Editorial Material
Cell Biology
Yuqing Lei, Ting Huang, Gaoyue Jiang, Yabin Zhang, Shiyan Liu, Huihui Li, Kefeng Lu
Summary: In yeast cells, the RNA polymerase II subunit Rpb9 upregulates the transcription of the autophagy gene ATG1 specifically and efficiently, with the mediation of Gcn4. This regulation is crucial for autophagic activities induced by starvation. Furthermore, the function of Rpb9 in autophagy and the activation of ATG1 transcription is conserved in mammalian cells.
Article
Multidisciplinary Sciences
Aileen Julia Riesle, Meijiang Gao, Marcus Rosenblatt, Jacques Hermes, Helge Hass, Anna Gebhard, Marina Veil, Bjorn Gruening, Jens Timmer, Daria Onichtchouk
Summary: This study investigates the combinatorial mechanisms of genome activation and shows that zebrafish genome activators Pou5f3 and Nanog exhibit different roles in the activation process. They act as pioneer-like transcription factors on synergistic enhancers, promoting histone acetylation and transcription activation. However, on antagonistic enhancers, one of the factors acts as a non-pioneer-like transcription factor, competing with the activator and blocking its effects. This activator-blocker mechanism restricts widespread transcriptional activation and prevents premature expression of late developmental genes in early embryos.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Plant Sciences
Rodrigo S. Reis
Summary: There is a significant gap in our understanding of thermomorphogenesis regulation, specifically in processes involving RNA. This gap presents opportunities for exciting new discoveries in post-transcriptional regulation, while also posing manageable challenges.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Shivani Nanda, Marc-Antoine Jacques, Wen Wang, Chad L. Myers, L. Safak Yilmaz, Albertha J. M. Walhout
Summary: A new study reveals that three-quarters of metabolic genes in the nematode Caenorhabditis elegans are transcriptionally regulated, and generates a co-regulated subpathway map of metabolism. The researchers also develop a web application to query gene associations with metabolic pathways. This study sheds light on the ubiquity of transcriptional regulation in metabolism and provides a blueprint for similar studies in other organisms.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Ka Lung Cheung, Anbalagan Jaganathan, Yuan Hu, Feihong Xu, Alannah Lejeune, Rajal Sharma, Cristina I. Caescu, Jamel Meslamani, Adam Vincek, Fan Zhang, Kyung Lee, Nilesh Zaware, Amina Abdul Qayum, Chunyan Ren, Mark H. Kaplan, John Cijiang He, Huabao Xiong, Ming-Ming Zhou
Summary: This study uncovers a previously unrecognized mechanism of self-directed cell type-specific regulation of the master transcription factor Stat3 through its own transcriptional target Hipk2 in Th17 cell differentiation. These findings provide insights into the regulation of Th17 cell immune functions and suggest a therapeutic strategy for developing targeted therapies for Th17-associated inflammatory disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Plant Sciences
William Agbemafle, Min May Wong, Diane C. Bassham
Summary: This review summarizes key regulatory mechanisms for modulating autophagy through post-translational modification or transcriptional regulation. Plants activate cellular responses to adapt to changing environmental conditions, one of which is autophagy, where cellular components are delivered to the vacuole for degradation. Autophagy is activated by various conditions, and the pathways controlling its activation are being elucidated. However, there is still much to discover regarding how these factors work together to properly modulate autophagy in response to specific signals.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Article
Biology
Miguel Turrero Garcia, Sarah K. Stegmann, Tiara E. Lacey, Christopher M. Reid, Sinisa Hrvatin, Caleb Weinreb, Manal A. Adam, M. Aurel Nagy, Corey C. Harwell
Summary: This study investigates how septal neuron diversity is established during neurogenesis, revealing that septal eminence progenitors differ from rostral septal progenitors in molecular profiles, proliferative capacity, and fate potential. Specifically, Nkx2.1-expressing septal eminence progenitors give rise to neurons of at least three morphological classes, born in temporal cohorts distributed across different septal nuclei in a sequential pattern.
Review
Biotechnology & Applied Microbiology
Georgette Femerling, Socorro Gama-Castro, Paloma Lara, Daniela Ledezma-Tejeida, Victor H. Tierrafria, Luis Muniz-Rascado, Cesar Bonavides-Martinez, Julio Collado-Vides
Summary: The ability to regulate gene expression is crucial for bacteria to adapt and interact with the environment. This article provides an overview of the transcriptional regulatory knowledge for Escherichia coli K-12, focusing on the sensing mechanisms and regulation of gene expression. It discusses the signal transduction pathways and the role of allosteric effectors in the sensing process. The article also introduces the concept of genetic sensory-response units and their functional heterogeneity.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
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)
Article
Plant Sciences
Chongmin Wang, Jun Li, Tao Zhou, Yongping Zhang, Haijun Jin, Xiaoqing Liu
Summary: This study analyzed the transcriptome of I. stachyodes roots to gain insights into the biosynthesis regulatory network of proanthocyanidins (PAs). It identified key structural genes and transcription factors involved in PA biosynthesis, and provided new insights into the molecular pathways underlying PA accumulation.
Review
Biochemistry & Molecular Biology
Emilie Bourdonnay, Thomas Henry
Summary: Gasdermins (GSDM) are a family of proteins that play important roles in cell death, immune response, disease susceptibility, and treatment response. The expression of GSDM genes is influenced by various factors and has been associated with diseases such as asthma, inflammatory bowel disease, and cancer.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Audrey R. Q. Lim, Que Kong, Sanjay K. Singh, Liang Guo, Ling Yuan, Wei Ma
Summary: This study identifies and characterizes HaWRI1, a sunflower ortholog of the transcription factor WRI1, which is highly expressed in developing seeds and stimulates oil accumulation. It is demonstrated that HaWRI1 acts as a pivotal transcription factor controlling the expression of genes involved in late glycolysis and fatty acid biosynthesis. The study also highlights the importance of an 80 amino-acid C-terminal domain of HaWRI1 for its transactivation. Additionally, seed-specific overexpression of HaWRI1 in Arabidopsis plants leads to enhanced seed oil content, suggesting its potential for bioengineering sunflower oil yield improvement.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Amanda Vaccalluzzo, Lisa Solieri, Davide Tagliazucchi, Alice Cattivelli, Serena Martini, Alessandra Pino, Cinzia Caggia, Cinzia L. Randazzo
Summary: This study identified a new candidate gene, bglH3, responsible for the beta-glucosidase-positive phenotype in L. plantarum, providing the basis for future marker-assisted selection of L. plantarum starter strains with a beta-glucosidase-positive phenotype. Additionally, the ability of selected strains to hydrolyze oleuropein at low temperatures is important for application as starter cultures on an industrial scale.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Review
Neurosciences
Erick Sousa, Nuria Flames
Summary: Neuronal diversity is an intrinsic feature of the nervous system, with transcription factors playing key roles in establishing different neuronal identities. Common features in transcription factor categories can be identified in both mammals and nematodes, highlighting their pleiotropic functions. Transcriptional repression is crucial in controlling neuronal diversity, and the acquisition of neuronal identities is considered a metastable process.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2022)