Article
Biochemistry & Molecular Biology
Ya Cui, Fanglue Peng, Dan Wang, Yumei Li, Jason Sheng Li, Lei Li, Wei Li
Summary: Genome-wide association studies have identified numerous non-coding SNPs associated with human traits and diseases, with functional interpretation remaining a challenge. The concept of 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) has been established to interpret a portion of GWAS SNPs. The 3'aQTL-atlas provides a comprehensive database of nearly 1.49 million SNPs associated with APA across 49 human tissues, aiming to explain genetic basis of APA and APA-linked susceptibility genes in human traits and diseases.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Cell Biology
Jia Jia Chan, Hossein Tabatabaeian, Yvonne Tay
Summary: The majority of human mRNAs generate alternative 3' UTRs through various processes, including RNA editing, m6A methylation, and alternative polyadenylation (APA), with 3' UTR splicing as an emerging mechanism. Regulation of these processes at the genome and transcriptome levels contribute to 3' UTR heterogeneity. Genomic variants in 3' UTR regions and aberrant 3' UTR processing are associated with cancer and their deregulation may contribute to cancer pathogenesis. In-depth characterization of these events will enhance our understanding of their significance and aid in therapeutic development.
TRENDS IN CELL BIOLOGY
(2023)
Article
Cell Biology
Jia Jia Chan, Bin Zhang, Xiao Hong Chew, Adil Salhi, Zhi Hao Kwok, Chun You Lim, Ng Desi, Nagavidya Subramaniam, Angela Siemens, Tyas Kinanti, Shane Ong, Avencia Sanchez-Mejias, Phuong Thao Ly, Omer An, Raghav Sundar, Xiaonan Fan, Shi Wang, Bei En Siew, Kuok Chung Lee, Choon Seng Chong, Bettina Lieske, Wai-Kit Cheong, Yufen Goh, Wee Nih Fam, Melissa G. Ooi, Bryan T. H. Koh, Shridhar Ganpathi Iyer, Wen Huan Ling, Jianbin Chen, Boon-Koon Yoong, Rawisak Chanwat, Glenn Kunnath Bonney, Brian K. P. Goh, Weiwei Zhai, Melissa J. Fullwood, Wilson Wang, Ker-Kan Tan, Wee Joo Chng, Yock Young Dan, Jason J. Pitt, Xavier Roca, Ernesto Guccione, Leah A. Vardy, Leilei Chen, Xin Gao, Pierce K. H. Chow, Henry Yang, Yvonne Tay
Summary: This study systematically reveals the role of 3' UTR splicing in cancer, finding its widespread presence in various types of cancer and its correlation with poor prognosis. Inhibiting 3' UTR splicing can effectively reduce oncogene expression and impede tumor progression, providing new directions for RNA-based anti-cancer therapeutics.
NATURE CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anob M. Chakrabarti, Ira A. Iosub, Flora C. Y. Lee, Jernej Ule, Nicholas M. Luscombe
Summary: The structure of mRNA molecules plays a crucial role in its interactions with RNA binding proteins (RBPs), but current experimental methods for studying these interactions are limited in sensitivity. In this study, the researchers extended the hiCLIP atlas of STAU1-bound duplexes by 10-fold through improved experimental assumptions and computational methods. They developed a computational pipeline called Tosca for processing and analyzing proximity ligation sequencing data, and used it to gain insights into the RNA selectivity of STAU1 and the effects of RBP-RNA structure interactions.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medicine, Research & Experimental
Siwei Pan, Jiaming Zhu, Pengfei Liu, Qiaochu Wei, Siyu Zhang, Wen An, Yuxin Tong, Zhenguo Cheng, Funan Liu
Summary: The study suggests that FN1 3'-UTR has stronger prognostic implications than FN1 protein in gastric cancer patients and can be a better therapeutic target for constructing targeted drugs.
Review
Biochemistry & Molecular Biology
Nitika Kandhari, Calvin A. Kraupner-Taylor, Paul F. Harrison, David R. Powell, Traude H. Beilharz
Summary: Alternative transcript cleavage and polyadenylation are associated with cancer cell transformation, proliferation, and outcome. Researchers have developed methods to detect and analyze alternative polyadenylation as potential cancer biomarkers, which, if integrated into standard prognostic measures, may advance cancer prognostic testing and guide therapy. This review focuses on existing methodologies, both experimental and computational, to support the use of alternative polyadenylation as cancer biomarkers.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Health Care Sciences & Services
Young-Joo Jeon, Sung-Hwan Cho, Eo-Jin Kim, Chang-Soo Ryu, Han-Sung Park, Jong-Woo Kim, Jeong-Yong Lee, Hui-Jeong An, Nam-Keun Kim
Summary: This study found an association between 3'-UTR variants in TS genes and colorectal cancer, suggesting they could potentially serve as biomarkers for CRC prognosis and prevention.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Pharmacology & Pharmacy
Marina Emelyanova, Ilya Pokataev, Igor Shashkov, Elena Kopantseva, Vladimir Lyadov, Rustam Heydarov, Vladimir Mikhailovich
Summary: This study focused on the relationship between gene polymorphisms and drug-induced toxicities in pancreatic ductal adenocarcinoma (PDAC) patients. It found an association between the TYMS rs11280056 polymorphism and neurotoxicity, as well as an association between the GSTP1 rs1695 polymorphism and hematological toxicity. These findings contribute to the understanding of individual differences in PDAC treatment and the development of more effective therapeutic strategies.
Article
Biochemistry & Molecular Biology
Daisuke Kaida, Kenta Shida
Summary: Pre-mRNA splicing is a critical mechanism in gene expression in eukaryotes, and splicing inhibition can impact various cellular functions. This study reveals that the potent splicing inhibitor spliceostatin A (SSA) causes stabilization of the p27 protein by increasing the stability of CDKN1B mRNA. The 3' untranslated region of CDKN1B mRNA is involved in this stabilization process.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Chidiebere U. Awah, Yana Glemaud, Fayola Levine, Kiseok Yang, Afrin Ansary, Fu Dong, Leonard Ash, Junfei Zhang, Olorunseun O. Ogunwobi
Summary: Resistance to targeted therapy is a challenge in breast, lung, and colorectal cancers, leading to a large number of deaths annually. We found that ERBB2+ cancer cells have mRNA-stabilizing sequences on their 3'UTR. By manipulating these sequences, we successfully degraded ERBB2 transcripts and reduced protein levels in various cancer cell types, providing a new approach to control oncogenic signals where current therapies fail.
FRONTIERS IN GENETICS
(2023)
Review
Biochemistry & Molecular Biology
Estanislao Navarro, Adrian Mallen, Miguel Hueso
Summary: This paper discusses the polymorphic nature of 3'UTR regions in mRNAs and the mechanisms that control their length and sequence, impacting the accessibility of functional effectors and ultimately gene expression regulation.
Article
Biochemistry & Molecular Biology
Alfredo Berzal-Herranz, Beatriz Berzal-Herranz, Sara Esther Ramos-Lorente, Cristina Romero-Lopez
Summary: This study provides evidence that West Nile virus promotes a cap-independent translation initiation mechanism in mammalian and insect cells, and suggests that its 3' UTR is involved in fine-tuned translation regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Buki Kwon, Mervin M. Fansler, Neil D. Patel, Jihye Lee, Weirui Ma, Christine Mayr
Summary: Multi-UTR genes express their alternative 3' UTR isoforms in a cell type-specific manner. Transcriptional enhancers, along with transcription factors, regulate the expression of these isoforms by influencing the cleavage activity of polyadenylation sites.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Yinglong Zhao, Guohui Zhong, Ruikai Du, Dingsheng Zhao, Jianwei Li, Yuheng Li, Wenjuan Xing, Xiaoyan Jin, Wenjuan Zhang, Weijia Sun, Caizhi Liu, Zizhong Liu, Xinxin Yuan, Guanghan Kan, Xuan Han, Qi Li, Yan-Zhong Chang, Yingxian Li, Shukuan Ling
Summary: Microgravity has a significant impact on cardiovascular health, leading to damage and mass loss in the heart. The role of Ckip-1 in atrophic heart growth after simulated microgravity involves inhibiting lipid accumulation and activating gene expression related to fatty acid oxidation. This study highlights the potential of Ckip-1 as an important regulator in maintaining cardiac function in space environments.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Antonela Blazekovic, Kristina Gotovacjercic, Fran Borovecki
Summary: The study aimed to assess differences in 3'UTR variants of the SNCA gene in a cohort of PD patients and control subjects from Croatia, identifying a significantly higher occurrence of a particular variant in the PD population which has not been reported previously. Further research is needed to explore the role of these variants in PD development and their impact on disease pathology.
Article
Microbiology
Antoine-Emmanuel Saliba, Lei Li, Alexander J. Westermann, Silke Appenzeller, Daphne A. C. Stapels, Leon N. Schulte, Sophie Helaine, Joerg Vogel
NATURE MICROBIOLOGY
(2017)
Article
Biochemical Research Methods
Ben Fan, Yu-Long Li, Lei Li, Xiao-Jun Peng, Chen Bu, Xiao-Qin Wu, Rainer Borriss
JOURNAL OF PROTEOMICS
(2017)
Article
Biochemistry & Molecular Biology
Yanjie Chao, Lei Li, Dylan Girodat, Konrad U. Foerstner, Nelly Said, Colin Corcoran, Michal Smiga, Kai Papenfort, Richard Reinhardt, Hans-Joachim Wieden, Ben F. Luisi, Joerg Vogel
Article
Biochemistry & Molecular Biology
Nadja Heidrich, Saskia Bauriedl, Lars Barquist, Lei Li, Christoph Schoen, Joerg Vogel
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Erik Holmqvist, Lei Li, Thorsten Bischler, Lars Barquist, Joerg Vogel
Article
Genetics & Heredity
Hyun Jung Park, Ping Ji, Soyeon Kim, Zheng Xia, Benjamin Rodriguez, Lei Li, Jianzhong Su, Kaifu Chen, Chioniso P. Masamha, David Baillat, Camila R. Fontes-Garfias, Ann-Bin Shyu, Joel R. Neilson, Eric J. Wagner, Wei Li
Article
Biochemistry & Molecular Biology
Yuan Chu, Nathan Elrod, Chaojie Wang, Lei Li, Tao Chen, Andrew Routh, Zheng Xia, Wei Li, Eric J. Wagner, Ping Ji
Article
Biochemistry & Molecular Biology
Seung Wook Yang, Lei Li, Jon P. Connelly, Shaina N. Porter, Kiran Kodali, Haiyun Gan, Jung Mi Park, Klementina Fon Tacer, Heather Tillman, Junmin Peng, Shondra M. Pruett-Miller, Wei Li, Patrick Ryan Potts
Article
Genetics & Heredity
Lei Li, Kai-Lieh Huang, Yipeng Gao, Ya Cui, Gao Wang, Nathan D. Elrod, Yumei Li, Yiling Elaine Chen, Ping Ji, Fanglue Peng, William K. Russell, Eric J. Wagner, Wei Li
Summary: The study presents a multi-tissue atlas of alternative polyadenylation (APA) quantitative trait loci (3 ' aQTLs) identifying approximately 0.4 million common genetic variants associated with the APA of target genes. About 16% of trait-associated variants colocalize with 3 ' aQTLs, indicating their substantial contribution to the molecular mechanisms behind human complex traits and diseases.
Article
Hematology
Yue Sheng, Jiangbo Wei, Fang Yu, Huanzhou Xu, Chunjie Yu, Qiong Wu, Yin Liu, Lei Li, Xiao-long Cui, Xueying Gu, Bin Shen, Wei Li, Yong Huang, Sumita Bhaduri-McIntosh, Chuan He, Zhijian Qian
Summary: YTHDC1 functions as a nuclear m(6)A reader in RNA metabolism regulation, with its overexpression shown in AML. Genetic deletion of Ythdc1 blocks AML development and maintenance, as well as LSCs self-renewal. YTHDC1 also plays a role in normal hematopoiesis and HSPC maintenance, with haploinsufficiency reducing LSCs self-renewal in vivo.
Article
Biochemistry & Molecular Biology
Ruofan Ding, Qixuan Wang, Lihai Gong, Ting Zhang, Xudong Zou, Kewei Xiong, Qi Liao, Mireya Plass, Lei Li
Summary: Researchers have developed a comprehensive database called scQTLbase for searching, analyzing, and visualizing single-cell expression quantitative trait loci (sc-eQTLs). The database includes 304 datasets spanning 57 cell types and 95 cell states. It offers various functionalities such as gene expression visualization, a genome browser, and colocalization visualization based on GWAS datasets.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Heather J. Zhou, Lei Li, Yumei Li, Wei Li, Jingyi Jessica Li
Summary: This study benchmarks popular hidden variable inference methods and finds that principal component analysis (PCA) not only underlies the statistical methodology behind these methods, but is also faster, better-performing, and easier to interpret and use. To help researchers use PCA in their QTL analysis, the authors provide an R package and a detailed guide, believing that using PCA will substantially improve and simplify hidden variable inference in QTL mapping, as well as increase the transparency and reproducibility of QTL research.
Article
Biochemical Research Methods
Xudong Zou, Ruofan Ding, Wenyan Chen, Gao Wang, Shumin Cheng, Qin Wang, Wei Li, Lei Li
Summary: This article describes a bioinformatic protocol for identifying 3'aQTLs using RNA-seq and genomic data, allowing analysis of dynamic APA events, identification of genetic variants associated with differential 3' UTR usage, and prediction of potential causal variants affecting APA.
Article
Multidisciplinary Sciences
Ben Fan, Yu-Long Li, Lei Li, Xiao-Jun Peng, Chen Bu, Xiao-Qin Wu, Rainer Borriss
