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)
Review
Biochemistry & Molecular Biology
Evangelos D. Karousis, Oliver Muehlemann
Summary: The article reviews the important role of NMD in mRNA degradation, discusses its impact on various diseases, and proposes strategies to modulate NMD as potential therapeutic approaches.
TRENDS IN BIOCHEMICAL 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.
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
Bosen You, Yin Sun, Jie Luo, Keliang Wang, Qing Liu, Ruizhe Fang, Bingmei Liu, Fuju Chou, Ronghao Wang, Jialin Meng, Chi-Ping Huang, Shuyuan Yeh, Chawnshang Chang, Wanhai Xu
Summary: The study suggests that androgen receptor (AR) promotes vasculogenic mimicry (VM) formation in ccRCC cells by regulating lncRNA-TANAR/TWIST1 signals, potentially impacting metastasis. This discovery provides a clue for the development of a novel anti-angiogenesis therapy to better suppress ccRCC progression.
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)
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
Cell Biology
Benjamin L. Zaepfel, Zhe Zhang, Kirstin Maulding, Alyssa N. Coyne, Weiwei Cheng, Lindsey R. Hayes, Thomas E. Lloyd, Shuying Sun, Jeffrey D. Rothstein
Summary: The study found that overexpression of UPF1 protein can mitigate neurotoxicity in C9orf72 ALS/FTD models by reducing the severity of known neurodegenerative phenotypes without affecting NMD function itself.
Article
Biochemistry & Molecular Biology
Sarah E. Fritz, Soumya Ranganathan, Clara D. Wang, J. Robert Hogg
Summary: This study reveals that an alternative isoform of the core NMD factor UPF1, UPF1(LL), can remodel the specificity of NMD in response to cellular stress. UPF1(LL) is able to bypass specific protective RNA binding proteins, bind and down-regulate transcripts with long 3'UTRs, and induce NMD in response to cellular stress conditions.
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
Immunology
Takuya Uehata, Osamu Takeuchi
Summary: The regulation of mRNA decay is crucial in controlling gene expression, involving both canonical pathways and endoribonucleolytic cleavage. Regnase-1 plays a critical role in immune regulation by dampening mRNA, particularly cytokines and inflammatory mediators. A group of Regnase-1-related RNases are also involved in immune regulation and antiviral host defense.
INTERNATIONAL IMMUNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Nikita Shepelev, Olga Dontsova, Maria Rubtsova
Summary: Telomere length is associated with cell proliferative potential and is maintained by telomerase. Telomerase is activated during cellular division and plays a crucial role in processes like regeneration, immune response, embryonic development, and cancer progression. Understanding the regulatory mechanisms of telomerase biogenesis and activity is important for manipulating telomerase and influencing these processes. This review focuses on the molecular mechanisms involved in telomerase regulation and the role of post-transcriptional and post-translational modifications in telomerase biogenesis and function in yeast and vertebrates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Jiani Liang, Margot Chirikjian, Utpal B. Pajvani, Alberto Bartolome
Summary: The expression of MafA, a key transcription factor, is decreased in type 2 diabetes, leading to beta-cell dysfunction. Understanding the regulatory factors of MafA expression may help identify potential therapeutic targets for improving beta-cell function.
Article
Chemistry, Applied
Liping Sun, Jingtian Huo, Jieya Liu, Jiayi Yu, Jialing Zhou, Chongde Sun, Yue Wang, Feng Leng
Summary: Anthocyanins play crucial roles in plant resistance, human health, and fruit coloring, making them highly valued. This review extensively covers the functions, classifications, distributions, biosynthesis, decoration, transportation, transcriptional regulation, DNA methylation, and post-translational regulation of anthocyanins in fruits.
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)
