Review
Biochemistry & Molecular Biology
Zubin Mehta, Marlin Touma
Summary: Advancements in genomics, bioinformatics, and genome editing have brought new insights into gene regulation. Alternative splicing of mRNA transcripts has been identified as a critical regulatory mechanism in gene expression. While there have been extensive studies on the role of alternative splicing in heart development and failure, little is known about its dysregulation in congenital heart defects (CHDs). This review provides an overview of the current understanding of alternative splicing and its implication in CHDs, emphasizing the roles of RNA binding proteins (RBPs) and causal splicing variants in key transcription factors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
Biochemistry & Molecular Biology
Narumi Sakaguchi, Mikita Suyama
Summary: Causative mutations for genetic disorders have been mainly identified in exonic regions, but recent research shows mutations in deep intronic regions can also cause disorders through pseudo-exon activation. In normal individuals, an average of 2.6 pseudo-exon activation events were found, more at the 5' donor splice sites. This suggests that pseudo-exon activation events can be observed in normal individuals at a certain frequency.
Article
Biochemical Research Methods
Ting Yu, Renmin Han, Zhaoyuan Fang, Zengchao Mu, Hongyu Zheng, Juntao Liu
Summary: RNA-seq technology is widely used in various research areas, and the TransRef computational algorithm has been shown to outperform several state-of-the-art assemblers in transcriptome assembly, particularly in identifying novel transcripts and transcripts with low-expression levels.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Microbiology
Qiang Wu, Huan Liu, Yixin Shi, Wanting Li, Jia Huang, Feifei Xue, Yongnan Liu, Gaoqiang Liu
Summary: This study characterized the genome of Ganoderma lingzhi, a genus of edible and medicinal mushrooms. The researchers identified a wide range of carbohydrate-active enzymes and characterized genes involved in sexual recognition and the biosynthesis of a key bioactive metabolite. Additionally, they discovered novel transcripts and genes with the possibility of alternative splicing. These resources provide valuable tools for studying the biology, genetics, and secondary metabolic pathways of G. lingzhi.
Article
Biotechnology & Applied Microbiology
Hiroki Ura, Sumihito Togi, Yo Niida
Summary: This study compared the advantages and disadvantages of three RNA-Seq library preparation methods and found that TruSeq detected transcripts and splicing events better than the other methods, accurately measuring gene expression levels and splicing events. TeloPrime had higher coverage at the transcription start site, while SMARTer performed better than TeloPrime in terms of the number of detected transcripts and splicing events among the studied full-length double-stranded cDNA methods.
Article
Biochemistry & Molecular Biology
Naima Ahmed Fahmi, Heba Nassereddeen, Jaewoong Chang, Meeyeon Park, Hsinsung Yeh, Jiao Sun, Deliang Fan, Jeongsik Yong, Wei Zhang
Summary: AS-Quant is a robust program for identifying alternative splicing events from RNA-seq data. It outperforms other widely used tools by calculating read coverage, categorizing event types, and generating short read coverage plots. The significant alternative splicing events identified by AS-Quant were validated using RT-PCR experiments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biotechnology & Applied Microbiology
Jinkai Wang
Summary: Post-transcriptional processing of RNAs is regulated by RNA binding proteins and transcription factors, as well as histone modifications. High-throughput sequencing techniques have allowed for the study of these processes using multiomics data, but deciphering the fundamental regulatory roles of these processes remains a challenge. This review discusses the regulatory mechanisms of post-transcriptional processes and outlines general principles and approaches for dissecting these mechanisms through integration of multiomics data and public resources.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2021)
Article
Plant Sciences
Xiaozeng Mi, Yi Yue, Mengsha Tang, Yanlin An, Hui Xie, Dahe Qiao, Zhiyu Ma, Shengrui Liu, Chaoling Wei
Summary: Alternative splicing (AS) increases transcript and protein diversity in plants and plays a key role in growth, development, and stress tolerance. The TeaAS database provides comprehensive information on AS in tea plants by integrating data from 66 RNA-seq datasets, allowing users to easily identify AS events and transcript expression levels. It also offers tools for sequence alignment and visualization of gene structure, making it a valuable resource for researchers studying AS in woody crops and gene regulation in tea plants.
Article
Immunology
Mengquan Yang, Xiaomin Shang, Yiqing Zhou, Changhong Wang, Guiying Wei, Jianxia Tang, Meihua Zhang, Yaobao Liu, Jun Cao, Qingfeng Zhang
Summary: This study utilized a full-length sequencing approach to generate a transcriptome dataset containing full-length transcripts of Plasmodium falciparum during asexual blood stages, revealing a variety of transcription events and non-coding RNAs. The integration of full-length transcriptomic data with shotgun proteome analysis validated the findings and identified novel small proteins, shedding light on the complex gene expression in malaria parasites and providing valuable resources for future research on P. falciparum genes.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Virology
Jia-min Yan, Wen-kang Zhang, Fei Li, Chuan-min Zhou, Xue-jie Yu
Summary: This study conducted a global transcriptome analysis of THP-1 macrophages infected with SFTSV, identifying differentially expressed mRNAs and lncRNAs. Differentially expressed mRNAs were associated with innate immune, cytokine signaling, systemic lupus erythematosus, and alcoholism, while differentially expressed lncRNAs were enriched in systemic lupus erythematosus, alcoholism, and ribosome. The study also revealed key regulatory genes and transcription factors playing important roles in SFTSV infection.
Review
Neurosciences
Cecilia Rocha, Panagiotis Prinos
Summary: Primary cilia play a critical role in directing cellular signaling events during brain development and neuronal differentiation. Genetic and epigenetic alterations, as well as RNA processing and post-translational modifications, contribute to the development of human neuronal disorders and brain tumors. This review summarizes research on mouse and human studies of ciliogenesis and primary cilia function in the brain, highlighting their role in maintaining neuronal progenitor populations, coordinating neuronal differentiation, and controlling key signaling pathways critical for neurogenesis. The impact of post-translational modifications and missplicing of ciliary genes leading to ciliopathies and cell cycle alterations is also discussed. Ultimately, genetic and epigenetic studies of cilia shed light on the cellular and molecular mechanisms underlying neurodevelopmental disorders and brain tumors.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Lirong Hu, Abdul Sammad, Congcong Zhang, Luiz F. Brito, Qing Xu, Yachun Wang
Summary: This study evaluated the changes in milk yield, physiological indicators, blood biochemical parameters, and alternative splicing patterns in lactating Holstein cows under heat stress conditions. The results showed that heat stress negatively impacted various biological processes of Holstein cows. Additionally, heat stress increased the occurrence of alternative splicing events, with genes involved in mRNA splicing, immune, and metabolic processes being enriched. Two candidate genes associated with heat stress responses in dairy cows were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Tun Xu, Xiaofei Yang, Yanyan Jia, Zihang Li, Guangbo Tang, Xiujuan Li, Bo Wang, Tingjie Wang, Jiadong Lin, Li Guo, Kai Ye
Summary: By applying IsoSeq on opium poppy, we enhanced gene annotation and identified tissue and development-specific alternative splicing modes using a custom-made correction tool. Through the newly discovered transcribed loci, we uncovered distinct characteristics of splicing sites between young and old genes.
Article
Forestry
Xianliang Zhu, Jiayue He, Changpin Zhou, Qijie Weng, Shengkan Chen, David Bush, Fagen Li
Summary: This study investigates the effects of gene transcription and alternative splicing on wood formation in Eucalyptus urophylla x tereticornis, an economically important tree species in southern China. The results suggest that gene transcription and alternative splicing play important regulatory roles in wood properties and are controlled by independent regulatory systems. Additionally, the study identifies potential molecular mechanisms involved in the regulation of wood properties, which may contribute to the genetic improvement of Eucalyptus.
Article
Hematology
Abd A. Alhasan, Osagie G. Izuogu, Haya H. Al-Balool, Jannetta S. Steyn, Amanda Evans, Maria Colzani, Cedric Ghevaert, Joanne C. Mountford, Lamin Marenah, David J. Elliott, Mauro Santibanez-Koref, Michael S. Jackson
Article
Multidisciplinary Sciences
Alicia Madgwick, Philippe Fort, Peter S. Hanson, Philippe Thibault, Marie-Claude Gaudreau, Georges Lutfalla, Tarik Moeroey, Sherif Abou Elela, Bill Chaudhry, David J. Elliott, Christopher M. Morris, Julian P. Venables
Article
Oncology
Jennifer Munkley, Sebastian Oltean, Daniel Vodak, Brian T. Wilson, Karen E. Livermore, Yan Zhou, Eleanor Star, Vasileios I. Floros, Bjarne Johannessen, Bridget Knight, Paul McCullagh, John McGrath, Malcolm Crundwell, Rolf I. Skotheim, Craig N. Robson, Hing Y. Leung, Lorna W. Harries, Prabhakar Rajan, Ian G. Mills, David J. Elliott
Article
Multidisciplinary Sciences
Jacqueline Stockley, Elke Markert, Yan Zhou, Craig N. Robson, David J. Elliott, Johan Lindberg, Hing Y. Leung, Prabhakar Rajan
SCIENTIFIC REPORTS
(2015)
Review
Biochemistry & Molecular Biology
Ingrid Ehrmann, Philippe Fort, David J. Elliott
BIOCHEMICAL SOCIETY TRANSACTIONS
(2016)
Article
Biochemical Research Methods
Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro Santibanez-Koref, David J. Elliot, Michael S. Jackson
BMC BIOINFORMATICS
(2016)
Correction
Biochemical Research Methods
Osagie G. Izuogu, Abd A. Alhasan, Hani M. Alafghani, Mauro Santibanez-Koref, David J. Elliott, Michael S. Jackson
BMC BIOINFORMATICS
(2016)
Review
Urology & Nephrology
Jennifer Munkley, Ian G. Mills, David J. Elliott
NATURE REVIEWS UROLOGY
(2016)
Article
Biochemistry & Molecular Biology
Marina Danilenko, Caroline Dalgliesh, Vittoria Pagliarini, Chiara Naro, Ingrid Ehrmann, Mikael Feracci, Mahsa Kheirollahi-Chadegani, Alison Tyson-Capper, Gavin J. Clowry, Philippe Fort, Cyril Dominguez, Claudio Sette, David J. Elliott
NUCLEIC ACIDS RESEARCH
(2017)
Article
Cell & Tissue Engineering
Irina Neganova, Evgenija Shmeleva, Jennifer Munkley, Valeria Chichagova, George Anyfantis, Rhys Anderson, Joao Passos, David J. Elliott, Lyle Armstrong, Majlinda Lako
Article
Multidisciplinary Sciences
Mikael Feracci, Jaelle N. Foot, Sushma N. Grellscheid, Marina Danilenko, Ralf Stehle, Oksana Gonchar, Hyun-Seo Kang, Caroline Dalgliesh, N. Helge Meyer, Yilei Liu, Albert Lahat, Michael Sattler, Ian C. Eperon, David J. Elliott, Cyril Dominguez
NATURE COMMUNICATIONS
(2016)
Article
Oncology
Jennifer Munkley, David J. Elliott
Article
Cell Biology
Ingrid Ehrmann, Matthew R. Gazzara, Vittoria Pagliarini, Caroline Dalgliesh, Mahsa Kheirollahi-Chadegani, Yaobo Xu, Eleonora Cesari, Marina Danilenko, Marie Maclennan, Kate Lowdon, Tanja Vogel, Piia Keskivali-Bond, Sara Wells, Heather Cater, Philippe Fort, Mauro Santibanez-Koref, Silvia Middei, Claudio Sette, Gavin J. Clowry, Yoseph Barash, Mark O. Cunningham, David J. Elliott
Article
Medicine, General & Internal
Jennifer Munkley, Daniel Vodak, Karen E. Livermore, Katherine James, Brian T. Wilson, Bridget Knight, Paul McCullagh, John Mcgrath, Malcolm Crundwell, Lorna W. Harries, Hing Y. Leung, Craig N. Robson, Ian G. Mills, Prabhakar Rajan, David J. Elliott
Article
Biochemistry & Molecular Biology
David J. Elliott, Caroline Dalgliesh, Gerald Hysenaj, Ingrid Ehrmann
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2019)