Article
Immunology
Zhaoqi Zhang, Elhusseny A. Bossila, Ling Li, Songnian Hu, Yong Zhao
Summary: This study used RNA-seq data to analyze transcriptome profiles and cell metabolism during monocyte development, revealing important genes and pathways involved in this process. The findings provide valuable insights into the dynamics of monocyte development in bone marrow.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Surama Biswas, Santosh Manicka, Erik Hoel, Michael Levin
Summary: Studies have shown that gene regulatory networks possess various types of memory, which is important for understanding the variability and time-dependent changes of drug action. Defining and identifying memory through a computational framework is beneficial for the biomedical field. Timed stimuli offer a powerful alternative for controlling complex in vivo dynamics.
Article
Multidisciplinary Sciences
Nozomu Takata, Jason M. Miska, Marc A. Morgan, Priyam Patel, Leah K. Billingham, Neha Joshi, Matthew J. Schipma, Zachary J. Dumar, Nikita R. Joshi, Alexander V. Misharin, Ryan B. Embry, Luciano Fiore, Peng Gao, Lauren P. Diebold, Gregory S. McElroy, Ali Shilatifard, Navdeep S. Chandel, Guillermo Oliver
Summary: Using eye organoids and mouse models, the authors demonstrate that lactate plays a bioenergetic independent role as a cell signaling molecule during early eye formation in mice. The study reveals the importance of aerobic glycolysis in retinal development and identifies specific glucose transporters and glycolytic genes involved. Lactate-mediated upregulation of eye-field transcription factors is controlled by epigenetic modifications.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Violaine Saint-Andre
Summary: The review discusses the main approaches and tools for mapping Transcriptional Regulatory Networks (TRNs) from high-throughput data, highlighting their advantages and limitations. It summarizes the main principles defining the topology and structure-function relationships in TRNs, and presents an overview of the work done to map TRNs from bulk transcriptomic data by methodological approach. Additionally, it touches upon recent modeling of TRNs using different types of molecular data and concludes with expected improvements in the field.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Hong Yang, Muhammad Arif, Meng Yuan, Xiangyu Li, Koeun Shong, Hasan Turkez, Jens Nielsen, Mathias Uhlen, Jan Boren, Cheng Zhang, Adil Mardinoglu
Summary: Researchers conducted network analysis and integrative systems analysis to reveal key transcriptional regulators and biological processes involved in the progression of NAFLD, enhancing the understanding of the disease mechanism.
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
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
R. Mondal, K. Madhurya, P. Saha, S. K. Chattopadhyay, S. Antony, A. Kumar, S. Roy, D. Roy
Summary: Recent research has highlighted the importance of sulphur and sulphur-containing molecules in fundamental plant processes, with a focus on hydrogen sulphide (H2S) as a signaling compound regulating plant development and stress responses. In silico analysis indicated differential expression patterns of H2S metabolic genes at different growth stages and tissue-specific expression under various stresses. Functional annotation of promoter structures revealed a variety of hormone and stress responsive cis-regulatory elements regulating H2S metabolism.
Article
Microbiology
Cortney R. Halsey, Rochelle C. Glover, Maureen K. Thomason, Michelle L. Reniere
Summary: Listeriosis is a deadly foodborne illness caused by Listeria monocytogenes. The redox-responsive regulator Rex plays a crucial role in the growth and pathogenesis of L. monocytogenes, particularly in bacterial replication in peripheral organs. Redox sensing and Rex-dependent regulation are important for metabolic adaptation and virulence of L. monocytogenes.
Article
Cell Biology
Matthew A. Reyer, Shriram Chennakesavalu, Emily M. Heideman, Xiangqian Ma, Magda Bujnowska, Lu Hong, Aaron R. Dinner, Carin K. Vanderpool, Jingyi Fei
Summary: Small RNAs (sRNAs) are important gene regulators in bacteria, acting post-transcriptionally by affecting translation and degradation of target mRNAs. Some sRNAs can regulate targets co-transcriptionally early in an mRNA's lifetime, potentially mediated by Rho-dependent termination. Data also reveals that certain kinetic steps and sRNA binding to target mRNA may dictate the regulation hierarchy within sRNA regulons.
Article
Biology
Erika Fox, Bree Cummins, William Duncan, Tomas Gedeon
Summary: A gene regulatory network is a summary of interactions between genes and regulatory gene products, including transcriptional regulation, protein activity regulation, and regulation of protein transport between compartments. DSGRN is a network modeling approach based on discrete-time Boolean models and continuous-time switching system models. This paper presents an extension of the DSGRN approach to modeling transport regulation across compartments such as cellular membranes, demonstrated through the search for potential stable periodic cycles in a model of the p53-Mdm2 network.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jiejie Zhang, Chen C. Li, Xin Li, Yaxi Liu, Qianhao Wang, Guangyu Zhang, Haiqing Xiong, Aibin He, Shanshan Ai
Summary: Distinct enhancer elements can regulate the cell type-specific expression of the developmental gene. We comprehensively studied enhancers U1 and U2 in controlling Nkx2-5 transcription during heart development. Our findings suggest that U1 and U2 have redundant functions at early stages, but U2 instead of U1 supports Nkx2-5 expression at later stages. Deletions of both enhancers result in reduced Nkx2-5 dosage and disturbed enhancer landscape in mouse hearts.
Review
Microbiology
Katie E. Shalvarjian, Dipti D. Nayak
Summary: Methanogenesis is a significant metabolic process carried out by methanogens in the Archaea domain. Although genes involved in methanogenic metabolism have been identified and characterized, the regulation of methane production in response to various signals remains less understood.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Anindita Mitra, Ana-Maria Raicu, Stephanie L. Hickey, Lori A. Pile, David N. Arnosti
Summary: Pleiotropically acting eukaryotic corepressors interact with widely expressed genes to modulate their expression within certain bounds, rather than turning off gene expression. Soft repression by corepressors is suggested to be a pervasive characteristic of most eukaryotic systems, playing a crucial role in metabolic adaptations.
Article
Biochemical Research Methods
Francis C. Motta, Robert C. Moseley, Bree Cummins, Anastasia Deckard, Steven B. Haase
Summary: This study demonstrates that a unified set of dynamic features of high-throughput time series gene expression data is more prominent in the core transcriptional regulators of cell and circadian cycles than in their outputs, even in the presence of external periodic stimuli. Additionally, the ability to discriminate between core and non-core genes is largely insensitive to the particular choice of quantification of these features.
BMC BIOINFORMATICS
(2022)