Article
Multidisciplinary Sciences
Praveen Kumar Kathare, Ruijiao Xin, Abirama Sundari Ganesan, Viviana M. June, Anireddy S. N. Reddy, Enamul Huq
Summary: Light signals have significant effects on the physiology, growth, and development of plants. SWAP1, an RNA-binding splicing factor, regulates light-regulated alternative splicing by interacting with other splicing factors and photoactivated phyB.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Shune Wang, Mei Xue, Chan He, Danyu Shen, Chunhao Jiang, Hongwei Zhao, Dongdong Niu
Summary: The study reveals that AtMC1 regulates plant immunity to bacterial pathogens and is physically associated with LSM4. The protein levels of AtMC1 and LSM4 increase with coexpression in vivo. Additionally, AtMC1 modulates the splicing of pre-mRNAs, including 4CL3, which regulates plant immunity.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2021)
Review
Plant Sciences
Praveen Kumar Kathare, Enamul Huq
Summary: The article summarizes the role of phytochromes in regulating plant growth and development, particularly in the regulation of pre-mRNA splicing process.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Jingya Lin, Ziqiang Zhu
Summary: This review discusses how plants adapt to high temperatures through pre-mRNA splicing, and the significance of this splicing regulation for plant growth and development.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Plant Sciences
Keiko Inaba-Hasegawa, Ayumi Ohmura, Masayo Nomura, Masahiro Sugiura
Summary: Chloroplast genomes in land plants contain approximately 20 intron-containing genes, similar to group II introns found in fungi, algae, and some bacteria, but lacking self-splicing capability. Researchers developed an in vitro system using tobacco chloroplasts to study splicing reactions, revealing differences in splicing mechanisms between chloroplast pre-mRNA and self-splicing group II introns.
PLANT AND CELL PHYSIOLOGY
(2021)
Review
Oncology
Sunkyung Choi, Namjoon Cho, Eun-Mi Kim, Kee K. Kim
Summary: Alternative pre-mRNA splicing plays a critical role in generating multiple mRNA and increasing protein diversity. Specific splicing isoforms have been found to be important in cellular processes, particularly in regulating cell numbers. Abnormal expression of splicing isoforms and factors, as well as disruptions in splicing caused by genetic mutations, are implicated in cancer development and progression. Alternative splicing has potential as a therapeutic target for cancer.
CANCER CELL INTERNATIONAL
(2023)
Review
Biochemistry & Molecular Biology
Sierra L. L. Love, Joseph D. D. Emerson, Kazunori Koide, Aaron A. A. Hoskins
Summary: Pre-mRNA splicing is a crucial step in human gene expression, carried out by a macromolecular machine known as the spliceosome. Mutations in this machinery can lead to various human diseases. This review provides an overview of the main features of the pre-mRNA splicing machinery in humans and how changes in its components' function can result in diseases ranging from blindness to cancers. The article also discusses drugs that interact with the spliceosome to alter splicing outcomes and speculates on future treatments for spliceosomopathies.
Article
Biochemistry & Molecular Biology
Christophe Rachez, Rachel Legendre, Mickael Costallat, Hugo Varet, Jia Yi, Etienne Kornobis, Christian Muchardt
Summary: HP1 proteins, known for marking heterochromatin and gene silencing, are also RNA-binding proteins. HP1 gamma, in particular, is targeted to hexameric RNA motifs and SINE transposable elements, tethering unspliced pre-mRNA to chromatin through intronic regions and limiting the usage of intronic cryptic splice sites during transcription. This reveals new insights into the relationship between chromatin and co-transcriptional splicing.
Review
Oncology
Shinsuke Araki, Momoko Ohori, Masato Yugami
Summary: This review summarizes recent progress in the relationship between druggable splicing-related molecules and cancer, highlights small-molecule splicing modulators, and discusses future perspectives of splicing modulation for personalized and combination therapies in cancer treatment.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Chunlei Tang, Qiang Xu, Jinren Zhao, Mingxing Yue, Jianfeng Wang, Xiaodong Wang, Zhensheng Kang, Xiaojie Wang
Summary: Alternative splicing is an important regulatory mechanism in plant resistance. This study identified a new effector protein, Pst_A23, produced by the wheat stripe rust pathogen, that targets the splicing process in wheat and suppresses the plant's defense response. The study also showed that Pst_A23 overexpression alters the splicing patterns of wheat genes and affects the production of functional transcripts, leading to decreased resistance to wheat stripe rust.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Yang Pan, John W. Phillips, Beatrice D. Zhang, Miyako Noguchi, Eric Kutschera, Jami McLaughlin, Pavlo A. Nesterenko, Zhiyuan Mao, Nathanael J. Bangayan, Robert Wang, Wendy Tran, Harry T. Yang, Yuanyuan Wang, Yang Xu, Matthew B. Obusan, Donghui Cheng, Alex H. Lee, Kathryn E. Kadash-Edmondson, Ameya Champhekar, Cristina Puig-Saus, Antoni Ribas, Robert M. Prins, Christopher S. Seet, Gay M. Crooks, Owen N. Witte, Yi Xing
Summary: This study describes a computational platform called IRIS that can discover tumor antigens derived from alternative splicing, providing potential targets for TCR and CAR-T immunotherapies. Through the analysis of transcriptomics and immuno-peptidomics data, the study demonstrates that the predicted targets by IRIS can bind with HLA molecules. The study illustrates the contribution of alternative splicing to the repertoire of tumor antigens and demonstrates the utility of IRIS in discovering AS-derived antigens and expanding cancer immunotherapies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Changshou Wang, Lin Xu, Chen Du, Hao Yun, Keyun Wang, Hui Liu, Mingliang Ye, Jing Fan, Yu Zhou, Hong Cheng
Summary: CDK11 is a potential druggable target for cancer therapy, as it plays important roles in phosphorylating transcription and splicing factors and facilitating cell cycle progression in cancer cells. This study reveals that CDK11 forms a tight complex with cyclins L1/L2 and SAP30BP, and that SAP30BP is a critical activator of CDK11, regulating global pre-mRNA splicing.
Article
Plant Sciences
Mohammed Albaqami
Summary: Plants adjust their biological processes to cope with environmental factors, such as high salt exposure. This study reveals that salt-induced long-distance calcium signaling is involved in the regulation of pre-mRNA splicing in response to salt stress. It suggests that calcium waves play a crucial role in molecular regulation of RNA splicing, contributing to plant salt stress tolerance.
PAKISTAN JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Hyun-Ji Park, Hae-Myeong Jung, Areum Lee, Seung-Hee Jo, Hyo-Jun Lee, Hyun-Soon Kim, Choon-Kyun Jung, Sung-Ran Min, Hye-Sun Cho
Summary: OsFKBP20-1b is SUMOylated under stress conditions in rice, leading to enhanced protein stability and interaction with OsSUMO1 and OsSUMO2. The low SUMOylation level of 5KR_OsFKBP20-1b results in inadequate association with U snRNAs in response to heat stress, affecting RNA processing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Plant Sciences
Varvara Dikaya, Nabila El Arbi, Nelson Rojas-Murcia, Sarah Muniz Nardeli, Daniela Goretti, Markus Schmid
Summary: Alternative splicing in plants is closely linked to their ability to perceive environmental stimuli, particularly temperature, which strongly influences plant development and morphology.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Salah E. Abdel-Ghany, Fahad Ullah, Asa Ben-Hur, Anireddy S. N. Reddy
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Yongsheng Wang, Huihui Wang, Feihu Xi, Huiyuan Wang, Ximei Han, Wentao Wei, Hangxiao Zhang, Qianyue Zhang, Yushan Zheng, Qiang Zhu, Markus Kohnen, Anireddy S. N. Reddy, Lianfeng Gu
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Jie Huang, Xinyu Lu, Hongwei Wu, Yuchen Xie, Qian Peng, Lianfeng Gu, Juyou Wu, Yuanchao Wang, Anireddy S N Reddy, Suomeng Dong
Review
Biochemistry & Molecular Biology
Anireddy S. N. Reddy, Jie Huang, Naeem H. Syed, Asa Ben-Hur, Suomeng Dong, Lianfeng Gu
BIOCHEMICAL SOCIETY TRANSACTIONS
(2020)
Article
Plant Sciences
Ibtissam Jabre, Saurabh Chaudhary, Wenbin Guo, Maria Kalyna, Anireddy S. N. Reddy, Weizhong Chen, Runxuan Zhang, Cornelia Wilson, Naeem H. Syed
Summary: Research suggests that nucleosome positioning affects cold-induced alternative splicing in plants. In Arabidopsis thaliana, different types of alternative splicing events are closely linked to characteristic nucleosome occupancy levels. Internal regions of protein-coding exons, known as exitrons, exhibit distinct nucleosome positioning patterns compared to other alternatively spliced regions.
Review
Biochemistry & Molecular Biology
Vesper Burjoski, Anireddy S. N. Reddy
Summary: RNAs transmit information from DNA to encode proteins and regulate gene expression. Recent studies have uncovered a hidden landscape of RNA-protein interactions in plants. Application of modern techniques has led to the discovery of close to 2000 putative RNA-binding proteins in plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Xuqing Liu, Yubang Gao, Jiakai Liao, Miao Miao, Kai Chen, Feihu Xi, Wentao Wei, Huihui Wang, Yongsheng Wang, Xi Xu, Anireddy S. N. Reddy, Lianfeng Gu
Summary: This study identified a large number of circRNAs and R-loops in the stem-differentiating xylem of Populus trichocarpa, and investigated their roles in modulating alternative splicing (AS). The results showed that they may play crucial roles in regulating AS in the xylem.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Peng Gao, Teagen D. Quilichini, Chun Zhai, Li Qin, Kirby T. Nilsen, Qiang Li, Andrew G. Sharpe, Leon Kochian, Jitao Zou, Anireddy S. N. Reddy, Yangdou Wei, Curtis Pozniak, Nii Patterson, C. Stewart Gillmor, Raju Datla, Daoquan Xiang
Summary: Research indicates that there is diversity in the regulation of alternative splicing in polyploid wheat and grass species, not only showing differences in different tissues but also between subgenomes. Analysis of homoeologous triads in polyploid wheat reveals evolutionary divergence in the regulation of embryogenesis between gene-level and transcript-level.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Plant Sciences
Huiyuan Wang, Sheng Liu, Xiufang Dai, Yongkang Yang, Yunjun Luo, Yubang Gao, Xuqing Liu, Wentao Wei, Huihui Wang, Xi Xu, Anireddy S. N. Reddy, Pankaj Jaiswal, Wei Li, Bo Liu, Lianfeng Gu
Summary: Researchers have developed a public database containing comprehensive measurements of gene expression and post-transcriptional regulation to study the response of secondary growth in Populus trichocarpa to different stresses. The database also includes data on alternative splicing, alternative polyadenylation, and alternative transcription initiation. The PSDX database provides tools for data query, visualization, a genome browser, and BLAST option, facilitating the study of genes related to secondary growth and stress response in Populus trichocarpa.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Haroon Butt, Jeremie Bazin, Sahar Alshareef, Ayman Eid, Moussa Benhamed, Anireddy S. N. Reddy, Martin Crespi, Magdy M. Mahfouz
Summary: Researchers used CRISPR technology to create rice mutants with different levels of salt stress sensitivity for spliceosome components SF3B1 and PHF5A, demonstrating that these mutants can be used to study functions of redundant paralogs in plants.
COMMUNICATIONS BIOLOGY
(2021)
Review
Biology
Showkat Ahmad Ganie, Anireddy S. N. Reddy
Summary: When facing environmental stresses, alternative splicing (AS) plays a crucial role in rice by rapidly regulating gene expression to help the plant adapt to various pressures. Studies have shown that AS is important for rice growth and development, especially under stress conditions. Understanding the impact of AS on rice and its pathogens can provide valuable insights for developing stress-resistant rice varieties in the future.
Article
Biochemical Research Methods
Don Neumann, Anireddy S. N. Reddy, Asa Ben-Hur
Summary: In this study, we benchmark a fully convolutional deep learning basecalling architecture and find that it outperforms Oxford nanopore's RNA basecallers.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Marcelo R. A. de Figueiredo, Anita Kuepper, Jenna M. Malone, Tijana Petrovic, Ana Beatriz T. B. de Figueiredo, Grace Campagnola, Olve B. Peersen, Kasavajhala V. S. K. Prasad, Eric L. Patterson, Anireddy S. N. Reddy, Martin F. Kubes, Richard Napier, Franck E. Dayan, Christopher Preston, Todd A. Gaines
Summary: A 27-nucleotide deletion removing nine amino acids in the degron tail of the auxin coreceptor Aux/IAA2 (SoIAA2) is associated with 2,4-D resistance in a Sisymbrium orientale weed population. The deletion reduces binding to TIR1 and increases dissociation rates, resulting in resistance to synthetic auxin herbicides.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Yu-Chen Song, Mo-Xian Chen, Kai-Lu Zhang, Anireddy S. N. Reddy, Fu-Liang Cao, Fu-Yuan Zhu
Article
Biotechnology & Applied Microbiology
Yubang Gao, Xuqing Liu, Bizhi Wu, Huihui Wang, Feihu Xi, Markus Kohnen, Anireddy S. N. Reddy, Lianfeng Gu
Summary: The study introduces a new pipeline, Nanom6A, for the identification and quantification of m(6)A modification at single-base resolution, providing transcriptome-wide quantification of m(6)A modification in stem-differentiating xylem.