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Ding J, Su Y, Liu Y, Xu Y, Yang D, Wang X, Hao S, Zhou H, Li H. The role of CSTF2 in cancer: from technology to clinical application. Cell Cycle 2023; 22:2622-2636. [PMID: 38166492 PMCID: PMC10936678 DOI: 10.1080/15384101.2023.2299624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024] Open
Abstract
A protein called cleavage-stimulating factor subunit 2 (CSTF2, additionally called CSTF-64) binds RNA and is needed for the cleavage and polyadenylation of mRNA. CSTF2 is an important component subunit of the cleavage stimulating factor (CSTF), which is located on the X chromosome and encodes 557 amino acids. There is compelling evidence linking elevated CSTF2 expression to the pathological advancement of cancer and on its impact on the clinical aspects of the disease. The progression of cancers, including hepatocellular carcinoma, melanoma, prostate cancer, breast cancer, and pancreatic cancer, is correlated with the upregulation of CSTF2 expression. This review provides a fresh perspective on the investigation of the associations between CSTF2 and various malignancies and highlights current studies on the regulation of CSTF2. In particular, the mechanism of action and potential clinical applications of CSTF2 in cancer suggest that CSTF2 can serve as a new biomarker and individualized treatment target for a variety of cancer types.
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Affiliation(s)
- Jiaxiang Ding
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical University, Bengbu, Anhui, China
| | - Yue Su
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical University, Bengbu, Anhui, China
| | - Youru Liu
- The People’s Hospital of Bozhou, Bozhou, Anhui, China
| | - Yuanyuan Xu
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China
| | - Dashuai Yang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province; School of Pharmacy, Anhui Medical University, Hefei, Anhui, China
| | - Xuefeng Wang
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China
| | - Shuli Hao
- The People’s Hospital of Bozhou, Bozhou, Anhui, China
| | - Huan Zhou
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
- School of Public Foundation, Bengbu Medical University, Bengbu, Anhui, China
- School of Pharmacy, Bengbu Medical University, Bengbu, Anhui, China
| | - Hongtao Li
- Clinical Trial Center of the First Affiliated Hospital of Bengbu Medical University, Bengbu, Anhui, China
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Kang B, Yang Y, Hu K, Ruan X, Liu YL, Lee P, Lee J, Wang J, Zhang X. Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain. Genome Res 2023; 33:1774-1787. [PMID: 37907328 PMCID: PMC10691540 DOI: 10.1101/gr.277864.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/12/2023] [Indexed: 11/02/2023]
Abstract
Differential polyadenylation sites (PAs) critically regulate gene expression, but their cell type-specific usage and spatial distribution in the brain have not been systematically characterized. Here, we present Infernape, which infers and quantifies PA usage from single-cell and spatial transcriptomic data and show its application in the mouse brain. Infernape uncovers alternative intronic PAs and 3'-UTR lengthening during cortical neurogenesis. Progenitor-neuron comparisons in the excitatory and inhibitory neuron lineages show overlapping PA changes in embryonic brains, suggesting that the neural proliferation-differentiation axis plays a prominent role. In the adult mouse brain, we uncover cell type-specific PAs and visualize such events using spatial transcriptomic data. Over two dozen neurodevelopmental disorder-associated genes such as Csnk2a1 and Mecp2 show differential PAs during brain development. This study presents Infernape to identify PAs from scRNA-seq and spatial data, and highlights the role of alternative PAs in neuronal gene regulation.
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Affiliation(s)
- Bowei Kang
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yalan Yang
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kaining Hu
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Xiangbin Ruan
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Yi-Lin Liu
- Department of Statistics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Pinky Lee
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jasper Lee
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jingshu Wang
- Department of Statistics, The University of Chicago, Chicago, Illinois 60637, USA;
| | - Xiaochang Zhang
- Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA;
- The Neuroscience Institute, The University of Chicago, Chicago, Illinois 60637, USA
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Biswal SR, Singh M, Dwibedy SLL, Kumari S, Muthuswamy S, Kumar A, Kumar S. Deciphering the RNA-binding protein interaction with the mRNAs encoded from human chromosome 15q11.2 BP1-BP2 microdeletion region. Funct Integr Genomics 2023; 23:174. [PMID: 37219715 DOI: 10.1007/s10142-023-01105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
Microdeletion of the 15q11.2 BP1-BP2 region, also known as Burnside-Butler susceptibility region, is associated with phenotypes like delayed developmental language abilities along with motor skill disabilities, combined with behavioral and emotional problems. The 15q11.2 microdeletion region harbors four evolutionarily conserved and non-imprinted protein-coding genes: NIPA1, NIPA2, CYFIP1, and TUBGCP5. This microdeletion is a rare copy number variation frequently associated with several pathogenic conditions in humans. The aim of this study is to investigate the RNA-binding proteins binding with the four genes present in 15q11.2 BP1-BP2 microdeletion region. The results of this study will help to better understand the molecular intricacies of the Burnside-Butler Syndrome and also the possible involvement of these interactions in the disease aetiology. Our results of enhanced crosslinking and immunoprecipitation data analysis indicate that most of the RBPs interacting with the 15q11.2 region are involved in the post-transcriptional regulation of the concerned genes. The RBPs binding to this region are found from the in silico analysis, and the interaction of RBPs like FASTKD2 and EFTUD2 with exon-intron junction sequence of CYFIP1 and TUBGCP5 has also been validated by combined EMSA and western blotting experiment. The exon-intron junction binding nature of these proteins suggests their potential involvement in splicing process. This study may help to understand the intricate relationship of RBPs with mRNAs within this region, along with their functional significance in normal development, and lack thereof, in neurodevelopmental disorders. This understanding will help in the formulation of better therapeutic approaches.
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Affiliation(s)
- Smruti Rekha Biswal
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India
| | - Mandakini Singh
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India
| | | | - Subhadra Kumari
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India
| | - Srinivasan Muthuswamy
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India
| | - Ajay Kumar
- Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology (NIT), Rourkela, Odisha, 769008, India.
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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Schwartz CE, Louie RJ, Toutain A, Skinner C, Friez MJ, Stevenson RE. X-Linked intellectual disability update 2022. Am J Med Genet A 2023; 191:144-159. [PMID: 36300573 DOI: 10.1002/ajmg.a.63008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/28/2022] [Accepted: 09/29/2022] [Indexed: 12/14/2022]
Abstract
Genes that are involved in the transcription process, mitochondrial function, glycoprotein metabolism, and ubiquitination dominate the list of 21 new genes associated with X-linked intellectual disability since the last update in 2017. The new genes were identified by sequencing of candidate genes (2), the entire X-chromosome (2), the whole exome (15), or the whole genome (2). With these additions, 42 (21%) of the 199 named XLID syndromes and 27 (25%) of the 108 numbered nonsyndromic XLID families remain to be resolved at the molecular level. Although the pace of discovery of new XLID genes has slowed during the past 5 years, the density of genes on the X chromosome that cause intellectual disability still appears to be twice the density of intellectual disability genes on the autosomes.
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Affiliation(s)
| | | | - Annick Toutain
- Department of Medical Genetics, Centre Hospitalier Universitaire, Tours, France
| | - Cindy Skinner
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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Zhang W, Wan Y, Zhang Y, Liu Q, Zhu X. CSTF2 Acts as a Prognostic Marker Correlated with Immune Infiltration in Hepatocellular Carcinoma. Cancer Manag Res 2022; 14:2691-2709. [PMID: 36117731 PMCID: PMC9481280 DOI: 10.2147/cmar.s359545] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background Cleavage stimulation factor 2 (CSTF2) encodes a nuclear protein that is implicated in the development of various cancers. However, the role of CSTF2 in hepatocellular carcinoma (HCC) has not been understood. This study aims to explore the function of CSTF2 in HCC. Methods The expression, diagnostic capability, prognostic value, and immune cell effect of CSTF2 in HCC were explored using various databases. The expression level of CSTF2 were validated in our cell lines. The effect of CSTF2 on hepatocarcinogenesis was explored by CSTF2 silencing. Results CSTF2 expression was significantly elevated in HCC and correlated with multiple clinicopathological characteristics. CSTF2 exhibited good diagnostic capability in discriminating HCC samples from nontumorous samples. High CSTF2 expression was significantly related to poor overall survival. Univariate and multivariate Cox regression analyses suggested that CSTF2 expression was an independent risk factor for HCC. These results were validated in ICGC cohorts. In addition, the nomogram based on CSTF2 showed better predictive performance than the AJCC staging system in TCGA and ICGC cohorts. Functional enrichment analysis revealed that CSTF2-related genes were involved in DNA/RNA processing and the cell cycle. In addition, we found that CSTF2 expression was closely related to the levels of various infiltrating immune cells, especially neutrophils. Moreover, some immune checkpoints had positive relationships with CSTF2 expression. CSTF2 silencing inhibited proliferation, invasion and migration, and promoted apoptosis in HepG2 cells. Western blotting analysis revealed that CSTF2 silencing inactivated the Wnt/β-catenin signaling pathway. Conclusion High CSTF2 expression not only correlates with unfavorable outcomes but also affects immune cell infiltration and immune checkpoint expression in HCC. CSTF2 silencing can alleviate the malignant phenotypes of hepatic cancer cell by inactivating the Wnt/β-catenin signaling pathway. These results indicate that CSTF2 can serve as a promising prognostic marker and therapeutic target for HCC patients.
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Affiliation(s)
- Wang Zhang
- Departments of Gastroenterology and Hepatology, First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Yipeng Wan
- Departments of Gastroenterology and Hepatology, First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Yue Zhang
- Departments of Gastroenterology and Hepatology, First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Qi Liu
- Departments of Gastroenterology and Hepatology, First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Xuan Zhu
- Departments of Gastroenterology and Hepatology, First Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
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Li L, Garg M, Wang Y, Wang W, Godbout R. DEAD Box 1 (DDX1) protein binds to and protects cytoplasmic stress response mRNAs in cells exposed to oxidative stress. J Biol Chem 2022; 298:102180. [PMID: 35752363 PMCID: PMC9293777 DOI: 10.1016/j.jbc.2022.102180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/13/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022] Open
Abstract
The integrated stress response is a network of highly orchestrated pathways activated when cells are exposed to environmental stressors. While global repression of translation is a well-recognized hallmark of the integrated stress response, less is known about the regulation of mRNA stability during stress. DEAD box proteins are a family of RNA unwinding/remodeling enzymes involved in every aspect of RNA metabolism. We previously showed that DEAD box 1 (DDX1) protein accumulates at DNA double-strand breaks during genotoxic stress and promotes DNA double-strand break repair via homologous recombination. Here, we examine the role of DDX1 in response to environmental stress. We show that DDX1 is recruited to stress granules (SGs) in cells exposed to a variety of environmental stressors, including arsenite, hydrogen peroxide, and thapsigargin. We also show that DDX1 depletion delays resolution of arsenite-induced SGs. Using RNA immunoprecipitation sequencing, we identify RNA targets bound to endogenous DDX1, including RNAs transcribed from genes previously implicated in stress responses. We show the amount of target RNAs bound to DDX1 increases when cells are exposed to stress, and the overall levels of these RNAs are increased during stress in a DDX1-dependent manner. Even though DDX1’s RNA-binding property is critical for maintenance of its target mRNA levels, we found RNA binding is not required for localization of DDX1 to SGs. Furthermore, DDX1 knockdown does not appear to affect RNA localization to SGs. Taken together, our results reveal a novel role for DDX1 in maintaining cytoplasmic mRNA levels in cells exposed to oxidative stress.
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Affiliation(s)
- Lei Li
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Mansi Garg
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Yixiong Wang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - Weiwei Wang
- Department of Medicine, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Roseline Godbout
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada.
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Feng L, Jing F, Qin X, Zhou L, Ning Y, Hou J, Kong W, Zhu Y. Cleavage Stimulation Factor Subunit 2: Function Across Cancers and Potential Target for Chemotherapeutic Drugs. Front Pharmacol 2022; 13:852469. [PMID: 35370655 PMCID: PMC8971630 DOI: 10.3389/fphar.2022.852469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 11/30/2022] Open
Abstract
The cleavage stimulation factor subunit complex is involved in the cleavage and polyadenylation of 3′-end pre-mRNAs that regulate mRNA formation and processing. However, cleavage stimulation factor subunit 2 (CSTF2) was found to play a more critical regulatory role across cancers. General cancer data sets from The Cancer Genome Atlas and Genotype-Tissue Expression project were thus downloaded for differential analysis, and the possible functions and mechanisms of CSTF2 in general cancer were analyzed using the Compartments database, cBioPortal database, Tumor Immune Single-cell Hub database, and Comparative Toxigenomics database using gene set enrichment analysis and R software. The results showed that CSTF2 could affect DNA repair and methylation in tumor cells. In addition, CSTF2 was associated with multiple tumor immune infiltrates in a wide range of cancers, and its high expression was associated with multiple immune checkpoints; therefore, it could serve as a potential target for many drug molecules. We also proved that CSTF2 promotes oral cell proliferation and migration. The high diagnostic efficacy of CSTF2 suggested that this gene may act as a new biomarker and personalized therapeutic target for a variety of tumors.
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Affiliation(s)
- Linfei Feng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fengyang Jing
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Hefei, China
| | - Xiaofeng Qin
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Hefei, China
| | - Liming Zhou
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Hefei, China
| | - Yujie Ning
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Hefei, China
| | - Jun Hou
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Weihao Kong
- Department of Emergency Surgery, Department of Emergency Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Weihao Kong, ; Youming Zhu,
| | - Youming Zhu
- Key Laboratory of Oral Diseases Research of Anhui Province, Department of Dental Implant Center, Stomatologic Hospital and College, Anhui Medical University, Hefei, China
- *Correspondence: Weihao Kong, ; Youming Zhu,
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Masoumzadeh E, Grozdanov PN, Jetly A, MacDonald CC, Latham MP. Electrostatic Interactions between CSTF2 and pre-mRNA Drive Cleavage and Polyadenylation. Biophys J 2022; 121:607-619. [PMID: 35090899 PMCID: PMC8873925 DOI: 10.1016/j.bpj.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 11/25/2022] Open
Abstract
Nascent pre-mRNA 3'-end cleavage and polyadenylation (C/P) involves numerous proteins that recognize multiple RNA elements. Human CSTF2 binds to a downstream U- or G/U-rich sequence through its RNA recognition motif (RRM) regulating C/P. We previously reported the only known disease-related CSTF2 RRM mutant (CSTF2D50A) and showed that it changed the on-rate of RNA binding, leading to alternative polyadenylation in brains of mice carrying the same mutation. In this study, we further investigated the role of electrostatic interactions in the thermodynamics and kinetics of RNA binding for the CSTF2 RRM and the downstream consequences for regulation of C/P. By combining mutagenesis with NMR spectroscopy and biophysical assays, we confirmed that electrostatic attraction is the dominant factor in RRM binding to a naturally occurring U-rich RNA sequence. Moreover, we demonstrate that RNA binding is accompanied by an enthalpy-entropy compensation mechanism that is supported by changes in pico-to-nanosecond timescale RRM protein dynamics. We suggest that the dynamic binding of the RRM to U-rich RNA supports the diversity of sequences it encounters in the nucleus. Lastly, in vivo C/P assays demonstrate a competition between fast, high affinity RNA binding and efficient, correct C/P. These results highlight the importance of the surface charge of the RRM in RNA binding and the balance between nascent mRNA binding and C/P in vivo.
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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