Article
Biochemistry & Molecular Biology
Armin Fuchs, Stefan Riegler, Zahra Ayatollahi, Nicola Cavallari, Luciana E. Giono, Barbara A. Nimeth, Krishna Mutanwad, Alois Schweighofer, Doris Lucyshyn, Andrea Barta, Ezequiel Petrillo, Maria Kalyna
Summary: The study revealed the importance of RNA interference in regulating gene expression, while its interactions with alternative splicing were not well understood. By using amiRNA to knockdown various splice variants of target genes, it was found that some transcript isoforms escaped degradation due to their nuclear localization. The isoforms of alternatively spliced genes that are nuclear localized and sensitive to NMD mask the action of RNA interference.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Yangang Lan, Kaimei Zhang, Ting He, Hao Wang, Chengzhi Jiang, Hanwei Yan, Yan Xiang
Summary: This study conducted a comprehensive analysis and functional research of SRs in poplar and other dicots, revealing the important role of a key gene PtSC27 in salt stress response. Overexpression of PtSC27 enhanced plant tolerance to salt stress by regulating enzyme activities and gene expression. These findings provide a foundation for understanding the structure and function of SRs and offer important gene resources for genetic engineering breeding.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Review
Plant Sciences
Rocio S. Tognacca, Florencia S. Rodriguez, Federico E. Aballay, Carla M. Cartagena, Lucas Servi, Ezequiel Petrillo
Summary: Alternative splicing is an important regulatory process that generates multiple transcripts from a single gene, affecting the transcriptome and potentially the proteome. This review summarizes recent advances in understanding the biological roles of alternative splicing isoforms in plant responses and development and highlights the need for improved research strategies. It also proposes a thorough strategy to analyze and evaluate the functions of alternative splicing isoforms of interest.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Miryam A. Cymerman, Helen Saul, Ronit Farhi, Karina Vexler, Dror Gottlieb, Irina Berezin, Orit Shaul
Summary: Translated upstream open reading frames (uORFs) can inhibit the translation of main open reading frames (ORFs) and lead to transcript degradation in eukaryotic cells. In mammalian cells, the length, structure, and reinitiation efficiency of translated uORFs play important roles in determining whether the transcripts will be targeted for degradation by the nonsense-mediated mRNA decay (NMD) pathway. However, the significance of these factors in NMD targeting for plants is still not well-studied.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
Zi-Chang Jia, Debatosh Das, Youjun Zhang, Alisdair R. Fernie, Ying-Gao Liu, Moxian Chen, Jianhua Zhang
Summary: Serine/arginine-rich (SR) proteins participate in RNA processing and maintain plant growth and stress responses through interactions with precursor mRNAs or other splicing factors. SR proteins are crucial for alternative splicing and play essential roles in the composition and alternative splicing of precursor mRNAs. However, their evolutionary trajectory, molecular function, and regulatory network in plants are still largely unknown compared to their animal counterparts. This article reviews the current understanding of the SR protein family in eukaryotes and proposes potential key research priorities for future functional studies.
Article
Plant Sciences
Steven Fanara, Marie Schloesser, Marc Hanikenne, Patrick Motte
Summary: The mutant sr45-1 in Arabidopsis exhibits a phenotype of constitutive iron deficiency, characterized by iron accumulation in root tissues and iron starvation in aerial parts. RNA-Sequencing reveals severe perturbations in metal homeostasis, phenylpropanoid pathway, oxidative stress responses, and reproductive development. Some developmental abnormalities of sr45-1 can be complemented by exogenous iron supply.
Article
Genetics & Heredity
Changhee Ha, Ja-Hyun Jang, Young-gon Kim, Jong-Won Kim
Summary: RNA sequence analysis is a useful tool for identifying aberrant splicing, but Sanger sequencing has limited sensitivity in certain cases. This study retrospectively reviewed the results of Sanger sequencing on potential splicing variants of tumor suppressor genes and assessed the possibility of false negativity caused by NMD through literature review. The findings suggest that despite most cases showing RNA changes expected to undergo NMD, they can still be interpreted using Sanger sequencing.
FRONTIERS IN GENETICS
(2023)
Article
Biotechnology & Applied Microbiology
Bo Sun, Liang Chen
Summary: Through genetical genomics, we elucidate the regulatory mechanism of NMD on individual genes across human tissues. We identify genetic variants that influence NMD regulation, which are often missed in traditional eQTL mapping. NMD regulation plays important roles in the brain and has specific genomic positions for NMD-QTLs.
Review
Virology
Md Robel Ahmed, Zhiyou Du
Summary: The interaction between viruses and hosts is dynamic and evolutionary. Eukaryotic hosts have multiple defense mechanisms against viral infection, including the nonsense-mediated mRNA decay (NMD) system. NMD ensures the accuracy of mRNA translation by degrading abnormal mRNAs. Many RNA viruses have internal stop codons (iTC), which activate NMD and lead to degradation of viral genomes. Some viruses are sensitive to NMD-mediated antiviral defense, while others have evolved mechanisms to overcome or escape NMD. This review summarizes the current understanding of NMD-mediated viral RNA degradation and the ways in which viruses compromise NMD for better infection.
Review
Genetics & Heredity
Marie Christine Martens, Steffen Emmert, Lars Boeckmann
Summary: Nucleotide excision repair is crucial for repairing UV-induced DNA damage, with alterations in NER genes possibly leading to disorders like Xeroderma pigmentosum. Recent research has focused on the functional relevance of splice variants and their connection to cancer.
Review
Cell Biology
Javier Duran, Lennart Nickel, Manuel Estrada, Johannes Backs, Maarten M. G. van den Hoogenhof
Summary: The study explores the role of RNA splicing in heart development and disease, focusing on the multifunctional Ca2+/calmodulin dependent protein kinase II delta (CaMKII delta) and its various splice variants. The review discusses the functions of different splice variants, particularly the involvement of CaMKII delta B, CaMKII delta C, CaMKII delta A, and CaMKII delta 9 in heart signaling. The translational perspective and future directions of CaMKII delta splicing research in healthy and diseased hearts are also examined.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
Cristina Nuevo-Tapioles, Mark R. Philips
Summary: The three mammalian RAS genes (HRAS, NRAS and KRAS) encode proteins important in cancer biology, with KRAS being the most frequently mutated oncogene. The pre-mRNA of KRAS produces two splice variants, KRAS4A and KRAS4B, which have different membrane targeting sequences. Recent studies have demonstrated the expression of KRAS4A in cancer and identified non-overlapping functions of the splice variants, including direct regulation of hexokinase 1.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hye-Yeon Seok, Sun-Young Lee, Swarnali Sarker, Md Bayzid, Yong-Hwan Moon
Summary: Plant roots exhibit distinct gene expression patterns compared to shoots under abiotic stress conditions. This study used mRNA sequencing to analyze the gene expression profiles of Arabidopsis roots subjected to osmotic stress caused by high salinity (NaCl) and drought (mannitol). The results showed significant changes in gene expression in the roots compared to the aerial parts under both NaCl and mannitol treatments. The study identified 68 transcription factor genes that are closely involved in osmotic stress signal transduction in roots. Additionally, alternative splice variants of 26 osmotic stress-responsive genes were found in the roots. The findings suggest that transcription factor families, alternative splicing, and resulting splice variants play important roles in the osmotic stress response in roots.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Jiawei Tang, Youquan Xie, Jingxun Huang, Liao Zhang, Weiye Jiang, Zhiyu Li, Jinlei Bian
Summary: This review discusses the impact of dysregulated alternative splicing on cancer and the role of SR proteins and SR protein-related kinases in cancer development. Small molecule inhibitors targeting SR proteins and SR protein-related kinases are categorized and summarized in terms of structure, inhibition target, mechanism of action, biological activity, and applicable diseases. This review aims to provide a timely summary of recent advances in alternative splicing regulated by kinases and an introduction to relevant small molecule inhibitors.
BIOORGANIC & MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Paul J. J. Russell, Jacob A. A. Slivka, Elaina P. P. Boyle, Arthur H. M. Burghes, Michael G. G. Kearse
Summary: It is estimated that almost half of mammalian transcripts contain uORFs, which are smaller than the main ORF. uORFs are usually inhibitory but can allow for translation reinitiation. However, translation reinitiation after uORFs is not a reliable method to prevent NMD. The decision of whether NMD occurs after translating uORFs happens before reinitiation in mammalian cells.