatory factors and trans-regulatory factors, revealing the crucial role of cell-type-specific regulatory elements in gene expression regulation, and developed the single-cell analysis software Socrates for studying cis-regulatory variation in various species.
Review
Cell Biology
Trine V. Dam, Nicolaj I. Toft, Lars Grontved
Summary: The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing rapidly. There are difficulties in diagnosing and treating NAFLD. Further insight into disease mechanisms and gene regulatory mechanisms associated with tissue remodeling is needed. Mapping the cis-regulatory genome and single-cell analysis are emerging technologies that provide more possibilities for research.
Article
Biotechnology & Applied Microbiology
Bahareh Nikparvar, Margarita Andreevskaya, Ilhan C. Duru, Florentina I. Bucur, Leontina Grigore-Gurgu, Daniela Borda, Anca I. Nicolau, Christian U. Riedel, Petri Auvinen, Nadav Bar
Summary: The pathogen Listeria (L.) monocytogenes exhibits different gene regulation modes in response to high pressure processing, including survival mode, repair mode, and re-growth mode. This allows for the timely activation of transcription factors associated with immediate stress response, followed by repair and re-growth to survive and recover from extreme conditions. The findings provide insights for potential design of specific strategies to target genes or mechanisms to prevent L. monocytogenes recovery during food storage under high pressure conditions.
Article
Oncology
Vito Alessandro Lasorsa, Annalaura Montella, Sueva Cantalupo, Matilde Tirelli, Carmen de Torres, Sanja Aveic, Gian Paolo Tonini, Achille Iolascon, Mario Capasso
Summary: This study focuses on noncoding cis-regulatory variants in neuroblastoma and identifies somatic mutations in regulatory elements that play a role in tumorigenesis. The findings highlight the importance of assessing these variants and long-range interactions in understanding the drivers of neuroblastoma.
Review
Biochemistry & Molecular Biology
Seungsoo Kim, Joanna Wysocka
Summary: Uncovering the cis-regulatory code that governs gene transcription in a given genome and cellular state remains a central goal of biology. This review discusses the different layers of regulation that influence transcriptional outputs, including the binding of transcription factors to specific DNA sequences, the role of cofactors in facilitating their function, and the complex interplay within regulatory landscapes. The authors propose that a quantitative, mechanistically informed model of transcriptional regulation is essential for ultimately understanding the cis-regulatory code.
Article
Multidisciplinary Sciences
Jonas Malkmus, Laurene Ramos Martins, Shalu Jhanwar, Bonnie Kircher, Victorio Palacio, Rushikesh Sheth, Francisca Leal, Amandine Duchesne, Javier Lopez-Rios, Kevin A. Peterson, Robert Reinhardt, Koh Onimaru, Martin J. Cohn, Aimee Zuniga, Rolf Zeller
Summary: The study on Grem1 enhancers in the mouse genome revealed the cis-regulatory logic behind the spatio-temporal control of Grem1 during limb bud development, showing that transcript levels are controlled in an additive manner and spatial regulation requires synergistic interactions among multiple enhancers. The research also discovered substantial spatial plasticity in Grem1 regulation, providing insights into the evolution process from fishes to tetrapods.
NATURE COMMUNICATIONS
(2021)
Review
Plant Sciences
Mohsen Hajheidari, Shao-shan Carol Huang
Summary: Transcription factors play a critical role in cell fate decisions, integrating developmental and environmental signals through binding to specific cis-regulatory modules. Precise identification of TF binding sites is essential for understanding regulatory networks and genetic variations.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Rebekah R. Starks, Haninder Kaur, Geetu Tuteja
Summary: The placenta is a temporary organ that provides nutrients, oxygen, and protection to the developing fetus in utero. Defects in its development may lead to severe consequences for both the mother and fetus due to misregulated gene expression. Analysis of ChIP-seq data for histone modifications in the mouse placenta identified associations of active and poised promoters and enhancers with different categories of genes, providing a foundation for future studies on gene regulation in the midgestation mouse placenta.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Jaya Krishnan, Chris W. Seidel, Ning Zhang, Narendra Pratap Singh, Jake VanCampen, Robert Peuss, Shaolei Xiong, Alexander Kenzior, Hua Li, Joan W. Conaway, Nicolas Rohner
Summary: Cis-regulatory changes have been found to contribute to the metabolic adaptation in different morphotypes of Astyanax mexicanus, with genetically diverged and differentially regulated elements identified between surface and cave populations. This study sheds light on the molecular mechanisms underlying metabolic adaptations to nutrient-deprived cave environments.
Article
Biochemical Research Methods
Neel Patel, William S. Bush
Summary: This study developed a general model of transcription factor influence on gene expression by incorporating both cis and trans gene regulatory features. The models performed significantly better compared to models containing only cis-regulatory features, and the inclusion of long distance chromatin interactions further improved accuracy. The refined effect estimates generated by the models allow for characterization of individual transcription factors' roles across the genome, providing a framework for integrating multiple data types into a single model of transcriptional regulation.
BMC BIOINFORMATICS
(2021)
Review
Plant Sciences
Alexandre P. Marand, Andrea L. Eveland, Kerstin Kaufmann, Nathan M. Springer
Summary: This article discusses the functions and identification methods of various classes of cis-regulatory elements in plant development and response to the environment. It also highlights the opportunities to exploit cis-regulatory variants for crop improvement efforts.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jian Sun, Yijun Lin, Nayoung Ha, Jianfei Zhang, Weiqi Wang, Xudong Wang, Qian Bian
Summary: In this study, researchers used single-cell RNA-Seq to investigate the transcriptional dynamics during mouse maxillary development. They identified distinct mesenchymal cell populations and their developmental trajectory, as well as key transcription factors associated with mesenchymal fate transitions. This study provides important insights for understanding craniofacial morphogenesis and abnormalities at a systems-level.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Editorial Material
Genetics & Heredity
Emily R. Miraldi, Xiaoting Chen, Matthew T. Weirauch
Summary: A new study introduces a novel deep-learning approach to decode the syntax of transcription-factor binding from high-resolution ChIP-nexus data. In silico simulations confirmed complex sequence-based predictions, including helical periodicity and directional cooperativity between transcription factors.
Article
Plant Sciences
Lydia Gramzow, Renu Sharma, Guenter Theissen
Summary: MADS-box genes are transcription factors that play important roles in plant development and evolution. The FLC-like clade of MADS-box genes, especially the MAF-like genes, show unusual evolutionary dynamics and have been found to have a key role in floral organ identity. By studying the genomic data of Brassicaceae species, we discovered that FLC-like genes in this family evolve under different strengths of purifying selection and that the tandem arrangement of MAF-like genes leads to high rates of duplication and loss. We hypothesize that the rapid evolution of MAF-like genes contributed to the successful adaptation of Brassicaceae to different environments.
Article
Biophysics
Nebojsa Murisic, Vincent Hakim, Ioannis G. Kevrekidis, Stanislav Y. Shvartsman, Basile Audoly
BIOPHYSICAL JOURNAL
(2015)
Article
Cell Biology
Victoria Tarle, Andrea Ravasio, Vincent Hakim, Nir S. Gov
INTEGRATIVE BIOLOGY
(2015)
Article
Neurosciences
Srdjan Ostojic, German Szapiro, Eric Schwartz, Boris Barbour, Nicolas Brunel, Vincent Hakim
JOURNAL OF NEUROSCIENCE
(2015)
Article
Neurosciences
Antonin Blot, Camille de Solages, Srdjan Ostojic, German Szapiro, Vincent Hakim, Clement Lena
JOURNAL OF PHYSIOLOGY-LONDON
(2016)
Article
Biochemistry & Molecular Biology
Marc Santolini, Iori Sakakibara, Morgane Gauthier, Francesc Ribas-Aulinas, Hirotaka Takahashi, Tatsuya Sawasaki, Vincent Mouly, Jean-Paul Concordet, Pierre-Antoine Defossez, Vincent Hakim, Pascal Maire
NUCLEIC ACIDS RESEARCH
(2016)
Article
Cell Biology
Veronica Perez-Schuster, Anirudh Kulkarni, Morgane Nouvian, Sebastian A. Romano, Konstantinos Lygdas, Adrien Jouary, Mario Dippopa, Thomas Pietri, Mathieu Haudrechy, Virginie Candat, Jonathan Boulanger-Weill, Vincent Hakim, German Sumbre
Review
Physics, Multidisciplinary
Vincent Hakim, Pascal Silberzan
REPORTS ON PROGRESS IN PHYSICS
(2017)
Article
Biochemical Research Methods
Jonas Ranft, Leandro G. Almeida, Pamela C. Rodriguez, Antoine Triller, Vincent Hakim
PLOS COMPUTATIONAL BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Herve Rouault, Marc Santolini, Francois Schweisguth, Vincent Hakim
NUCLEIC ACIDS RESEARCH
(2014)
Article
Multidisciplinary Sciences
Marc Santolini, Thierry Mora, Vincent Hakim
Article
Biology
Guy Bouvierm, Johnatan Aljadeff, Claudia Clopath, Celian Bimbard, Jonas Ranft, Antonin Blot, Jean-Pierre Nadel, Nicolas Brunel, Vincent Hakim, Boris Barbour
Article
Biophysics
Thomas Chapdelaine, Vincent Hakim, Antoine Triller, Jonas Ranft, Christian G. Specht
Summary: Postsynaptic scaffold proteins immobilize neurotransmitter receptors at synapses for efficient transmission. Gephyrin and GlyRs form complexes at inhibitory synapses, with dynamics influenced by their interactions. This reciprocal stabilization provides quantitative insights into the organization of synaptic proteins.
BIOPHYSICAL JOURNAL
(2021)
Article
Biology
Ling Kang, Jonas Ranft, Vincent Hakim
Summary: This article presents a simple model of motor cortex that accurately reproduces the statistical characteristics of recorded data during movement preparation. The model suggests that traveling waves in the motor cortex are result of the dephasing caused by external inputs rather than solely a product of recurrent connectivity.
Article
Materials Science, Multidisciplinary
Vincent Hakim, Simon Pigeon, Amandine Aftalion
Summary: Motivated by recent experiments, this article theoretically analyzes the flow past an obstacle of a one-dimensional quantum fluid of light, which is resonantly driven and exhibits bistability. The flow undergoes multiple abrupt transitions when the fluid velocity or the obstacle potential strength is increased. Unlike usual fluids and superfluids, these transitions occur between stationary states and are closely related to the fluid bistability. Interestingly, at the transition points, the fluid in the obstacle wake is in an unstable intermediate density state.
Article
Physics, Fluids & Plasmas
Vincent Hakim, Jonas Ranft