Review
Biochemistry & Molecular Biology
Ricardo De Paoli-Iseppi, Josie Gleeson, Michael B. Clark
Summary: Alternative splicing of RNA is a key mechanism leading to the expression of multiple transcript isoforms from a single gene, increasing the complexity of the transcriptome and proteome. Long-read sequencing technologies can address the limitations of short-read sequencing in resolving complex isoforms and distinguish changes that may impact RNA regulation or protein function. Integration of long-read sequencing with other technologies allows for detailed profiling of alternative splicing at the isoform level and determination of the impact of genetic variation on isoform expression.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Theodore M. Nelson, Sankar Ghosh, Thomas S. Postler
Summary: Long-read sequencing (LRS) provides more accurate and quantitative records of RNA, including splicing patterns, compared to conventional high-throughput sequencing. However, mining and analyzing publicly available LRS data can be challenging due to the complexity of software tools and difficulties in comparing results across different studies. To address these challenges, we have developed a user-friendly and free pipeline for the rapid and standardized analysis of LRS datasets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Shuang-Yan Zheng, Lu-Xia Pan, Fu-Ping Cheng, Meng-Jie Jin, Zi-Long Wang
Summary: In this study, the full-length transcriptome of A. mellifera was sequenced using PacBio technology. A total of 116,535 transcripts and 30,045 genes were identified. Compared to the reference genome, 18,915 gene loci and 96,176 transcripts were newly identified. Additionally, alternative splicing events, alternative polyadenylation sites and long non-coding RNAs were detected. These findings expand our understanding of the complexity and diversity of the honey bee transcriptome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Genetics & Heredity
Qiang Sun, Ye Han, Jianxing He, Jie Wang, Xuejie Ma, Qianqian Ning, Qing Zhao, Qian Jin, Lili Yang, Shuang Li, Yang Li, Qiaoming Zhi, Junnian Zheng, Dong Dong
Summary: This study investigates the transcriptome complexity in colorectal cancer (CRC) using long-read sequencing technology and short-read RNA-seq methods. A novel splicing isoform, TIMP1 ?4-5, is identified and its ectopic expression is found to suppress tumor cell growth and metastasis. Furthermore, a CRISPR/dCasRx-based strategy is introduced to induce TIMP1 exon 4-5 exclusion, which has the potential to restrain CRC growth.
Article
Biochemical Research Methods
Karim Rahimi, Anne Faerch Nielsen, Morten T. Veno, Jorgen Kjems
Summary: Circular RNA (circRNA) are highly stable RNA molecules with suggested roles in development and disease, derived from linear pre-mRNAs through a process called back-splicing. Identification of circRNAs depends on the detection of unique back-splice-junction sequence reads. Long-read nanopore sequencing has expanded our understanding of circRNA size distribution and internal splicing patterns.
Article
Biotechnology & Applied Microbiology
Esther Ng, Mihaela-Olivia Dobrica, James M. Harris, Yanxia Wu, Senko Tsukuda, Peter A. C. Wing, Paolo Piazza, Peter Balfe, Philippa C. Matthews, M. Azim Ansari, Jane A. McKeating
Summary: This study used oligonucleotide enrichment and PacBio long read sequencing to identify the repertoire of HBV RNAs. The method allowed for the detection of up to 25% viral sequences and the identification of canonical and non-canonical viral-human transcripts. RNA isolated from de novo HBV infected cells and transfected cells were used to assess the viral transcriptome and annotate truncations and polyadenylation profiles. The enrichment capture and PacBio sequencing method provides an accurate mapping of the HBV transcriptome.
JOURNAL OF GENERAL VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas, Michaela A. Boti, Andreas Scorilas
Summary: The study examined the role of human RAS proteins in cancer, discovering 39 novel RAS mRNA transcript variants and analyzing their expression profiles in a wide range of human cell lines. While shedding light on hidden aspects of the RAS gene family, further research is necessary to uncover the biological function of these novel alternative transcript variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zhao Li, Linqian Han, Zi Luo, Lin Li
Summary: This study utilized single-molecule long-read sequencing to analyze cDNA libraries from the teosinte inbred line TIL11, identifying 70,044 nonredundant transcript isoforms. A machine learning-based bioinformatics pipeline, DenovoAS_Finder, was developed to annotate the TIL11 transcriptome without a complete reference genome with up to 91% accuracy. Additionally, a draft TIL11 genome was constructed with 16,633 high-quality contigs by Nanopore sequencing, revealing insights into maize domestication and providing a valuable resource for utilizing wild germplasm in maize breeding.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Oncology
Liwei Song, Mengjun Yu, Renjing Jin, Meng Gu, Ziyu Wang, Dailun Hou, Shaofa Xu, Jinghui Wang, Teng Ma
Summary: In this study, we utilized the PacBio Single Molecule, Real-Time (SMRT) Sequencing platform to investigate the transcriptome after DNA-PK inactivation. We identified a large number of new transcripts and gene structures, and validated some of the new transcripts. These findings contribute to our understanding of the role of DNA-PK in transcriptome regulation and RNA metabolism.
FRONTIERS IN ONCOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Cheng-Yan Mou, Qiang Li, Zhi-Peng Huang, Hong-Yu Ke, Han Zhao, Zhong-Meng Zhao, Yuan-Liang Duan, Hua-Dong Li, Yu Xiao, Zhou-Ming Qian, Jun Du, Jian Zhou, Lu Zhang
Summary: This study generated a full-length transcriptome of oriental river prawn muscle using the PacBio Sequel platform, and identified 6,599 error-corrected isoforms. Transcriptome structural analysis revealed thousands of alternative splicing and polyadenylation events. This study provides valuable information for understanding the genomic structure and improving the genome annotation of oriental river prawn.
Article
Genetics & Heredity
Xindan Li, Jinming Wu, Xinping Xiao, Yifeng Rong, Haile Yang, Junyi Li, Qiong Zhou, Weiguo Zhou, Jianquan Shi, Hongfang Qi, Hao Du
Summary: The Tibetan Schizothoracinae fish Gymnocypris przewalskii, known for its ability to adapt to the extreme plateau environment, has been studied for its transcriptome features using long-read sequencing technology. A total of 159,053 full-length transcripts were captured, with a significant amount of them well-annotated and containing complete open reading frames. The FL transcriptome provides a solid foundation for future research on G. przewalskii.
Article
Biochemistry & Molecular Biology
Alejandra Tamayo, Gonzalo Nunez-Moreno, Carolina Ruiz, Julie Plaisancie, Alejandra Damian, Jennifer Moya, Nicolas Chassaing, Patrick Calvas, Carmen Ayuso, Pablo Minguez, Marta Corton
Summary: PAX6 haploinsufficiency causes aniridia, a congenital eye disorder that involves the iris, and foveal hypoplasia. Comprehensive screening of the PAX6 locus revealed four deep-intronic variants with potential effects on pre-RNA splicing. Functional analysis using in vitro minigene splicing assays and nanopore-based long-read sequencing confirmed the impact of two variants on aberrant splicing, while the other two variants were found to have no effect on splicing. This study emphasizes the importance of integrating functional studies into diagnostic algorithms to achieve conclusive genetic diagnoses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Juan-Carlos A. Padilla, Seda Barutcu, Ludovic Malet, Gabrielle Deschamps-Francoeur, Virginie Calderon, Eunjeong Kwon, Eric Lecuyer
Summary: This study provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs and highlights the potential usefulness of nanopore sequencing in interrogating secreted RNA transcriptomes.
Article
Biochemistry & Molecular Biology
Elizaveta Sarygina, Anna Kozlova, Kseniia Deinichenko, Sergey Radko, Konstantin Ptitsyn, Svetlana Khmeleva, Leonid K. Kurbatov, Pavel Spirin, Vladimir S. Prassolov, Ekaterina Ilgisonis, Andrey Lisitsa, Elena Ponomarenko
Summary: The long-read RNA sequencing developed by Oxford Nanopore Technology allows for direct quantification of transcript isoforms and can be used in alternative splicing profiling. By using principal component analysis (PCA) to visualize the transcriptomic data, biospecimens can be grouped into clusters based on their gene expression. This method is useful for studying drug metabolism and transcriptome analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Genetics & Heredity
Qi A. Song, Nathan S. Catlin, W. Brad Barbazuk, Song Li
Article
Multidisciplinary Sciences
Jason O. Brant, J. Lucas Boatwright, Ruth Davenport, Aaron Gabriel W. Sandoval, Malcolm Maden, W. Brad Barbazuk
Article
Plant Sciences
Julian R. Dupuis, Yohan Pillon, Tomoko Sakishima, Chrissen E. C. Gemmill, Srikar Chamala, W. Brad Barbazuk, Scott M. Geib, Elizabeth A. Stacy
PLANT SYSTEMATICS AND EVOLUTION
(2019)
Article
Multidisciplinary Sciences
Martha Rendon-Anaya, Enrique Ibarra-Laclette, Alfonso Mendez-Bravo, Tianying Lan, Chunfang Zheng, Lorenzo Carretero-Paulet, Claudia Anahi Perez-Torres, Alejandra Chacon-Lopez, Gustavo Hernandez-Guzman, Tien-Hao Chang, Kimberly M. Farr, W. Brad Barbazuk, Srikar Chamala, Marek Mutwil, Devendra Shivhare, David Alvarez-Ponce, Neena Mitter, Alice Hayward, Stephen Fletcher, Julio Rozas, Alejandro Sanchez Gracia, David Kuhn, Alejandro F. Barrientos-Priego, Jarkko Salojarvi, Pablo Librado, David Sankoff, Alfredo Herrera-Estrella, Victor A. Albert, Luis Herrera-Estrella
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Plant Sciences
Jerald D. Noble, Kelly M. Balmant, Christopher Dervinis, Gustavo de los Campos, Marcio F. R. Resende, Matias Kirst, William Brad Barbazuk
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Biochemistry & Molecular Biology
Kelly M. Balmant, Jerald D. Noble, Filipe C. Alves, Christopher Dervinis, Daniel Conde, Henry W. Schmidt, Ana Vazquez, William B. Barbazuk, Gustavo de los Campos, Marcio F. R. Resende, Matias Kirst
Article
Plant Sciences
Guanqiao Feng, Mi-Jeong Yoo, Ruth Davenport, J. Lucas Boatwright, Jin Koh, Sixue Chen, W. Brad Barbazuk
Article
Cell & Tissue Engineering
Janak Gaire, Justin A. Varholick, Sabhya Rana, Michael D. Sunshine, Sylvain Dore, W. Brad Barbazuk, David D. Fuller, Malcolm Maden, Chelsey S. Simmons
Summary: The spiny mouse is an exciting research organism due to its remarkable scarless healing abilities in various tissues beyond the skin, which could shed light on numerous clinically relevant human diseases. However, there are challenges in working with this emerging research organism that require future strategies and methods.
NPJ REGENERATIVE MEDICINE
(2021)
Article
Biochemical Research Methods
Tongjun Gu, Xiwu Zhao, William Bradley Barbazuk, Ji-Hyun Lee
Summary: A novel hybrid deep learning-based approach combining CNN and RNN was developed to predict miRNA targets more accurately. The approach showed superior performance compared to previous methods on test datasets, and delivered substantial improvements on independent datasets. Additionally, a unified model was developed that is robust on fitting different input datasets.
BMC BIOINFORMATICS
(2021)
Article
Plant Sciences
J. Lucas Boatwright, Cheng-Ting Yeh, Heng-Cheng Hu, Alfonso Susanna, Douglas E. Soltis, Pamela S. Soltis, Patrick S. Schnable, William B. Barbazuk
Summary: Polyploidization can have a significant impact on genetic material, with Tragopogon offering a unique opportunity to study repeated allopolyploid formation and genome evolution over time.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Tongjun Gu, Mingyi Xie, W. Brad Barbazuk, Ji-Hyun Lee
Summary: Research shows that miTAR can capture both known and multiple novel features in miRNA:target interactions.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Jessie A. Pelosi, Emily H. Kim, W. Brad Barbazuk, Emily B. Sessa
Summary: In this study, we assembled the largest nuclear dataset for ferns and investigated the fern phylogeny, whole genome duplications (WGDs), and gene retention patterns following WGDs. Our results revealed high levels of gene tree-species tree conflict in the fern phylogeny and identified multiple WGDs events. We also found that functions of retained genes following WGDs were largely convergent.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Dawei Dai, Janaki S. Mudunkothge, Mary Galli, Si Nian Char, Ruth Davenport, Xiaojin Zhou, Jeffery L. Gustin, Gertraud Spielbauer, Junya Zhang, W. Brad Barbazuk, Bing Yang, Andrea Gallavotti, A. Mark Settles
Summary: The paternal imprinting of Ded1 in maize contributes to the xenia effect by regulating the pace of endosperm development. This study provides evidence for the existence of xenia effects and reveals the regulatory mechanism of endosperm development.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Amy E. Siebert, Jacob Corll, J. Paige Gronevelt, Laurel Levine, Linzi M. Hobbs, Catalina Kenney, Christopher L. E. Powell, Fabia U. Battistuzzi, Ruth Davenport, A. Mark Settles, W. Brad Barbazuk, Randal J. Westrick, Gerard J. Madlambayan, Shailesh Lal
Summary: U12-type introns are widely present in multicellular eukaryotes and are associated with developmental defects. Mutations in RBM48 gene in humans disrupt U12-type intron splicing and are associated with myelodysplastic syndrome. Comparison of human and maize genetic data identifies candidate genes that likely mediate mutant phenotypes of U12-type splicing defects.
Article
Plant Sciences
Mi-Jeong Yoo, Jin Koh, J. Lucas Boatwright, Douglas E. Soltis, Pamela S. Soltis, W. Brad Barbazuk, Sixue Chen
Summary: Polyploidy is an important evolutionary process in eukaryotes, particularly in flowering plants. Understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. This study compared the leaf transcriptomes of recently formed natural allotetraploids and their diploid parents, and found that there were significant differences in gene expression between the old and new polyploids. Some loci showed novel expression bias patterns in the newly formed polyploids, indicating ongoing evolutionary processes.