Review
Immunology
Frank Fang Yao Lee, Scott Alper
Summary: While TLR signaling is necessary to combat infection, persistent inflammation can cause damage and contribute to various inflammatory disorders. Alternative pre-mRNA splicing plays a role in terminating TLR signaling by producing dominant negative inhibitors that limit inflammation. Understanding the production and function of these alternative isoforms may provide insights into inflammatory disease.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Plant Sciences
Ewa Sybilska, Agata Daszkowska-Golec
Summary: Seed germination is a vital process in a plant's life that is regulated by various mechanisms and external factors. Alternative splicing (AS) plays a significant role in abscisic acid (ABA) signaling and gene expression control. This review discusses the current understanding of AS regulators and ABA-related changes in AS during seed germination, as well as the impact of these changes on protein functionality. The advances in sequencing technology provide better tools for studying the role of AS in gene regulation.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Hongbin Li, Vishaal Rajani, Lu Han, Danielle Chung, James E. Cooke, Ameet S. Sengar, Michael W. Salter
Summary: NMDA receptors (NMDARs) are a principal subtype of excitatory neurotransmitter receptor, composed of two GluN1 and two GluN2 subunits. Alternative splicing of GluN1 can affect the signaling of glycine, which is crucial for the nonionotropic signaling by NMDARs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Li Ji, Xiangrui Yang, Feifei Qi
Summary: This article summarizes the role of innate immunity in plant-microbe interactions, including the mechanisms of recognizing and responding to different microbes and how microbes manipulate plant signaling pathways to evade immunity. It also raises some questions that need to be addressed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Galia Maik-Rachline, Inbal Wortzel, Rony Seger
Summary: The MAPK cascades transmit external stimuli signals to various cellular processes through specific phosphorylation and activation, ensuring proper cell fate. The involvement of specific genes and alternatively spliced isoforms extends the signaling specificity of the MAPK cascades, enabling different cellular responses to various stimuli.
Review
Biochemical Research Methods
Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li
Summary: Alternative splicing (AS), a key pathway for transcriptional regulation, has been shown to be associated with complex diseases. Computational approaches for detecting disease-associated AS events have been developed. This review discusses the metrics used for characterizing AS events quantitatively. It also reviews and discusses three types of methods for detecting disease-associated splicing events: differential splicing analysis, aberrant splicing detection, and splicing-related network analysis. Additionally, methods for detecting genetic variants that potentially regulate splicing are described. Experimental comparisons are conducted to illustrate the performance of each method. The limitations of these methods are discussed, as well as potential ways to address them. This review aims to provide a systematic understanding of computational approaches for analyzing disease-associated splicing.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Genetics & Heredity
Shefali Banerjee, Gaddiel Galarza-Munoz, Mariano A. Garcia-Blanco
Summary: This review emphasizes the importance of RNA alternative splicing in regulating immune T cell function and discusses the relationship between mutations and diseases, as well as potential therapeutic strategies.
Article
Plant Sciences
Qi Zhang, Wei Zhang, Jianbo Wei, Zhaoxu Gao, Jianing Guan, Zhibo Cui, Xiaoxue Wang
Summary: This study reveals that the splicing factor SKIP plays a positive regulatory role in ABA signaling in plants. It regulates the splicing of ABA signaling-related genes, affecting the expression of ABA-positive regulators. The study also found that SKIP is involved in the regulation of ABA-mediated genome-wide alternative splicing and differential gene expression.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Immunology
Sanqi An, Yueqi Li, Yao Lin, Jiemei Chu, Jinming Su, Qiuli Chen, Hailong Wang, Peijiang Pan, Ruili Zheng, Jingyi Li, Junjun Jiang, Li Ye, Hao Liang
Summary: The study found that genes with APA in COVID-19 patients were enriched in gene ontology categories related to innate immunity, and APA events may provide better predictions than AS. This suggests that APA could act as a potential therapeutic target and novel biomarker in COVID-19 patients.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Oncology
Jamal Elhasnaoui, Giulio Ferrero, Valentina Miano, Santina Cutrupi, Michele De Bortoli
Summary: This study reveals a novel mechanism of gene regulation mediated by estrogen receptor alpha in breast cancer cells, involving the control of RNA-binding protein expression and effects on isoform usage and alternative splicing. These regulatory mechanisms play a significant role in cell proliferation and epithelial-to-mesenchymal transition in breast cancer.
Article
Pharmacology & Pharmacy
Xu-Xiao Chen, Bao-Hua Zhang, Yan-Cen Lu, Zi-Qiang Li, Cong-Yan Chen, Yu-Chen Yang, Yong-Jun Chen, Di Ma
Summary: This study established a robust 16-gene AS signature for predicting tumor relapse in stage I-III HCC, which is significantly associated with the immune status of the HCC microenvironment.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Cell Biology
Kuo-Chieh Liao, Mariano A. Garcia-Blanco
Summary: The review discusses the functional significance of alternative splicing in innate immune responses to viral infection, highlighting its role in regulating interferon pathways, splicing factors in antiviral immunity, and the regulation of cell death pathways by alternative splicing.
Article
Environmental Sciences
Cheng Gui Wang, Wei Wang, Li Li Shi, Yu Chun Shen, Siuming F. Chan
Summary: This research identified two different four-exon CHH genes in lobsters and found that their transcripts produced different variants through alternative splicing. These transcripts were widely expressed in various non-eyestalk tissues of female lobsters and played important roles in the reproductive cycle.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Plant Sciences
Richard A. Hill, Johanna Wong-Bajracharya, Sidra Anwar, Donovin Coles, Mei Wang, Anna Lipzen, Vivian Ng, Igor Grigoriev, Francis Martin, Ian C. Anderson, Christopher Cazzonelli, Thomas Jeffries, Krista L. Plett, Jonathan M. Plett
Summary: The pathways regulated in ectomycorrhizal plant hosts during the establishment of symbiosis are not as well understood, but a study on Eucalyptus grandis using RNA sequencing and metabolomics revealed specific and core responses to symbiosis. Despite being mutualistic, a large number of disease signaling genes were induced, with a dynamic transcriptional regulation observed in E. grandis across colonization stages, including genes associated with the carotenoid/ABA pathway.
Review
Biochemistry & Molecular Biology
Alexandra Moisand, Mathilde Madery, Thomas Boyer, Charlotte Domblides, Celine Blaye, Nicolas Larmonier
Summary: Breast cancers are a heterogeneous group of diseases with varying responses to current therapies. Hormone receptor-positive breast cancers can benefit from endocrine therapies, but metastatic disease remains a challenge. Immunotherapies have had limited success in breast cancer, only benefiting patients with hormone receptor-negative tumors. Current research focuses on the role of hormone receptor signaling in the sensitivity of breast cancer cells to anti-tumor immune responses and the potential of hormone therapy agents to enhance immune-based interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Thomas Roule, Martin Crespi, Thomas Blein
Summary: As sessile organisms, plants have evolved sophisticated mechanisms of gene regulation to cope with changing environments, and long non-coding RNAs (lncRNAs) play important roles in controlling root growth and development by regulating gene expression. They are involved in fine-tuning primary root growth and the development of root lateral organs, as well as in plant responses to stresses and the regulation of nutrient assimilation and homeostasis, ultimately leading to modifications in root architecture. Targeting lncRNAs in plant breeding programs could offer a promising approach to subtly acclimate crops to upcoming environmental changes.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Biochemistry & Molecular Biology
Thomas Roule, Aurelie Christ, Nosheen Hussain, Ying Huang, Caroline Hartmann, Moussa Benhamed, Jose Gutierrez-Marcos, Federico Ariel, Martin Crespi, Thomas Blein
Summary: Clustered organization of biosynthetic non-homologous genes in plant genomes is regulated by epigenetic reprogramming and chromatin conformation. This study identified a long non-coding RNA (lncRNA) called MARS that controls the local epigenetic activation in response to ABA in Arabidopsis marneral cluster. MARS modulates the binding of PRC1 component LHP1, leading to changes in H3K27me3 deposition and chromatin condensation. This study suggests that co-regulated lncRNAs play a role in the evolution of biosynthetic pathways.
Editorial Material
Plant Sciences
Martin Crespi, Federico Ariel
Summary: Non-B DNA structures, including G-quadruplexes, R-loops, and various DNA alternate conformations, have been found to impact gene regulation in plant genomes. The recent identification of intercalated-motifs in rice expands the understanding of how non-B DNA contributes to plant gene regulation.
TRENDS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Haroon Butt, Jeremie Bazin, Kasavajhala V. S. K. Prasad, Nourelislam Awad, Martin Crespi, Anireddy S. N. Reddy, Magdy M. Mahfouz
Summary: Abiotic stresses have significant impacts on plant growth, development, and crop productivity. The plant-specific splicing factor RS33 plays an important role in regulating pre-mRNA splicing and abiotic stress responses in rice.
Article
Plant Sciences
Sombir Rao, Sarita Jha, Chandni Bansal, Apoorva Gupta, Celine Sorin, Martin Crespi
Summary: Heat stress transcription factors (HSFs) and microRNAs (miRNAs) play a critical role in the regulation of heat stress response in plants by regulating different stress and developmental networks through regulatory feedback mechanisms.
Review
Biochemistry & Molecular Biology
Pablo A. Manavella, Micaela A. Godoy Herz, Alberto R. Kornblihtt, Reed Sorenson, Leslie E. Sieburth, Kentaro Nakaminami, Motoaki Seki, Yiliang Ding, Qianwen Sun, Hunseung Kang, Federico D. Ariel, Martin Crespi, Axel J. Giudicatti, Qiang Cai, Hailing Jin, Xiaoqi Feng, Yijun Qi, Craig S. Pikaard
Summary: This article presents and discusses new and long-standing open questions in plant RNA biology, covering topics such as alternative splicing, dynamics, translation, structures, epitranscriptomics, long non-coding RNAs, small RNA production and functions, and more. It provides insights into the current state-of-the-art in the field and aims to provoke future discoveries and reflections.
Article
Multidisciplinary Sciences
Ying Huang, Jing An, Sanchari Sircar, Clara Bergis, Chloe Dias Lopes, Xiaoning He, Barbara Da Costa, Feng-Quan Tan, Jeremie Bazin, Javier Antunez-Sanchez, Maria Florencia Mammarella, Ravi-sureshbhai Devani, Rim Brik-Chaouche, Abdelhafid Bendahmane, Florian Frugier, Chongjing Xia, Christophe Rothan, Aline V. Probst, Zouine Mohamed, Catherine Bergounioux, Marianne Delarue, Yijing Zhang, Shaojian Zheng, Martin Crespi, Sotirios Fragkostefanakis, Magdy M. Mahfouz, Federico Ariel, Jose Gutierrez-Marcos, Cecile Raynaud, David Latrasse, Moussa Benhamed
Summary: This study examines the changes in chromatin and gene expression in response to heat stress in tomato. They found that heat stress rapidly alters chromatin structure and leads to the formation of temporary contacts between promoters and enhancers, which drive the expression of genes responsive to heat stress. The researchers also discovered that this spatial reorganization of chromatin requires the transcription factor HSFA1a.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jeremie Bazin, Emilie Elvira-Matelot, Thomas Blein, Vincent Jauvion, Nathalie Bouteiller, Jun Cao, Martin D. Crespi, Herve Vaucheret
Summary: In addition to regulating splicing, the spliceosome components SmD1 and PRP39 also promote posttranscriptional gene silencing in Arabidopsis thaliana. However, their actions are distinct in both splicing and gene silencing. The double mutant analysis suggests that PRP39 and SmD1 work together to limit degradation of transgene-derived aberrant RNAs, thus promoting the initiation of posttranscriptional gene silencing in the cytoplasm.
Article
Plant Sciences
Li Liu, Michel Heidecker, Thomas Depuydt, Nicolas Manosalva Perez, Martin Crespi, Thomas Blein, Klaas Vandepoele
Summary: A study identified 6599 high-confidence lincRNA loci in Arabidopsis and constructed a TF-lincRNA regulatory network containing 2659 lincRNAs and 15686 interactions. Experimental validation confirmed the role of three transcription factors in controlling root-specific lincRNA expression.
Article
Biochemistry & Molecular Biology
Thomas Roule, Maria Florencia Legascue, Andana Barrios, Nicolas Gaggion, Martin Crespi, Federico Ariel, Thomas Blein
Summary: Long noncoding RNAs (lncRNAs) play a crucial role in regulating gene expression in plants, including various molecular mechanisms. In Arabidopsis, lncRNAs have been identified and associated with plant development and environmental response. This study identified a lncRNA called ARES downstream of the key gene IAA14/SOLITARYROOT (SLR) involved in root development. Knockdown and knockout experiments revealed that ARES affects the induction of the neighboring gene NF-YB3 in response to exogenous auxin and leads to a root developmental phenotype. Transcriptomic analysis showed deregulation of ARF7-dependent genes. These findings suggest that ARES functions as a novel regulator of auxin response and lateral root development.
Article
Biochemistry & Molecular Biology
Wil Prall, Arsheed H. Sheikh, Jeremie Bazin, Jean Bigeard, Marilia Almeida-Trapp, Martin Crespi, Heribert Hirt, Brian D. Gregory
Summary: Posttranscriptional regulation of mRNA mediated by m6A has significant impacts on transcriptome regulation in plants. This study provides a comprehensive understanding of the effects of m6A on both short-term and long-term responses to pathogen signaling in Arabidopsis. The results show that m6A-deficient plants exhibit enhanced resistance to bacterial and fungal pathogen infections with altered immune responses. Furthermore, m6A deposition on defense and immunity-related transcripts is specifically coordinated prior to and during pathogen signal flagellin, and correlates with changes in transcript abundance and cleavage.
Article
Biochemistry & Molecular Biology
Maria Florencia Mammarella, Leandro Lucero, Nosheen Hussain, Aitor Munoz-Lopez, Ying Huang, Lucia Ferrero, Guadalupe L. Fernandez-Milmanda, Pablo Manavella, Moussa Benhamed, Martin Crespi, Carlos L. Ballare, Jose Gutierrez Marcos, Pilar Cubas, Federico Ariel
Summary: The long noncoding RNA APOLO regulates the shade avoidance syndrome in Arabidopsis thaliana by dynamically modulating expression of key factors. APOLO deregulation leads to the repression of the BRC1 gene and an increase in shoot branching. It also plays a role in leaf hyponasty and influences auxin homeostasis by modulating auxin synthesis and efflux genes.
Article
Biology
Martin Crespi
Summary: With the advancement of modern sequencing technologies, a large number of non-coding RNAs have been discovered, which may play important regulatory roles in gene expression and are crucial for plants in response to environmental stresses and adaptation to changing conditions.
COMPTES RENDUS BIOLOGIES
(2022)
Article
Biotechnology & Applied Microbiology
Camille Fonouni-Farde, Aurelie Christ, Thomas Blein, Maria Florencia Legascue, Lucia Ferrero, Michael Moison, Leandro Lucero, Juan Sebastian Ramirez-Prado, David Latrasse, Daniel Gonzalez, Moussa Benhamed, Leandro Quadrana, Martin Crespi, Federico Ariel
Summary: This study uncovers a novel mechanism in which a plant lncRNA coordinates Polycomb action and DNA methylation through its interaction with VIM1. It also suggests that evolutionarily unrelated lncRNAs may have similar functions by interacting with homologous proteins.
Article
Biotechnology & Applied Microbiology
Runxuan Zhang, Richard Kuo, Max Coulter, Cristiane P. G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, Linda Milne, Stefan Riegler, Akihiro Matsui, Maho Tanaka, Sarah Harvey, Yubang Gao, Theresa Wiessner-Kroh, Alejandro Paniagua, Martin Crespi, Katherine Denby, Asa Ben Hur, Enamul Huq, Michael Jantsch, Artur Jarmolowski, Tino Koester, Sascha Laubinger, Qingshun Quinn Li, Lianfeng Gu, Motoaki Seki, Dorothee Staiger, Ramanjulu Sunkar, Zofia Szweykowska-Kulinska, Shih-Long Tu, Andreas Wachter, Robbie Waugh, Liming Xiong, Xiao-Ning Zhang, Ana Conesa, Anireddy S. N. Reddy, Andrea Barta, Maria Kalyna, John W. S. Brown
Summary: This study introduces a new comprehensive Arabidopsis transcriptome dataset, AtRTD3, which contains over 169,000 transcripts and provides accurate splice junctions and transcription start/end sites. Additionally, novel methods for identifying accurate splice junctions and transcription start/end sites have been developed, and the effectiveness of AtRTD3 has been validated through analysis of a cold response RNA-seq time-series.