Article
Biochemistry & Molecular Biology
Aleksandra Glowacka, Pawel Bieganowski, Ewelina Jurewicz, Wieslawa Lesniak, Tomasz Wilanowski, Anna Filipek
Summary: S100A10, a Ca2+-binding protein, is involved in various cellular and extracellular processes. Its main roles include regulating plasminogen conversion to plasmin via interaction with annexin A2 and influencing neurotransmitter binding through interaction with 5-HT1B receptor, impacting depressive symptoms. Strict control of S100A10 expression is crucial due to its involvement in tumor progression and neurotransmitter regulation. Our study reveals a new regulatory mechanism of S100A10 expression by the transcription factor GRHL2 through direct binding to specific sites in the gene.
Article
Biochemistry & Molecular Biology
Sarah Janati-Idrissi, Mariana Roza de Abreu, Cervin Guyomar, Fernanda de Mello, Thaovi Nguyen, Nazim Mechkouri, Stephanie Gay, Jerome Montfort, Anne Alicia Gonzalez, Marzieh Abbasi, Jerome Bugeon, Violette Thermes, Herve Seitz, Julien Bobe
Summary: This study provides a proof of concept for the successful identification of miRNA phenotypic targets from RNA-seq data. The researchers identified tead3b as a target of miR-202-5p, which is involved in ovarian function and egg production. This study highlights the importance of understanding miRNA functions and their targets in order to better understand biological processes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Aileen Julia Riesle, Meijiang Gao, Marcus Rosenblatt, Jacques Hermes, Helge Hass, Anna Gebhard, Marina Veil, Bjorn Gruening, Jens Timmer, Daria Onichtchouk
Summary: This study investigates the combinatorial mechanisms of genome activation and shows that zebrafish genome activators Pou5f3 and Nanog exhibit different roles in the activation process. They act as pioneer-like transcription factors on synergistic enhancers, promoting histone acetylation and transcription activation. However, on antagonistic enhancers, one of the factors acts as a non-pioneer-like transcription factor, competing with the activator and blocking its effects. This activator-blocker mechanism restricts widespread transcriptional activation and prevents premature expression of late developmental genes in early embryos.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Mengyuan Wang, Qian Li, Lingbo Liu
Summary: Gene expression regulation involves multiple processes and various regulatory factors. This review provides an overview of key factors involved in gene expression regulation, such as transcription factors, chromatin accessibility, histone modifications, DNA methylation, and RNA modifications. Additionally, methods for detecting these regulatory factors are also described.
Article
Multidisciplinary Sciences
Xuan Wang, Jia-Ning Han, Xu Zhang, Yue-Yuan Ma, Yina Lin, Huan Wang, Dian-Jie Li, Tao-Ran Zheng, Fu-Qing Wu, Jian-Wen Ye, Guo-Qiang Chen
Summary: The researchers designed a thermosensitive switch for spatial and temporal control of colony pattern, cell shape and polymer production.
NATURE COMMUNICATIONS
(2021)
Review
Biotechnology & Applied Microbiology
Seung-Woon Jung, Jinho Yeom, Jong Seong Park, Seung Min Yoo
Summary: This article reviews the current trends and advances in tuning gene expression and regulation in microbial cell factories for sustainable and eco-friendly development. By balancing growth and production through gene expression and regulation, metabolic fluxes can be optimized and precisely controlled to improve productivity and yield of microbial cell factories. Various genetic-engineering-based tools and strategies for constructing microbial cell factories are discussed, with a focus on the prospects for tuning gene expression and regulation systems.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Biotechnology & Applied Microbiology
Derrick Shih-Wei Chuang, James C. Liao
Summary: This study revealed the important role of phosphoketolase (Xpk) in primary metabolism of cyanobacteria, particularly in energy regulation and dark conditions. Additionally, Xpk is involved in the pathway producing ATP from glycogen to acetate. Deletion of xpk leads to glucose secretion under dark, anaerobic conditions.
METABOLIC ENGINEERING
(2021)
Article
Biochemical Research Methods
Mengying Zhang, Xiyun Jin, Junyi Li, Yi Tian, Qi Wang, Xinhui Li, Juan Xu, Yongsheng Li, Xia Li
Summary: CeRNASeek is an R package that integrates multiple-omics data to identify and analyze ceRNA-ceRNA interactions. It provides six computational methods and various downstream analyses, suitable for studying the function of ceRNAs in complex diseases.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Cell Biology
Elly I. Lewerissa, Nael Nadif Kasri, Katrin Linda
Summary: Autophagy is a crucial metabolic process for maintaining cellular homeostasis and survival. Recent studies have shown the importance of autophagy in brain function, particularly in neuronal development and functioning. Mutations in autophagy-related genes as well as genes involved in epigenetic regulation have been linked to neurodevelopmental disorders (NDDs). This suggests that aberrant autophagic regulation may contribute to nervous system impairments in NDDs with disturbed epigenetic regulation.
Article
Cell Biology
Anna Alvarez-Guaita, Satish Patel, Koini Lim, Afreen Haider, Liang Dong, Olivia J. Conway, Marcella K. L. Ma, Davide Chiarugi, Vladimir Saudek, Stephen O'Rahilly, David B. Savage
Summary: Adig is a crucial protein in adipocytes, and its deficiency can affect adipogenesis and leptin levels in vivo, leading to leaner mice.
Article
Biochemistry & Molecular Biology
Barbara Michalec-Wawiorka, Jakub Czapinski, Kamil Filipek, Patrycja Rulak, Arkadiusz Czerwonka, Marek Tchorzewski, Adolfo Rivero-Muller
Summary: This study presents an optimized inducible expression system that enables rapid generation of doxycycline-responsive cells. The modifications of the Tet-On system provide high, stable, and homogenous expression of the Tet-On3G transactivator.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Shanshan Wang, Wei Lv, Tao Li, Shubing Zhang, Huihui Wang, Xuemei Li, Lianzi Wang, Dongyue Ma, Yan Zang, Jilong Shen, Yuanhong Xu, Wei Wei
Summary: N-6-Methyladenosine (m6A) is the most abundant internal modification associated with eukaryotic mRNAs, and it plays a dynamic regulatory role in gene expression by affecting various steps of mRNA metabolism. This review discusses the general role of m6A, focusing on the three major types of enzymes that determine the level of m6A modification and the regulatory mechanism by which m6A influences RNA metabolism. Understanding the role of m6A in physiological and pathophysiological processes, especially in tumorigenesis, is of great importance.
CANCER CELL INTERNATIONAL
(2022)
Article
Plant Sciences
Qian Zhang, Wei Yuan, Qianwen Wang, Yiying Cao, Feiyun Xu, Ian C. Dodd, Weifeng Xu
Summary: The study reveals that ABA plays a crucial role in regulating root growth of tomato plants under drought stress. Wild-type plants showed increased primary root growth during moderate drying, maintained more lateral roots and longer primary and total root length under severe drying, and produced more roots after re-watering. RNA-Seq analysis indicated different expression patterns of auxin-related genes in roots between wild-type and ABA-deficient plants under drying or re-watering conditions, suggesting ABA regulation of tomato root growth may involve auxin response.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Chao Wang, Jonathan Leavenworth, Chao Zhang, Zhichao Liu, Katherine Y. Yuan, Yicun Wang, Guangxin Zhang, Shuaibin Wang, Xuelian Cui, Yue Zhang, Sejong Bae, Jiangbing Zhou, Lizhong Wang, Runhua Liu
Summary: In prostate cancer, high expression of eIF4A1 is regulated by DNA methylation and it plays an oncogenic role through the BRD2 signaling pathway.
Article
Biochemistry & Molecular Biology
Jian-Ping Lian, Yu-Wei Yang, Rui-Rui He, Lu Yang, Yan-Fei Zhou, Meng-Qi Lei, Zhi Zhang, Jia-Hui Huang, Yu Cheng, Yu-Wei Liu, Yu-Chan Zhang, Yue-Qin Chen
Summary: MEL1, a rice AGO protein, is ubiquitinated and degraded by a monocot-specific E3 ligase XBOS36 post-meiosis, leading to semi-sterility if abnormally accumulated. Inhibition of MEL1 degradation disrupts pollen formation at the microspore stage. This study provides insight into the interaction between a monocot-specific E3 ligase and an AGO protein during plant reproductive development.
Article
Biochemical Research Methods
Siqi Li, Xiang Li, Wei Xue, Lin Zhang, Liang-Zhong Yang, Shi-Meng Cao, Yun-Ni Lei, Chu-Xiao Liu, Si-Kun Guo, Lin Shan, Man Wu, Xiao Tao, Jia-Lin Zhang, Xiang Gao, Jun Zhang, Jia Wei, Jinsong Li, Li Yang, Ling-Ling Chen
Summary: The study demonstrates that CRISPR-RfxCas13d can effectively discriminate circRNAs from mRNAs and has identified important circRNAs involved in cell growth, such as the pro-proliferative circFAM120A and the regulatory circMan1a2 in mouse embryo preimplantation development.
Article
Biochemical Research Methods
Si-Kun Guo, Fang Nan, Chu-Xiao Liu, Li Yang, Ling-Ling Chen
Summary: Circular RNAs are produced from the back-splicing of precursor mRNAs and exhibit structural differences and potentially different functions from their linear RNA counterparts. This study outlines experimental and computational methods to probe circular RNA secondary structure at single-nucleotide resolution in living cells.
Article
Cell Biology
Jiaquan Liu, Liang-Zhong Yang, Ling-Ling Chen
Summary: This mini-review outlines molecular methods for identifying lncRNA-protein interactions, including large-scale and individual level approaches, as well as imaging and single-molecule methods. Despite some limitations, these methods enable quantification and comprehensive analysis of RNA-protein interactions.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Chu-Xiao Liu, Si-Kun Guo, Fang Nan, Yi-Feng Xu, Li Yang, Ling-Ling Chen
Summary: Exon back-splicing-generated circular RNAs can suppress PKR in cells. We synthesized immunogenicity-free RNA circles containing short dsRNA and found that they induce an immune response. Directly ligated circular RNAs efficiently suppress PKR activation.
Review
Cell Biology
Li Yang, Jeremy E. Wilusz, Ling-Ling Chen
Summary: Covalently closed, single-stranded circular RNAs can be produced from viral RNA genomes as well as from the processing of cellular RNAs. Recent studies have revealed that many protein-coding genes can undergo backsplicing, leading to widespread expression of circular RNAs (circRNAs) in eukaryotic cells. circRNAs play various roles in gene regulation, acting as noncoding RNAs or encoding functional peptides. They are involved in physiological processes including early development, immune responses, neurogenesis, and tumorigenesis.
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Chu-Xiao Liu, Ling-Ling Chen
Summary: In this review, we discuss the methods used in circular RNA studies and the current understanding of their regulatory roles and potential applications. Circular RNAs can modulate transcription and splicing, regulate the stability and translation of mRNAs, interfere with signaling pathways, and play important roles in cellular processes and immune responses.
Article
Biochemical Research Methods
Siqi Li, Hao Wu, Ling-Ling Chen
Summary: This study presents a detailed protocol based on the RfxCas13d/BSJ-gRNA system for large-scale functional circRNA screening in human cell lines. The protocol allows for the differentiation between circRNAs and mRNAs and the identification of highly expressed circRNAs affecting cell growth.
Editorial Material
Biochemical Research Methods
Ling-Ling Chen
Summary: This article highlights the recent progress and technological advances in understanding lncRNA biogenesis, modes of action, and cellular phenotypes, and discusses the challenges and opportunities for higher-resolution and in vivo studies in this field.
Article
Biochemical Research Methods
Guo-Hua Yuan, Ying Wang, Guang-Zhong Wang, Li Yang
Summary: In this study, a machine learning model called RNAlight was developed to identify nucleotide features related to the subcellular localizations of mRNAs and lncRNAs. By extracting nucleotide features and mapping them to RBPs, the sequence basis for distinct RNA subcellular localizations was revealed. Furthermore, RNAlight could also predict the subcellular localizations of other types of RNAs, highlighting its generality in RNA subcellular localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Editorial Material
Cell Biology
Ling-Ling Chen, Albrecht Bindereif, Irene Bozzoni, Howard Y. Y. Chang, A. Gregory Matera, Myriam Gorospe, Thomas B. B. Hansen, Jorgen Kjems, Xu-Kai Ma, Jun Wei Pek, Nikolaus Rajewsky, Julia Salzman, Jeremy E. E. Wilusz, Li Yang, Fangqing Zhao
Summary: This Comment calls for a common nomenclature for naming circRNAs to ensure clarity and reproducibility in studies.
NATURE CELL BIOLOGY
(2023)
Review
Cell Biology
John S. S. Mattick, Paulo P. P. Amaral, Piero Carninci, Susan Carpenter, Howard Y. Y. Chang, Ling-Ling Chen, Runsheng Chen, Caroline Dean, Marcel E. E. Dinger, Katherine A. A. Fitzgerald, Thomas R. R. Gingeras, Mitchell Guttman, Tetsuro Hirose, Maite Huarte, Rory Johnson, Chandrasekhar Kanduri, Philipp Kapranov, Jeanne B. B. Lawrence, Jeannie T. T. Lee, Joshua T. T. Mendell, Timothy R. R. Mercer, Kathryn J. J. Moore, Shinichi Nakagawa, John L. L. Rinn, David L. L. Spector, Igor Ulitsky, Yue Wan, Jeremy E. E. Wilusz, Mian Wu
Summary: Genes encoding lncRNAs are abundant in complex organisms and are transcribed by RNA polymerase I, II, and III, as well as processed introns. The classification and annotation of lncRNAs are challenging due to their various functions, isoforms, and interactions with other genes. These lncRNAs evolve rapidly, are cell type-specific, and regulate multiple cellular processes, including gene expression and translation control.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lin Shan, Guang Xu, Run-Wen Yao, Peng-Fei Luan, Youkui Huang, Pei-Hong Zhang, Yu-Hang Pan, Lin Zhang, Xiang Gao, Ying Li, Shi-Meng Cao, Shuai-Xin Gao, Zheng-Hu Yang, Siqi Li, Liang-Zhong Yang, Ying Wang, Catharine C. L. Wong, Li Yu, Jinsong Li, Li Yang, Ling-Ling Chen
Summary: The nucleolus, composed of hundreds of proteins, plays a crucial role in ribosomal RNA transcription and processing. Through screening and imaging studies, researchers identified a static protein, URB1, enriched in the periphery of the dense fibrillar component of nucleolus. URB1 is responsible for proper pre-rRNA anchoring and folding, and its depletion disrupts nucleolar organization and leads to aberrant pre-rRNA intermediates, resulting in decreased rRNA production and developmental defects.
Article
Biochemical Research Methods
Wenyan Han, Bao-Qing Gao, Junjie Zhu, Zongxing He, Jianfeng Li, Li Yang, Jia Chen
Summary: This article introduces a new gene editing technology, transformer base editor (tBE), which enables efficient base editing without observed off-target mutations. The method can be applied in mammalian cells and mice, and a detailed experimental protocol is provided.
Article
Biotechnology & Applied Microbiology
Xiang Gao, Xu-Kai Ma, Xiang Li, Guo-Wei Li, Chu-Xiao Liu, Jun Zhang, Ying Wang, Jia Wei, Jia Chen, Ling-Ling Chen, Li Yang
Summary: This study uses base editors to deplete circRNA. By targeting splice sites, both circular and linear RNAs can be repressed. This provides an efficient method for the study of circRNA functions.
