Review
Physiology
Mian Muhammad Awais, Muhammad Shakeel, Jingchen Sun
Summary: miRNAs are small non-coding RNAs of about 22 nucleotides that have been reported to regulate gene expression at the posttranscriptional level, involved in various biological processes such as immunity, development, metabolism, and host-pathogen interactions. Both cellular and viral miRNAs may play vital roles in host-pathogen interactions, with viral infections altering host miRNA expression profiles.
FRONTIERS IN PHYSIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Asahiro Morishita, Kyoko Oura, Tomoko Tadokoro, Koji Fujita, Joji Tani, Tsutomu Masaki
Summary: The liver is a non-immunological organ involved in metabolic activities, nutrient storage, and detoxification. Resident immune cells in the liver drive immunological reactions and certain microRNAs are associated with the immune response to pathogens, although the exact mechanism of miRNA interference in these interactions remains unclear.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Pharmacology & Pharmacy
Sapna Sehrawat, Mariano A. Garcia-Blanco
Summary: It is well-known that viral infection significantly changes the expression of host genes, which have both pro- and anti-viral functions. While the effects of viral infection on transcription and translation have been extensively studied, the impact on alternative splicing of pre-messenger RNAs has received less attention. In this review, we highlight notable examples of how viral infection alters alternative splicing and discuss the implications of these changes on infection.
ANTIVIRAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Yongtao Yu, Yuxiang Liufu, Yi Ren, Jie Zhang, Maoying Li, Shouwei Tian, Jinfang Wang, Shengjin Liao, Guoyi Gong, Haiying Zhang, Shaogui Guo
Summary: This study used PacBio single-molecule long-read sequencing to identify alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. The results showed that these post-transcriptional mechanisms play important roles in fruit ripening, particularly the splicing isoforms associated with fruit ripening. Additionally, KEGG analysis revealed that fructose and mannose metabolism, starch and sucrose metabolism, and carotenoid biosynthesis were enriched in genes undergoing AS and APA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Multidisciplinary Sciences
Nisrine Chelkha, Anthony Levasseur, Bernard La Scola, Philippe Colson
Summary: Giant viruses challenge the traditional view of the virosphere with their large size and complex interactions with hosts, exhibiting defense mechanisms against hosts and competing microorganisms. Comparative genomics may aid in identifying genes involved in defense strategies against giant viruses.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2021)
Article
Cell Biology
Shi-lu Chen, Zhong-xu Zhu, Xia Yang, Li-li Liu, Yang-fan He, Ming-ming Yang, Xin-yuan Guan, Xin Wang, Jing-ping Yun
Summary: APA plays a crucial role in HCC, with CPSF1 identified as a key regulator contributing to unfavorable survival outcomes in HCC. Knockdown of CPSF1 inhibits HCC cell proliferation and migration, while overexpression has the opposite effect. Knockdown of CPSF1 not only induces APA but also increases AS events.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Carmelo Gurnari, Simona Pagliuca, Valeria Visconte
Summary: Alternative RNA splicing is an essential physiological function that plays a crucial role in cellular development. RNA splicing dysfunction has been implicated in the development of several cancers, including myeloid malignancies. Cancer cells exhibit marked gene expression alterations, including different usage of AS isoforms, potentially causing tissue-specific effects and disruptions of downstream pathways.
Article
Biochemistry & Molecular Biology
Rebecca M. Sena, Jeffery L. Twiss, Amy S. Gardiner, Michela Dell'Orco, David N. Linsenbardt, Nora Perrone-Bizzozero
Summary: Neuronal Hu/ELAV-like proteins HuB, HuC, and HuD play key roles in the proper development and maintenance of the nervous system by regulating mRNA stability, transport, translation, as well as alternative splicing and polyadenylation. Deletion of HuD has a greater impact on alternative splicing with 310 genes affected, although it also influences polyadenylation of 53 genes. This study provides insights into the transcriptomic effects of HuD deletion on nuclear events in the neocortex.
Review
Endocrinology & Metabolism
Panyisha Wu, Moya Zhang, Nicholas J. G. Webster
Summary: Alternative RNA splicing is an important biological process that has been linked to various clinical syndromes, but its applicability to common diseases is still uncertain. This review focuses on the changes in alternative RNA splicing in fatty liver disease and the role of splicing regulation in disease progression.
FRONTIERS IN ENDOCRINOLOGY
(2021)
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)
Review
Immunology
Davia Blake, Kristen W. Lynch
Summary: The latest advances in next-generation sequencing studies have revealed a high frequency of genes regulated by RNA processing mechanisms in the immune system, particularly alternative splicing and alternative polyadenylation. These mechanisms have the potential to alter protein identity, control protein abundance, localization, and association with other factors. This review focuses on how control of apoptosis by alternative splicing and alternative polyadenylation is utilized to tune cell fate during an immune response.
IMMUNOLOGICAL REVIEWS
(2021)
Article
Plant Sciences
Ping Lu, Daipeng Chen, Zhaomei Qi, Haoming Wang, Yitong Chen, Qinhu Wang, Cong Jiang, Jin-Rong Xu, Huiquan Liu
Summary: This study investigates the landscape and regulation of alternative splicing (AS) and alternative polyadenylation (APA) in Fusarium graminearum, a filamentous fungus. The results reveal that AS and APA play important roles in gene expression regulation, with the majority of AS events affecting coding sequences. Unexpectedly, AS transcripts with premature-termination codons are not degraded. Distal APA sites have strong signals, while proximal APA isoforms are highly expressed in F. graminearum. The study also uncovers the roles of 3'-end processing factors in promoting proximal APA site usage and intron splicing. Furthermore, the study suggests intron inclusion and 3'-untranslated region lengthening as novel mechanisms in regulating aging and dormancy in fungi.
Article
Plant Sciences
Zhongxin Jin, Xinning Lv, Yushuai Sun, Zongbao Fan, Guangqing Xiang, Yuxin Yao
Summary: The study identified a total of 8,453 AS events in grapevine roots, with retained intron (RI) being the most dominant type, and showed a global decrease in inclusion isoforms proportion under salt stress. Only a small overlap was found between salt-responsive AS events and differentially expressed genes, while differentially spliced genes were mainly related to RNA processing, nucleic acid binding, and ion channel activity. Additionally, the study identified salt-induced spliceosomal protein genes LSM2 and SRSF1 in grapevine roots and proposed a method to explore interactions between AS and alternative polyadenylation (APA) using Iso-Seq data.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Genetics & Heredity
Leonard Scharfen, Dagmar Zigackova, Kirsten A. Reimer, Martha R. Stark, Viktor A. Slat, Nancy J. Francoeur, Melissa L. Wells, Lecong Zhou, Perry J. Blackshear, Karla M. Neugebauer, Stephen D. Rader
Summary: By studying a highly diverged red alga, researchers discovered the presence of alternative polyadenylation (APA) in this non-model organism, suggesting its potential importance in regulating gene expression.
FRONTIERS IN GENETICS
(2022)
Review
Cell Biology
Prakash Dharmalingam, Rajasekaran Mahalingam, Hari Krishna Yalamanchili, Tingting Weng, Harry Karmouty-Quintana, Ashrith Guha, Rajarajan A. Thandavarayan
Summary: Research has shown that alternative cleavage and polyadenylation (APA) play a crucial role in the pathogenesis of various human diseases, leading to dysfunctional gene regulation and abnormal cell proliferation. While the functions of the core APA machinery and its role in disease conditions remain largely unknown, the mechanism of APA has become a hot topic in disease research.
JOURNAL OF CELLULAR PHYSIOLOGY
(2022)
Article
Virology
Masahiko Ajiro, Shuang Tang, John Doorbar, Zhi-Ming Zheng
JOURNAL OF VIROLOGY
(2016)
Article
Virology
Yoshiki Kawamura, Marta Bosch-Marce, Shuang Tang, Amita Patel, Philip R. Krause
JOURNAL OF VIROLOGY
(2018)
Article
Virology
Julianna R. Pieknik, Andrea S. Bertke, Shuang Tang, Philip R. Krause
Article
Immunology
Shasta D. McClenahan, Philip R. Krause
Article
Immunology
Kirsten S. Vannice, M. Cristina Cassetti, Robert W. Eisinger, Joachim Hombach, Ivana Knezevic, Hilary D. Marston, Annelies Wilder-Smith, Marco Cavaleri, Philip R. Krause
Article
Virology
Julianna R. Pieknik, Andrea S. Bertke, Philip R. Krause
JOURNAL OF VIROLOGY
(2019)
Article
Microbiology
Shuang Tang, Amita Patel, Philip R. Krause
Article
Immunology
Philip R. Krause, Jett Roberts
JOURNAL OF INFECTIOUS DISEASES
(2020)
Editorial Material
Medicine, General & Internal
Philip R. Krause, Marion F. Gruber
NEW ENGLAND JOURNAL OF MEDICINE
(2020)
Article
Medicine, General & Internal
Philip R. Krause, Thomas R. Fleming, Ira M. Longini, Richard Peto, Sylvie Briand, David L. Heymann, Valerie Beral, Matthew D. Snape, Helen Rees, Alba-Maria Ropero, Ran D. Balicer, Jakob P. Cramer, Cesar Munoz-Fontela, Marion Gruber, Rogerio Gaspar, Jerome A. Singh, Kanta Subbarao, Maria D. Van Kerkhove, Soumya Swaminathan, Michael J. Ryan, Ana-Maria Henao-Restrepo
NEW ENGLAND JOURNAL OF MEDICINE
(2021)
Editorial Material
Immunology
Philip R. Krause, Narendra Arora, William Dowling, Cesar Munoz-Fontela, Simon Funnell, Rogerio Gaspar, Marion F. Gruber, Adam Hacker, Ana Maria Henao-Restrepo, Stanley Plotkin, Helen Rees, Dean K. Smith, Soumya Swaminathan