Article
Biochemistry & Molecular Biology
Jie Zhang, Yijun Yang, Xinhua Li, Gen Li, Takuya Mizukami, Yanli Liu, Yuan Wang, Guoqiang Xu, Heinrich Roder, Li Zhang, Zeng-jie Yang
Summary: PDLIM3 plays a crucial role in ciliogenesis and hedgehog signaling transduction in SHH-MB cells, promoting cell proliferation and tumor growth. It can serve as a molecular marker for defining MB.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Biochemistry & Molecular Biology
Zakaria Louadi, Kevin Yuan, Alexander Gress, Olga Tsoy, Olga Kalinina, Jan Baumbach, Tim Kacprowski, Markus List
Summary: Alternative splicing plays a crucial role in regulating the functional diversity of the proteome, but its isoform-specific effects on protein-protein interactions are often overlooked. By integrating various interaction information, researchers have developed a user-friendly database called DIGGER to study mechanistic consequences of alternative splicing, providing a valuable resource for exploring the functional role of individual exons on a network level.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Oncology
Xinyuan Jiang, Zhiyong Xu, Sujing Jiang, Huan Wang, Mingshu Xiao, Yueli Shi, Kai Wang
Summary: PDZ-LIM family proteins are scaffolding proteins that contain PDZ and LIM interaction domains. The PDZ and LIM domains function as scaffolds to bind to various proteins. PDLIMs are evolutionarily conserved proteins found in different species. They mediate the interaction of signal molecules and are involved in important physiological processes such as cell differentiation, proliferation, migration, and maintenance of cellular structural integrity. Dysregulation of PDLIMs has been linked to tumor formation and development. This paper reviews and integrates the current knowledge on PDLIMs, describing the structure and function of PDZ and LIM domains and the role of PDLIMs in tumor development.
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
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
Immunology
Wencui Wan, Yang Long, Xuemin Jin, Qiuming Li, Weiwei Wan, Hongzhuo Liu, Yu Zhu
Summary: This study demonstrated that miR-200a may serve as a potential therapeutic target in DR through down-regulating PDLIM1, significantly affecting cell viability and inflammation.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Review
Cell Biology
Lucas A. B. Fisher, Frieder Schock
Summary: The ability of multicellular animals to move is achieved through rearrangement of cytoskeleton. ALP/Enigma family proteins, characterized by PDZ and LIM domains, play a crucial role in facilitating this process in various cellular environments, and have implications in muscle-related diseases.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Delong Zhou, Yvan Tran, Sherif Abou Elela, Michelle S. Scott
Summary: SAPFIR is a predictor of protein features associated with alternative splicing events, allowing for rapid identification of functional alternative splicing events and analysis of proteins generated from diverse genes, providing guidance on the impact on cellular functions.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Sandhya Malla, Devi Prasad Bhattarai, Paula Groza, Dario Melguizo-Sanchis, Ionut Atanasoai, Carlos Martinez-Gamero, Angel-Carlos Roman, Dandan Zhu, Dung-Fang Lee, Claudia Kutter, Francesca Aguilo
Summary: This study reveals the role of ZFP207 in mouse embryonic stem cells through multiple functional analyses. Unlike human ESCs, mouse ZFP207 mainly exerts its effects by controlling AS networks and acting as RNA-binding proteins (RBPs) to maintain ESC identity and regulate neural fate commitment.
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)
Article
Biochemistry & Molecular Biology
Chiharu Hidaka, Shinichi Mitsui, Yoij Osako, Kou Takahashi, Kenjiro Tanaka, Kazunari Yuri
Summary: This study investigated the expression patterns of Sez6 splicing isoforms in the mouse brain and cultured neurons, revealing brain area-specific expression. Furthermore, neuronal activation and certain drugs were found to modulate the splicing patterns of Sez6.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Michael D. Healy, Joanna Sacharz, Kerrie E. McNally, Calum McConville, Vikas A. Tillu, Ryan J. Hall, Molly Chilton, Peter J. Cullen, Mehdi Mobli, Rajesh Ghai, David A. Stroud, Brett M. Collins
Summary: SNX17 controls the endosomal recycling of transmembrane cargo proteins through its association with the Commander trafficking complex and the PDLIM family of proteins. The interaction between SNX17 and PDLIM is mediated by a unique peptide interaction involving electrostatic contacts and a conserved proline-containing loop sequence. This interaction may play a role in regulating the activity of SNX17 in conjunction with Commander and actin-rich endosomal trafficking domains.
Article
Biochemistry & Molecular Biology
Stephen A. Peter, Jessica S. Isaac, Franz Narberhaus, Julia E. Weigand
Summary: Proteome integrity is crucial for cellular homeostasis and adaptation to stress conditions like hypoxia, with alternative splicing being a mechanism for rapid adaptation. The isoE degron, generated under hypoxia, represents a universal protein degradation signal functional in mammalian cells, yeast, and bacteria. The conserved (F/W)xxW motif is essential for efficient protein decay mediated by the proteasome in eukaryotes and Lon protease in bacteria.
JOURNAL OF MOLECULAR 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
Plant Sciences
Fengzhong Lu, Wanchen Li, Yalin Peng, Yang Cao, Jingtao Qu, Fuai Sun, Qingqing Yang, Yanli Lu, Xuehai Zhang, Lanjie Zheng, Fengling Fu, Haoqiang Yu
Summary: This study characterized a maize PP2C family member, ZmPP2C26, which negatively regulated drought tolerance in maize by dephosphorylating ZmMAPK3 and ZmMAPK7. Alternative splicing generated ZmPP2C26L and ZmPP2C26S isoforms, with ZmPP2C26S showing higher phosphatase activity. The expression of ZmPP2C26L and ZmPP2C26 was inhibited by drought stress, and the zmpp2c26 mutant exhibited enhanced drought tolerance. However, overexpression of ZmPP2C26L and ZmPP2C26S decreased drought tolerance in Arabidopsis and rice. Phosphoproteomic analysis revealed that ZmPP2C26 also altered phosphorylation levels of proteins involved in photosynthesis. This study provides insights into the mechanism of PP2C in response to abiotic stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Jumpei Ito, Masumi Iijima, Nobuo Yoshimoto, Tomoaki Niimi, Shun'ichi Kuroda, Andres D. Maturana
CELLULAR SIGNALLING
(2015)
Article
Multidisciplinary Sciences
Hideaki E. Kato, Keiichi Inoue, Rei Abe-Yoshizumi, Yoshitaka Kato, Hikaru Ono, Masae Konno, Shoko Hososhima, Toru Ishizuka, Mohammad Razuanul Hoque, Hirofumi Kunitomo, Jumpei Ito, Susumu Yoshizawa, Keitaro Yamashita, Mizuki Takemoto, Tomohiro Nishizawa, Reiya Taniguchi, Kazuhiro Kogure, Andres D. Maturana, Yuichi Iino, Hiromu Yawo, Ryuichiro Ishitani, Hideki Kandori, Osamu Nureki
Article
Multidisciplinary Sciences
Hideaki E. Kato, Motoshi Kamiya, Seiya Sugo, Jumpei Ito, Reiya Taniguchi, Ayaka Orito, Kunio Hirata, Ayumu Inutsuka, Akihiro Yamanaka, Andres D. Maturana, Ryuichiro Ishitani, Yuki Sudo, Shigehiko Hayashi, Osamu Nureki
NATURE COMMUNICATIONS
(2015)
Article
Biochemistry & Molecular Biology
Miyuki Nakatani, Jumpei Ito, Riko Koyama, Masumi Iijima, Nobuo Yoshimoto, Tomoaki Niimi, Shun'ichi Kuroda, Andres D. Maturana
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2016)
Article
Biochemistry & Molecular Biology
Jumpei Ito, Masatoshi Takita, Koichi Takimoto, Andres D. Maturana
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2013)
Article
Biochemistry & Molecular Biology
Riko Koyama, Tiphaine Mannic, Jumpei Ito, Laurence Amar, Maria-Christina Zennaro, Michel Florian Rossier, Andres Daniel Maturana
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2018)
Article
Chemistry, Physical
Gennaro Pescitelli, Hideaki E. Kato, Satomi Oishi, Jumpei Ito, Andres Daniel Maturana, Osamu Nureki, Robert W. Woody
JOURNAL OF PHYSICAL CHEMISTRY B
(2014)
Article
Multidisciplinary Sciences
Hideaki E. Kato, Feng Zhang, Ofer Yizhar, Charu Ramakrishnan, Tomohiro Nishizawa, Kunio Hirata, Jumpei Ito, Yusuke Aita, Tomoya Tsukazaki, Shigehiko Hayashi, Peter Hegemann, Andres D. Maturana, Ryuichiro Ishitani, Karl Deisseroth, Osamu Nureki
Article
Multidisciplinary Sciences
Mizuki Takemoto, Hideaki E. Kato, Michio Koyama, Jumpei Ito, Motoshi Kamiya, Shigehiko Hayashi, Andres D. Maturana, Karl Deisseroth, Ryuichiro Ishitani, Osamu Nureki
Review
Cardiac & Cardiovascular Systems
Nina Kaludercic, Maria Chiara Maiuri, Susmita Kaushik, Alvaro F. Fernandez, Jenny de Bruijn, Francesca Castoldi, Yun Chen, Jumpei Ito, Risa Mukai, Tomokazu Murakawa, Jihoon Nah, Federico Pietrocola, Toshiro Saito, Salwa Sebti, Martina Semenzato, Lorenza Tsansizi, Sebastiano Sciarretta, Julio Madrigal-Matute
CARDIOVASCULAR RESEARCH
(2020)
Article
Cardiac & Cardiovascular Systems
Shigemiki Omiya, Yosuke Omori, Manabu Taneike, Tomokazu Murakawa, Jumpei Ito, Yohei Tanada, Kazuhiko Nishida, Osamu Yamaguchi, Takashi Satoh, Ajay M. Shah, Shizuo Akira, Kinya Otsu
Article
Biology
Jumpei Ito, Shigemiki Omiya, Mara-Camelia Rusu, Hiromichi Ueda, Tomokazu Murakawa, Yohei Tanada, Hajime Abe, Kazuki Nakahara, Michio Asahi, Manabu Taneike, Kazuhiko Nishida, Ajay M. Shah, Kinya Otsu
Summary: Iron metabolism plays a crucial role in the development of heart failure, with ferritinophagy leading to iron overload and increased lipid peroxidation. Inhibiting this process can protect the heart from hemodynamic stress.
Article
Biochemistry & Molecular Biology
Jumpei Ito, Tomomi Minemura, Sebastien Walchli, Tomoaki Niimi, Yoshitaka Fujihara, Shun'ichi Kuroda, Koichi Takimoto, Andres D. Maturana
Summary: Research shows that Id2 functions as a transcriptional repressor for L- and T-type Ca2+ channels in cardiomyocytes, with its expression being controlled by aldosterone. The presence of Id2 prevents the occurrence of channels associated with a pathological state, potentially acting as a protective mechanism in cardiomyocytes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Hajime Abe, Yohei Tanada, Shigemiki Omiya, Mihai-Nicolae Podaru, Tomokazu Murakawa, Jumpei Ito, Ajay M. Shah, Simon J. Conway, Masahiro Ono, Kinya Otsu
Summary: This study demonstrates that a subset of mouse cardiac fibroblasts become activated by pressure overload and recruit inflammatory Ly6C(hi) monocytes to the heart. The involvement of NF-kappa B in activated cardiac fibroblasts attenuates heart function damage and offers new insights into potential therapeutic strategies for heart failure.