Review
Plant Sciences
Eun-Deok Kim, Keiko U. Torii
Summary: The formation of stomata is a significant model system for understanding stem cell fate commitment. The regulatory strategies governing cell fate commitment differ between embryonic and postembryonic stomatal development. The interplay of transcription factors and cell cycle machineries is crucial for cell differentiation. Recent studies have provided insights into the molecular mechanisms underlying the interaction between transcription factors and epigenetic machineries.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Biochemistry & Molecular Biology
Bethany M. Moore, Yun Sun Lee, Peipei Wang, Christina Azodi, Erich Grotewold, Shin-Han Shiu
Summary: The modeling and experimental validation of transcriptional response to wounding and jasmonic acid identified temporal cis-regulatory codes and new regulatory sequences important for wound response. The study provides a global predictive model for wound response and highlights the significance of regulatory factors and open chromatin regions in different types of wound response.
Article
Biochemistry & Molecular Biology
Zhen Sun, Yuan Lin, Mohammed T. Islam, Richard Koche, Lin Hedehus, Dingyu Liu, Chang Huang, Thomas Vierbuchen, Charles L. Sawyers, Kristian Helin
Summary: Nuclear receptor-binding SET-domain protein 1 (NSD1) is a crucial methyltransferase involved in transcriptional regulation and is dysregulated in diseases like Sotos syndrome. NSD1 associates with H3K36me2 at regulatory elements, particularly enhancers. It promotes enhancer-dependent gene transcription by facilitating RNA polymerase II pause release, affecting cell fate transition and Sotos syndrome development.
Article
Immunology
Alison Mary Farley, An Chengrui, Sam Palmer, Dong Liu, Anastasia I. Kousa, Paul Rouse, Viktoria Major, Joanna Sweetman, Jan Morys, Andrea Corsinotti, Jennifer Nichols, Janice Ure, Renee McLay, Luke Boulter, S. Jon Chapman, Simon R. Tomlinson, C. Clare Blackburn
Summary: A recent study has challenged the widely held view that a common thymic epithelial progenitor cell (TEPC) dominates the early thymus development. Instead, the researchers found evidence of sublineage-primed progenitors that exhibit cell-fate plasticity. This discovery provides a significant advancement in understanding fetal thymic epithelial development and has implications for thymus-related clinical research.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Deepak A. Kaji, Angela M. Montero, Roosheel Patel, Alice H. Huang
Summary: This study identifies transcriptional regulators involved in the induction and differentiation of dense connective tissues. By generating tendon and fibrocartilage cells from mouse embryonic stem cells and utilizing scRNA-seq, the authors reveal molecular mechanisms underlying cell fate switch between these lineages. Additionally, the research demonstrates successful generation of 3D engineered tissues using these differentiation protocols for modeling development and disease.
NATURE COMMUNICATIONS
(2021)
Review
Cell Biology
Jordan H. Driskill, Duojia Pan
Summary: The characters YAP and TAZ play important roles in controlling stem cell functions, translating biological cues into genome-wide effects. Aberrant activity of YAP and TAZ leads to stem cell dysfunction, while therapeutic targeting of the Hippo pathway and YAP/TAZ can enhance stem cell activity for regeneration. Modulating YAP/TAZ may have potential applications in regenerative medicine and cancer therapy.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Developmental Biology
Yanyan Ding, Zhenxin Liu, Feng Liu
Summary: This study reviews recent advances in transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates, offering important insights for the generation and expansion of engraftable HSCs in vitro.
DEVELOPMENTAL BIOLOGY
(2021)
Review
Chemistry, Multidisciplinary
Ying Kong, Jiazhi Duan, Feng Liu, Lin Han, Gang Li, Chunhui Sun, Yuanhua Sang, Shuhua Wang, Fan Yi, Hong Liu
Summary: The application of physical signals in tissue engineering has the potential to regulate stem cell fate through nanostructure mediation. This method provides a new perspective for research and is expected to aid in the development of remote-controlled and wireless platforms to guide stem cell differentiation.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Cell Biology
Shanel Tsuda, Matthew E. Pipkin
Summary: This passage discusses the role of antigen-specific CD8 T cells in robust immunity to intracellular infections and explores the regulation of gene expression programs that determine cell fate. It proposes a model to describe the development of CD8 T cells and discusses insights from transcriptional control and chromatin regulation.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY
(2022)
Article
Biology
Maria Abou Chakra, Ruth Isserlin, Thinh N. Tran, Gary D. Bader
Summary: The duration of the cell cycle changes dramatically during development, acting as a transcriptional filter to control gene transcript expression, cell diversity, and the number of different cell types. Fast-developing organisms have a narrow genomic distribution of gene lengths while slower developers have more long genes. These findings support the importance of cell cycle dynamics in controlling gene transcript expression and cell fate across multicellular animals.
Article
Multidisciplinary Sciences
Marlies P. Rossmann, Karen Hoi, Victoria Chan, Brian J. Abraham, Song Yang, James Mullahoo, Malvina Papanastasiou, Ying Wang, Ilaria Elia, Julie R. Perlin, Elliott J. Hagedorn, Sara Hetzel, Raha Weigert, Sejal Vyas, Partha P. Nag, Lucas B. Sullivan, Curtis R. Warren, Bilguujin Dorjsuren, Eugenia Custo Greig, Isaac Adatto, Chad A. Cowan, Stuart L. Schreiber, Richard A. Young, Alexander Meissner, Marcia C. Haigis, Siegfried Hekimi, Steven A. Carr, Leonard Zon
Summary: The transcription factor TIF1 gamma directly controls the expression of Coenzyme Q synthesis genes, and loss of TIF1 gamma leads to decreased CoQ levels and increased histone methylation, which ultimately affects cell fate decisions. Mitochondrial metabolism plays a key role as an output of lineage transcription factors in driving early blood lineage cell fate decisions.
Article
Multidisciplinary Sciences
Huan Chen, Min Li, Guang Qi, Ming Zhao, Longyu Liu, Jingyi Zhang, Gongyou Chen, Daowen Wang, Fengquan Liu, Zheng Qing Fu
Summary: The phytohormone salicylic acid (SA) plays a key role in plant defense against biotrophic and hemibiotrophic pathogens. NPR1 and EDS1 synergistically activate pathogenesis-related (PR) genes and plant defenses by forming a protein complex and recruiting Mediator. EDS1 functions as an autonomous transcriptional coactivator with intrinsic transactivation domains and physically interacts with the CDK8 subunit of Mediator.
Article
Multidisciplinary Sciences
Rong Zhang, Hanah Goetz, Juan Melendez-Alvarez, Jiao Li, Tian Ding, Xiao Wang, Xiao-Jun Tian
Summary: Resource competition between gene circuit modules can lead to unexpected circuit functions. By building cascading bistable switches to achieve two successive cell fate transitions, a 'winner-takes-all' behavior was observed which was overcome by a division of labor strategy.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Yan Wu, Jiaqi Wu, Minghua Deng, Yihan Lin
Summary: Recent single-cell studies have revealed a new cell fate control mechanism mediated by temporal redundancy modulation during yeast stress response, which might represent an evolutionarily important strategy for maintaining functional redundancy between gene duplicates.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Yasuhiko Kondo, Himeka Hayashi
Summary: This article discusses the mechanisms and regulation of sexual preference for opposite-sex chemosensory signals in small rodents, focusing on laboratory mice, rats, and hamsters. Hormonal and central regulation, as well as the influence of sexual experience on the brain reward system, are highlighted. Additionally, the role of neuropeptides such as oxytocin, vasopressin, and kisspeptin in regulating sexual preference is reviewed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zuzana Gelova, Michelle Gallei, Marketa Pernisova, Geraldine Brunoud, Xixi Zhang, Matous Glanc, Lanxin Li, Jaroslav Michalko, Zlata Pavlovicova, Inge Verstraeten, Huibin Han, Jakub Hajny, Robert Hauschild, Milada Covanova, Marta Zwiewka, Lukas Hoermayer, Matyas Fendrych, Tongda Xu, Teva Vernoux, Jiri Friml
Summary: ABP1 is a key player in plant development with broad expression and possible involvement in additional auxin perception mechanisms. While it is not essential for transcriptional auxin signaling, gain-of-function alleles of ABP1 exhibit a wide range of growth and developmental defects.
Article
Biology
Rasmus Kristoffer Pedersen, Morten Andersen, Thomas Stiehl, Johnny T. Ottesen
Summary: This study presents and analyzes a mechanism-based mathematical model to investigate the interaction between HSC and the stem cell niche. The importance of HSC self-renewal and their role in long-term maintenance of blood cell production is revealed. Two reduced models of different complexity are proposed, one of which aligns well with clinical data and offers a potential prediction of patient prognosis. The mathematical model and reduced forms have the potential to provide insights into the regulation of HSC dynamics and blood cell formation, advancing the treatment of hematologic malignancies in the future.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Biology
Salvador Chulian, Alvaro Martinez-Rubio, Anna Marciniak-Czochra, Thomas Stiehl, Cristina Blazquez Goni, Juan Francisco Rodriguez Gutierrez, Manuel Ramirez Orellana, Ana Castillo Robleda, Victor M. Perez-Garcia, Maria Rosa
Summary: The study focused on developing mathematical models of lymphopoiesis, investigating the self-regulation characteristics of lymphocytes and their regulatory mechanisms in pediatric bone marrow, and using numerical simulations to explore the impact of proliferation and maturation rates on B-cell reconstitution.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Physiology
Thomas Stiehl, Anna Marciniak-Czochra
Summary: This study introduces a computational algorithm that can identify all clonal hierarchies compatible with bulk variant allele frequencies in patient samples, providing insights into the evolution of leukemia cells.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Cell Biology
Natalia Nikonorova, Evan Murphy, Cassio Flavio Fonseca de Lima, Shanshuo Zhu, Brigitte van de Cotte, Lam Dai Vu, Daria Balcerowicz, Lanxin Li, Xiangpei Kong, Gieljan De Rop, Tom Beeckman, Jiri Friml, Kris Vissenberg, Peter C. Morris, Zhaojun Ding, Ive De Smet
Summary: Auxin plays a crucial role in plant growth by either promoting or inhibiting processes like division and expansion. Research has shown that different concentrations of the synthetic auxin NAA can impact the proteome and phosphoproteome of root tips, leading to the discovery of novel growth regulators. These findings highlight the complex pathways involved in growth regulation in plants.
Review
Genetics & Heredity
Sarah Balderston, Gabrielle Clouse, Juan-Jose Ripoll, Grace K. Pratt, Giedrius Gasiunas, Jens-Ole Bock, Eric Paul Bennett, Kiana Aran
Summary: The discovery of CRISPR has revolutionized genome engineering and its potential goes beyond gene editing. CRISPR technology can control gene expression, image the genome in vivo, and detect specific nucleic acid sequences for diagnostics. New technologies are being developed to improve CRISPR quality control and reliability in therapeutics and beyond. The toolbox of CRISPR tools is continuing to diversify with new advancements.
Article
Multidisciplinary Sciences
Lanxin Li, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez, Jack Merrin, Jian Chen, Lana Shabala, Wouter Smet, Hong Ren, Steffen Vanneste, Sergey Shabala, Bert De Rybel, Dolf Weijers, Toshinori Kinoshita, William M. Gray, Jiri Friml
Summary: Plant growth is regulated by environmental factors, such as how plants respond to gravity by bending shoots up and roots down. Research has shown that the plant hormone auxin affects root growth by regulating cell expansion and contraction in the roots.
Review
Plant Sciences
Lanxin Li, Michelle Gallei, Jiri Friml
Summary: In this review, recent unexpected insights into the mechanisms underlying auxin regulation of growth are discussed, challenging existing models. The divergent mechanisms of apoplastic pH regulation in shoots and roots are focused on, revisiting the classical Acid Growth Theory and discussing coordinated involvement of multiple auxin signaling pathways.
TRENDS IN PLANT SCIENCE
(2022)
Article
Medicine, Research & Experimental
Lukas P. M. Kremer, Santiago Cerrizuela, Sascha Dehler, Thomas Stiehl, Jonas Weinmann, Heike Abendroth, Susanne Kleber, Alexander Laure, Jihad El Andari, Simon Anders, Anna Marciniak-Czochra, Dirk Grimm, Ana Martin-Villalba
Summary: The study identified AAV variants with high regional tropism towards adult neural stem cells, paving the way for preclinical testing of regenerative gene therapy.
MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT
(2021)
Article
Hematology
Ursula S. A. Stalmann, Fabio Ticconi, Inge A. M. Snoeren, Ronghui Li, Helene F. E. Gleitz, Glenn S. Cowley, Marie E. McConkey, Aaron B. Wong, Stephani Schmitz, Stijn N. R. Fuchs, Shubhankar Sood, Nils B. Leimkuehler, Sergio Martinez-Hoyer, Bella Banjanin, David Root, Tim H. Bruemmendorf, Juliette E. Pearce, Andreas Schuppert, Eric M. J. Bindels, Marieke A. Essers, Dirk Heckl, Thomas Stiehl, Ivan G. Costa, Benjamin L. Ebert, Rebekka K. Schneider
Summary: Genetic haploinsufficiency plays a crucial role in the clonal dominance of 5q-HSCs, providing a unique competitive advantage through increased HSC self-renewal and proliferation capacity, as well as increased fitness under inflammatory stress.
Article
Multidisciplinary Sciences
Lanxin Li, Huihuang Chen, Saqer S. Alotaibi, Ales Pencik, Maciek Adamowski, Ondrej Novak, Jiri Friml
Summary: This study investigates the mechanism of rapid alkalinization factors (RALFs) in regulating plant growth. It is found that RALF1 inhibits the growth of Arabidopsis thaliana roots by inducing apoplast alkalinization, which is mediated by the receptor FERONIA (FER) through net H+ influx. Additionally, the study reveals cross-talk between RALF1 and auxin signaling pathways, where RALF1 up-regulates auxin biosynthesis to regulate root growth. The biphasic action of RALF1 on growth allows plants to respond rapidly to environmental stimuli and reprogram growth and development in the long term.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Jennifer Saile, Theresa Wiessner-Kroh, Katarina Erbstein, Dominik M. Obermueller, Anne Pfeiffer, Denis Janocha, Jan Lohmann, Andreas Wachter
Summary: The central energy sensor kinases SnRK1 and TOR regulate light-dependent alternative splicing and developmental characteristics in Arabidopsis seedlings. They are required for skotomorphogenesis, cotyledon opening, and regular development in light. SnRK1 and TOR also act upstream of light- and sugar-regulated alternative splicing events, expanding their known action spectra in energy signaling.
Article
Cell Biology
Laura Orsatti, Thomas Stiehl, Katharina Dischinger, Roberto Speziale, Pamela Di Pasquale, Edith Monteagudo, Carsten Mueller-Tidow, Aleksandar Radujkovic, Peter Dreger, Thomas Luft
Summary: The study identified specific Kyn metabolism patterns and cytokines that may influence the severity and manifestation of fibrosing chronic graft-versus-host disease (cGVHD), especially in the case of fibrosing cGVHD with a distinct pathway shift. This research provides new biomarkers and potential clinical trial evidence for the prevention of cGVHD.
CELL REPORTS MEDICINE
(2021)
Article
Plant Sciences
Madhumitha Narasimhan, Michelle Gallei, Shutang Tan, Alexander Johnson, Inge Verstraeten, Lanxin Li, Lesia Rodriguez, Huibin Han, Ellie Himschoot, Ren Wang, Steffen Vanneste, Judit Sanchez-Simarro, Fernando Aniento, Maciek Adamowski, Jiri Friml
Summary: This study reexamined the effects of auxin on PIN endocytic trafficking and found that high concentrations of NAA and IAA have nonspecific effects on the endomembrane system, while low concentrations specifically promoted endocytosis of PIN2. This contributes to polarity maintenance and highlights the nonspecific effects of high auxin levels on trafficking and endomembrane compartments.
