Review
Biochemical Research Methods
Mattia Furlan, Stefano de Pretis, Mattia Pelizzola
Summary: Despite RNA abundance being commonly assumed as a proxy for transcriptional activity, it is now possible to calculate how synthesis, processing, and degradation rates collectively determine the abundance of each gene's RNA. Different transcriptional outputs can correspond to different combinations of kinetic rates, indicating the existence of markedly different modes of gene expression regulation and their profound effects on gene self-expression regulation.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Geysson Javier Fernandez, Julieta M. Ramirez-Mejia, Silvio Urcuqui-Inchima
Summary: This study reveals that ZIKV-infected macrophages activate a genetic program involving inflammatory and antiviral responses, with changes in various signaling pathways. Key transcription factors, long non-coding RNAs, and miRNAs play regulatory roles in controlling gene expression and post-transcriptional control. Additionally, RNA binding proteins are involved in this regulatory mechanism.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2022)
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.
Review
Biochemistry & Molecular Biology
Chandramohan Muthu Lakshmi Bavithra, Marimuthu Murugan, Shanmugasundaram Pavithran, Kathirvel Naveena
Summary: Insecticide resistance in insects is a major threat to human health and agriculture, leading to pest management failures, increased costs, decreased crop yields, and public health disasters. The resistance is caused by factors such as indiscriminate insecticide usage and selection pressure on insect populations. Insects respond to insecticide stress at the cellular level through genetic propagations, transcriptional and post-transcriptional regulatory signals, and physiological changes. Understanding these cellular intricacies can help develop alternative pest control methods targeting insect vulnerabilities and using technologies like RNA interference to manage resistance-related genes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Multidisciplinary Sciences
Rakesh Kaundal, Naveen Duhan, Biswa R. Acharya, Manju V. Pudussery, Jorge F. S. Ferreira, Donald L. Suarez, Devinder Sandhu
Summary: This study investigated salt tolerance mechanisms in alfalfa, revealing that reduced salt uptake under salinity may contribute to the lower salt tolerance index in the salt-tolerant genotype G03 compared to the salt-sensitive G09. Differential expressions of genes regulating shoot number explained the differences in shoot biomass between the two genotypes. Additionally, genes involved in hormone, calcium, and redox signaling pathways showed treatment- and genotype-specific differences, providing insights into improving salinity tolerance in alfalfa.
SCIENTIFIC REPORTS
(2021)
Review
Cardiac & Cardiovascular Systems
Sven Danckwardt, David-Alexandre Tregouet, Elisabetta Castoldi
Summary: The haemostatic system plays a crucial role in maintaining vascular integrity and is involved in inflammation and immunity. Disruptions in haemostasis are common in diseases such as sepsis, cardiovascular disorders, and COVID-19. Posttranscriptional mechanisms regulate the biogenesis of haemostatic components and can be hijacked in disease processes. This review highlights the importance of posttranscriptional mechanisms in haemostatic control and their potential therapeutic implications for treating global medical threats.
CARDIOVASCULAR RESEARCH
(2023)
Article
Cell Biology
Ruifan Wu, Shengchun Feng, Fan Li, Gang Shu, Lina Wang, Ping Gao, Xiaotong Zhu, Canjun Zhu, Songbo Wang, Qingyan Jiang
Summary: Obesity is a global health problem associated with metabolic diseases. This study investigates the role of YBX1 in adipogenesis and adipose tissue expansion. The researchers found that YBX1 deficiency inhibited adipocyte differentiation and that YBX1 promotes adipogenesis through ULK1- and ULK2-mediated autophagy. The findings provide insights into the molecular mechanisms and functional importance of YBX1 in regulating autophagy and adipogenesis, highlighting its potential as a therapeutic target for obesity and metabolic diseases.
CELL DEATH & DISEASE
(2023)
Article
Multidisciplinary Sciences
Alireza Akbari, Ahmad Ismaili, Nazanin Amirbakhtiar, Masoumeh Pouresmael, Zahra-Sadat Shobbar
Summary: This study used RNA sequencing to investigate the gene expression differences between two cold tolerant and sensitive chickpea genotypes. The results showed that the sensitive genotype had significant down-regulation of genes related to photosynthesis under cold stress, while the tolerant genotype exhibited several protective and signaling genes. These findings are important for improving cold tolerance in chickpea through molecular breeding or genetic engineering.
SCIENTIFIC REPORTS
(2023)
Article
Neurosciences
Soren N. Andreassen, Trine L. Toft-Bertelsen, Jonathan H. Wardman, Rene Villadsen, Nanna MacAulay
Summary: This study provides important molecular tools for studying pathologies related to disturbed brain fluid homeostasis by analyzing the transcriptome of the choroid plexus in rats. The results show similarities in transport protein transcript abundance between species and provide a list of potential transport mechanisms and regulatory candidates involved in cerebrospinal fluid secretion.
FLUIDS AND BARRIERS OF THE CNS
(2022)
Article
Cell Biology
Sai Aung Phyo, Keita Uchida, Christina Yingxian Chen, Matthew A. Caporizzo, Kenneth Bedi, Joanna Griffin, Kenneth Margulies, Benjamin L. Prosser
Summary: This study investigates the transcriptional, autoregulatory, and post-translational mechanisms that contribute to microtubule network remodeling in different stages of heart disease using heart failure patient samples and murine models. The study reveals the operability of autoregulation across tubulin isoforms in the heart and the rapid induction of microtubule detyrosination after hypertrophic stimulus. It provides insights into the rapid rewriting of the tubulin code and the tunable autoregulation of tubulin during pathological progression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Rania Bassiouni, Lee D. Gibbs, David W. Craig, John D. Carpten, Troy A. McEachron
Summary: Spatial transcriptional profiling is a method that provides gene expression information within tissue architecture, making it well suited for studying solid tumors. It can investigate spatial relationships among cell populations and reveal spatial patterns of relevant oncogenic genetic events. The broad utility and flexibility of this approach have been reflected in the development of various strategies and commercial platforms, allowing its widespread applicability in research settings.
Article
Biochemistry & Molecular Biology
Alison C. Greenlaw, Kris G. Alavattam, Toshio Tsukiyama
Summary: To ensure cell survival during quiescence, cells modulate their gene expression and transcription. By studying the nascent transcriptome, researchers identified over a thousand noncoding RNAs in quiescent and G1 yeast cells, revealing that noncoding transcription plays a larger role in the quiescent state. Furthermore, post-transcriptional regulation is increased in quiescence, affecting both mRNA and ncRNA. The nuclear exosome-NNS pathway was found to regulate the abundance of mRNAs involved in various cellular processes during quiescent entry, highlighting its important biological role in mRNA regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Lulu Yu, Vladimir Majerciak, Zhi-Ming Zheng
Summary: Human papillomaviruses (HPV) are a group of viruses that cause cancer, with HPV16 and HPV18 being the most common types responsible for majority of cases. The expression of their genome is regulated by alternative RNA splicing, and epigenetic modifications also play a role in HPV infections and carcinogenesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Vivek Kumar Raxwal, Somya Singh, Manu Agarwal, Karel Riha
Summary: The study revealed that new genes in rice have relatively low expression levels, possibly controlled by distal enhancers and chromatin conformation at their TSS; the chromatin in TSS regions may be remodeled in response to abiotic stress, indicating conditional expression of young genes. Furthermore, transcripts of young genes in Arabidopsis are prone to nonsense-mediated RNA decay, restricting their expression.
Review
Biochemistry & Molecular Biology
Joshua L. Schwartz, Krysten Leigh Jones, Gene W. Yeo
Summary: This study discusses the pathological mechanisms and therapeutic potential of various neurological disorders caused by short repeat expansions, including RNA processes, RAN translation, and reducing toxic RNA levels. Promising therapeutic strategies have emerged for these disorders, although treatments are still lacking for most of them.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2021)