1
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Cheng K, Zhang C, Lu Y, Li J, Tang H, Ma L, Zhu H. The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3504. [PMID: 37836244 PMCID: PMC10575402 DOI: 10.3390/plants12193504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.
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Affiliation(s)
- Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Yao Lu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hui Tang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
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2
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Li Y, Mokrani A, Fu H, Shi C, Li Q, Liu S. Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas. Genomics 2023; 115:110697. [PMID: 37567397 DOI: 10.1016/j.ygeno.2023.110697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The Pacific oyster (Crassostrea gigas) is a widely cultivated shellfish in the world, while its transcriptome diversity remains less unexplored due to the limitation of short reads. In this study, we used Oxford Nanopore sequencing to develop the full-length transcriptome database of C. gigas. We identified 77,920 full-length transcripts from 21,523 genes, and uncovered 9668 alternative splicing events and 87,468 alternative polyadenylation sites. Notably, a total of 16,721 novel transcripts were annotated in this work. Furthermore, integrative analysis of 25 publicly available RNA-seq datasets revealed the transcriptome diversity involved in post-transcriptional regulation in C. gigas. We further developed a Drupal based webserver, Cgtdb, which can be used for transcriptome visualization, sequence alignment, and functional genome annotation analyses. This work provides valuable resources and a useful tool for integrative analysis of various transcriptome datasets in C. gigas, which will serve as an essential reference for functional annotation of the oyster genome.
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Affiliation(s)
- Yin Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Ahmed Mokrani
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Huiru Fu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Chenyu Shi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, and College of Fisheries, Ocean University of China, Qingdao 266003, China.
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3
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Li Y, Chen F, Yang Y, Han Y, Ren Z, Li X, Soppe WJJ, Cao H, Liu Y. The Arabidopsis pre-mRNA 3' end processing related protein FIP1 promotes seed dormancy via the DOG1 and ABA pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37035898 DOI: 10.1111/tpj.16239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/05/2023] [Indexed: 06/19/2023]
Abstract
Seed dormancy is an important adaptive trait to prevent germination occurring at an inappropriate time. The mechanisms governing seed dormancy and germination are complex. Here, we report that FACTOR INTERACTING WITH POLY(A) POLYMERASE 1 (FIP1), a component of the pre-mRNA 3' end processing machinery, is involved in seed dormancy and germination processes in Arabidopsis thaliana. FIP1 is mainly expressed in seeds and the knockout of FIP1 causes reduced seed dormancy, indicating that FIP1 positively influences seed dormancy. Meanwhile, fip1 mutants are insensitive to exogenous ABA during seed germination and early seedling establishment. The terms 'seed maturation' and 'response to ABA stimulus' are significantly enriched in a gene ontology analysis based on genes differentially expressed between fip1-1 and the wild type. Several of these genes, including ABI5, DOG1 and PYL12, show significantly decreased transcript levels in fip1. Genetic analysis showed that either cyp707a2 or dog1-5 partially, but in combination completely, represses the reduced seed dormancy of fip1, indicating that the double mutant cyp707a2 dog1-5 is epistatic to fip1. Moreover, FIP1 is required for CFIM59, another component of pre-mRNA 3' end processing machinery, to govern seed dormancy and germination. Overall, we identified FIP1 as a regulator of seed dormancy and germination that plays a crucial role in governing these processes through the DOG1 and ABA pathways.
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Affiliation(s)
- Yu Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
| | - Yue Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
| | - Yi Han
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan, 250102, China
| | - Ziyun Ren
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wim J J Soppe
- Rijk Zwaan Breeding B.V., De Lier, 2678 ZG, the Netherlands
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100094, China
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4
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Huang K, Wu S, Yang X, Wang T, Liu X, Zhou X, Huang L. CAFuncAPA: a knowledgebase for systematic functional annotations of APA events in human cancers. NAR Cancer 2023; 5:zcad004. [PMID: 36694725 PMCID: PMC9869079 DOI: 10.1093/narcan/zcad004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/12/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
Alternative polyadenylation (APA) is a widespread posttranscriptional regulation process. APA generates diverse mRNA isoforms with different 3' UTR lengths, affecting mRNA expression, miRNA binding regulation and alternative splicing events. Previous studies have demonstrated the important roles of APA in tumorigenesis and cancer progression through diverse aspects. Thus, a comprehensive functional landscape of diverse APA events would aid in a better understanding of the underlying mechanisms related to APA in human cancers. Here, we built CAFuncAPA (https://relab.xidian.edu.cn/CAFuncAPA/) to systematically annotate the functions of 15478 APA events in human pan-cancers. Specifically, we first identified APA events associated with cancer survival and tumor progression. We annotated the potential downstream effects of APA on genes/isoforms expression, regulation of miRNAs, RNA binding proteins (RBPs) and alternative splicing events. Moreover, we also identified up-regulators of APA events, including the effects of genetic variants on poly(A) sites and RBPs, as well as the effect of methylation phenotypes on APA events. These findings suggested that CAFuncAPA can be a helpful resource for a better understanding of APA regulators and potential functions in cancer biology.
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Affiliation(s)
- Kexin Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
- West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Sijia Wu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Xiaotong Yang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Xi Liu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi, P.R. China
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5
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Muthmann N, Albers M, Rentmeister A. CAPturAM, a Chemo-Enzymatic Strategy for Selective Enrichment and Detection of Physiological CAPAM-Targets. Angew Chem Int Ed Engl 2023; 62:e202211957. [PMID: 36282111 PMCID: PMC10107118 DOI: 10.1002/anie.202211957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Modified nucleotides impact all aspects of eukaryotic mRNAs and contribute to regulation of gene expression at the transcriptional and translational level. At the 5' cap, adenosine as first transcribed nucleotide is often N6 -methyl-2'-O-methyl adenosine (m6 Am ). This modification is tissue dependent and reversible, pointing to a regulatory function. CAPAM was recently identified as methyltransferase responsible for m6 Am formation, however, the direct assignment of its target transcripts proves difficult. Antibodies do not discriminate between internal N6 -methyl adenosine (m6 A) and m6 Am . Here we present CAPturAM, an antibody-free chemical biology approach for direct enrichment and probing of physiological CAPAM-targets. We harness CAPAM's cosubstrate promiscuity to install propargyl groups on its targets. Subsequent functionalization with an affinity handle allows for their enrichment. Using wildtype and CAPAM-/- cells, we successfully applied CAPturAM to confirm or disprove CAPAM-targets, facilitating the verification and identification of CAPAM targets.
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Affiliation(s)
- Nils Muthmann
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
| | - Marvin Albers
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of BiochemistryUniversity of MünsterCorrensstrasse 3648149MünsterGermany
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6
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Berry CW, Olivares GH, Gallicchio L, Ramaswami G, Glavic A, Olguín P, Li JB, Fuller MT. Developmentally regulated alternate 3' end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage. Genes Dev 2022; 36:916-935. [PMID: 36175033 PMCID: PMC9575692 DOI: 10.1101/gad.349689.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/12/2022] [Indexed: 02/03/2023]
Abstract
Alternative polyadenylation (APA) generates transcript isoforms that differ in the position of the 3' cleavage site, resulting in the production of mRNA isoforms with different length 3' UTRs. Although widespread, the role of APA in the biology of cells, tissues, and organisms has been controversial. We identified >500 Drosophila genes that express mRNA isoforms with a long 3' UTR in proliferating spermatogonia but a short 3' UTR in differentiating spermatocytes due to APA. We show that the stage-specific choice of the 3' end cleavage site can be regulated by the arrangement of a canonical polyadenylation signal (PAS) near the distal cleavage site but a variant or no recognizable PAS near the proximal cleavage site. The emergence of transcripts with shorter 3' UTRs in differentiating cells correlated with changes in expression of the encoded proteins, either from off in spermatogonia to on in spermatocytes or vice versa. Polysome gradient fractionation revealed >250 genes where the long 3' UTR versus short 3' UTR mRNA isoforms migrated differently, consistent with dramatic stage-specific changes in translation state. Thus, the developmentally regulated choice of an alternative site at which to make the 3' end cut that terminates nascent transcripts can profoundly affect the suite of proteins expressed as cells advance through sequential steps in a differentiation lineage.
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Affiliation(s)
- Cameron W Berry
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gonzalo H Olivares
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Center for Genome Regulation (CRG), Universidad de Chile, Santiago 7810000, Chile
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago 7810000, Chile
- Program of Human Genetics, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Huechuraba 8580745, Chile
- Center of Integrative Biology (CIB), Universidad Mayor, Huechuraba 8580745, Chile
| | - Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alvaro Glavic
- Center for Genome Regulation (CRG), Universidad de Chile, Santiago 7810000, Chile
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago 7810000, Chile
| | - Patricio Olguín
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Program of Human Genetics, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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7
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Xia L, Han Q, Duan X, Zhu Y, Pan J, Dong B, Xia W, Xue W, Sha J. m6A-induced repression of SIAH1 facilitates alternative splicing of androgen receptor variant 7 by regulating CPSF1. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:219-230. [PMID: 35402071 PMCID: PMC8965770 DOI: 10.1016/j.omtn.2022.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/12/2022] [Indexed: 01/22/2023]
Affiliation(s)
- Lei Xia
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Qing Han
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Xuehui Duan
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Yinjie Zhu
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Jiahua Pan
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Baijun Dong
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Weiliang Xia
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Wei Xue
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
- Corresponding author. Wei Xue, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Shandong Middle road, Shanghai 200001, China.
| | - Jianjun Sha
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
- Corresponding author. Jianjun Sha, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Shandong Middle road, Shanghai 200001, China.
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8
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Zhong W, Wu Y, Zhu M, Zhong H, Huang C, Lin Y, Huang J. Alternative splicing and alternative polyadenylation define tumor immune microenvironment and pharmacogenomic landscape in clear cell renal carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:927-946. [PMID: 35211354 PMCID: PMC8829526 DOI: 10.1016/j.omtn.2022.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/17/2022] [Indexed: 12/29/2022]
Abstract
Two major posttranscriptional mechanisms—alternative splicing (AS) and alternative polyadenylation (APA)—have attracted much attention in cancer research. Nevertheless, their roles in clear cell renal carcinoma (ccRCC) are still ill defined. Herein, this study was conducted to uncover the implications of AS and APA events in ccRCC progression. Through consensus molecular clustering analysis, two AS or APA RNA processing phenotypes were separately constructed with distinct prognosis, tumor-infiltrating immune cells, responses to immunotherapy, and chemotherapy. The AS or APA score was constructed to quantify AS or APA RNA processing patterns of individual ccRCCs with principal-component analysis. Both high AS and APA scores were characterized by undesirable survival outcomes, relatively high response to immunotherapy, and low sensitivity to targeted drugs, such as sorafenib and pazopanib. Moreover, several small molecular compounds were predicted for patients with a high AS or APA score. There was a positive correlation between AS and APA scores. Their interplay contributed to poor prognosis and reshaped the tumor immune microenvironment. Collectively, this study is the first to comprehensively analyze two major posttranscriptional events in ccRCC. Our findings uncovered the potential functions of AS and APA events and identified their therapeutic potential in immunotherapy and targeted therapy.
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Affiliation(s)
- Weimin Zhong
- Central Laboratory at The Fifth Hospital of Xiamen, Xiamen 361101, Fujian Province, China
| | - Yulong Wu
- Department of Urology at The Fifth Hospital of Xiamen, Xiamen 361101, Fujian Province, China
| | - Maoshu Zhu
- Central Laboratory at The Fifth Hospital of Xiamen, Xiamen 361101, Fujian Province, China
| | - Hongbin Zhong
- Department of Nephrology at The Fifth Hospital of Xiamen, Xiamen 361101, Fujian Province, China
| | - Chaoqun Huang
- Central Laboratory at The Fifth Hospital of Xiamen, Xiamen 361101, Fujian Province, China
| | - Yao Lin
- Central Laboratory at The Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Innovation and transformation center, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Jiyi Huang
- Department of Nephrology at The Fifth Hospital of Xiamen, Xiamen 361101, Fujian Province, China
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9
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Polymorphism in the human arylamine N-acetyltransferase 1 gene 3’-untranslated region determines polyadenylation signal usage. Biochem Pharmacol 2022; 200:115020. [DOI: 10.1016/j.bcp.2022.115020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 11/22/2022]
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10
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Pereira-Castro I, Garcia BC, Curinha A, Neves-Costa A, Conde-Sousa E, Moita LF, Moreira A. MCL1 alternative polyadenylation is essential for cell survival and mitochondria morphology. Cell Mol Life Sci 2022; 79:164. [PMID: 35229202 PMCID: PMC11072748 DOI: 10.1007/s00018-022-04172-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/07/2022] [Accepted: 01/27/2022] [Indexed: 02/02/2023]
Abstract
Alternative polyadenylation in the 3' UTR (3' UTR-APA) is a mode of gene expression regulation, fundamental for mRNA stability, translation and localization. In the immune system, it was shown that upon T cell activation, there is an increase in the relative expression of mRNA isoforms with short 3' UTRs resulting from 3' UTR-APA. However, the functional significance of 3' UTR-APA remains largely unknown. Here, we studied the physiological function of 3' UTR-APA in the regulation of Myeloid Cell Leukemia 1 (MCL1), an anti-apoptotic member of the Bcl-2 family essential for T cell survival. We found that T cells produce two MCL1 mRNA isoforms (pA1 and pA2) by 3' UTR-APA. We show that upon T cell activation, there is an increase in both the shorter pA1 mRNA isoform and MCL1 protein levels. Moreover, the less efficiently translated pA2 isoform is downregulated by miR-17, which is also more expressed upon T cell activation. Therefore, by increasing the expression of the more efficiently translated pA1 mRNA isoform, which escapes regulation by miR-17, 3' UTR-APA fine tunes MCL1 protein levels, critical for activated T cells' survival. Furthermore, using CRISPR/Cas9-edited cells, we show that depletion of either pA1 or pA2 mRNA isoforms causes severe defects in mitochondria morphology, increases apoptosis and impacts cell proliferation. Collectively, our results show that MCL1 alternative polyadenylation has a key role in the regulation of MCL1 protein levels upon T cell activation and reveal an essential function for MCL1 3' UTR-APA in cell viability and mitochondria dynamics.
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Affiliation(s)
- Isabel Pereira-Castro
- Gene Regulation, i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal.
- Gene Regulation, IBMC, Instituto de Biologia Molecular E Celular, Universidade Do Porto, Porto, Portugal.
| | - Beatriz C Garcia
- Gene Regulation, i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal
- Gene Regulation, IBMC, Instituto de Biologia Molecular E Celular, Universidade Do Porto, Porto, Portugal
| | - Ana Curinha
- Gene Regulation, IBMC, Instituto de Biologia Molecular E Celular, Universidade Do Porto, Porto, Portugal
- Department of Molecular Biology and Genetics, John Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Eduardo Conde-Sousa
- i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal
- INEB, Instituto de Engenharia Biomédica, Universidade Do Porto, Porto, Portugal
| | - Luís F Moita
- Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal
| | - Alexandra Moreira
- Gene Regulation, i3S, Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, Porto, Portugal.
- Gene Regulation, IBMC, Instituto de Biologia Molecular E Celular, Universidade Do Porto, Porto, Portugal.
- ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade Do Porto, Porto, Portugal.
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11
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Implications of Poly(A) Tail Processing in Repeat Expansion Diseases. Cells 2022; 11:cells11040677. [PMID: 35203324 PMCID: PMC8870147 DOI: 10.3390/cells11040677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/21/2022] Open
Abstract
Repeat expansion diseases are a group of more than 40 disorders that affect mainly the nervous and/or muscular system and include myotonic dystrophies, Huntington’s disease, and fragile X syndrome. The mutation-driven expanded repeat tract occurs in specific genes and is composed of tri- to dodeca-nucleotide-long units. Mutant mRNA is a pathogenic factor or important contributor to the disease and has great potential as a therapeutic target. Although repeat expansion diseases are quite well known, there are limited studies concerning polyadenylation events for implicated transcripts that could have profound effects on transcript stability, localization, and translation efficiency. In this review, we briefly present polyadenylation and alternative polyadenylation (APA) mechanisms and discuss their role in the pathogenesis of selected diseases. We also discuss several methods for poly(A) tail measurement (both transcript-specific and transcriptome-wide analyses) and APA site identification—the further development and use of which may contribute to a better understanding of the correlation between APA events and repeat expansion diseases. Finally, we point out some future perspectives on the research into repeat expansion diseases, as well as APA studies.
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12
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Ogorodnikov A, Danckwardt S. TRENDseq-A highly multiplexed high throughput RNA 3' end sequencing for mapping alternative polyadenylation. Methods Enzymol 2021; 655:37-72. [PMID: 34183130 DOI: 10.1016/bs.mie.2021.03.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alternative polyadenylation (APA) is a widespread and highly dynamic mechanism of gene regulation. It affects more than 70% of all genes, resulting in transcript isoforms with distinct 3' end termini. APA thereby considerably expands the diversity of the transcriptome 3' end (TREND). This leads to mRNA isoforms with profoundly different physiological effects, by affecting protein output, production of distinct protein isoforms, or modulating protein localization. APA is globally regulated in various conditions, including developmental and adaptive programs. Since perturbations of APA can disrupt biological processes, ultimately resulting in most devastating disorders, querying the APA landscape is crucial to decipher underlying mechanisms, resulting consequences and potential diagnostic and therapeutic implications. Here we provide a detailed step-by-step protocol for TRENDseq, a method for transcriptome-wide high-throughput sequencing of polyadenylated RNA 3' ends in a highly multiplexed fashion. TRENDseq exploits linear amplification of the starting material to improve sensitivity while significantly reducing the amount of input material. It thereby represents a powerful tool to study APA in numerous experimental set-ups and/or limited human samples in a highly multiplexed and reproducible manner.
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Affiliation(s)
- Anton Ogorodnikov
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany; Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany; Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany; Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany; Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany; German Centre for Cardiovascular Research (DZHK), Berlin, Germany.
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13
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Pereira-Castro I, Moreira A. On the function and relevance of alternative 3'-UTRs in gene expression regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1653. [PMID: 33843145 DOI: 10.1002/wrna.1653] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022]
Abstract
Messanger RNA (mRNA) isoforms with alternative 3'-untranslated regions (3'-UTRs) are produced by alternative polyadenylation (APA), which occurs during transcription in most eukaryotic genes. APA fine-tunes gene expression in a cell-type- and cellular state-dependent manner. Selection of an APA site entails the binding of core cleavage and polyadenylation factors to a particular polyadenylation site localized in the pre-mRNA and is controlled by multiple regulatory determinants, including transcription, pre-mRNA cis-regulatory sequences, and protein factors. Alternative 3'-UTRs serve as platforms for specific RNA binding proteins and microRNAs, which regulate gene expression in a coordinated manner by controlling mRNA fate and function in the cell. Genome-wide studies illustrated the full extent of APA prevalence and revealed that specific 3'-UTR profiles are associated with particular cellular states and diseases. Generally, short 3'-UTRs are associated with proliferative and cancer cells, and long 3'-UTRs are mostly found in polarized and differentiated cells. Fundamental new insights on the physiological consequences of this widespread event and the molecular mechanisms involved have been revealed through single-cell studies. Publicly available comprehensive databases that cover all APA mRNA isoforms identified in many cellular states and diseases reveal specific APA signatures. Therapies tackling APA mRNA isoforms or APA regulators may be regarded as innovative and attractive tools for diagnostics or treatment of several pathologies. We highlight the function of APA and alternative 3'-UTRs in gene expression regulation, the control of these mechanisms, their physiological consequences, and their potential use as new biomarkers and therapeutic tools. This article is categorized under: RNA Processing > 3' End Processing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Isabel Pereira-Castro
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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14
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Marini F, Scherzinger D, Danckwardt S. TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. Nucleic Acids Res 2021; 49:D243-D253. [PMID: 32976578 PMCID: PMC7778938 DOI: 10.1093/nar/gkaa722] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/06/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3′ end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3′ end maturation is closely linked to transcription, RNA processing and even epigenetic (histone/DNA/RNA) modifications. Here, we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes. TREND-DB visualizes the dynamics of transcriptome 3′ end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA-binding sites and RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps identify their diagnostic and therapeutic potential.
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Affiliation(s)
- Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, 55131 Mainz, Germany
| | - Denise Scherzinger
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, 55131 Mainz, Germany
| | - Sven Danckwardt
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, 55131 Mainz, Germany.,Posttranscriptional Gene Regulation, Cancer Research and Experimental Hemostasis, University Medical Center Mainz, 55131 Mainz, Germany.,Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Rhine-Main, 55131 Mainz, Germany
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15
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Levin M, Zalts H, Mostov N, Hashimshony T, Yanai I. Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms. Nucleic Acids Res 2020; 48:5926-5938. [PMID: 32421815 PMCID: PMC7293032 DOI: 10.1093/nar/gkaa359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/11/2020] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Alternative polyadenylation (APA) produces isoforms with distinct 3′-ends, yet their functional differences remain largely unknown. Here, we introduce the APA-seq method to detect the expression levels of APA isoforms from 3′-end RNA-Seq data by exploiting both paired-end reads for gene isoform identification and quantification. We detected the expression levels of APA isoforms in individual Caenorhabditis elegans embryos at different stages throughout embryogenesis. Examining the correlation between the temporal profiles of isoforms led us to distinguish two classes of genes: those with highly correlated isoforms (HCI) and those with lowly correlated isoforms (LCI) across time. We hypothesized that variants with similar expression profiles may be the product of biological noise, while the LCI variants may be under tighter selection and consequently their distinct 3′ UTR isoforms are more likely to have functional consequences. Supporting this notion, we found that LCI genes have significantly more miRNA binding sites, more correlated expression profiles with those of their targeting miRNAs and a relative lack of correspondence between their transcription and protein abundances. Collectively, our results suggest that a lack of coherence among the regulation of 3′ UTR isoforms is a proxy for selective pressures acting upon APA usage and consequently for their functional relevance.
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Affiliation(s)
- Michal Levin
- Quantitative Proteomics, Institute of Molecular Biology, Mainz 55128, Germany
| | - Harel Zalts
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Natalia Mostov
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Tamar Hashimshony
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Itai Yanai
- Institute for Computational Medicine, NYU Grossman School of Medicine, New York 10016, USA
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16
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Tamaddon M, Shokri G, Hosseini Rad SMA, Rad I, Emami Razavi À, Kouhkan F. Involved microRNAs in alternative polyadenylation intervene in breast cancer via regulation of cleavage factor "CFIm25". Sci Rep 2020; 10:11608. [PMID: 32665581 PMCID: PMC7360588 DOI: 10.1038/s41598-020-68406-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 06/24/2020] [Indexed: 12/22/2022] Open
Abstract
Cleavage factor “CFIm25”, as a key repressor at proximal poly (A) site, negatively correlates to cell proliferation and tumorigenicity in various cancers. Hence, understanding CFIm25 mechanism of action in breast cancer would be a great benefit. To this aim four steps were designed. First, potential miRNAs that target 3′-UTR of CFIm25 mRNA, retrieved from Targetscan web server. Second, screened miRNAs were profiled in 100 breast cancer and 100 normal adjacent samples. Third, miRNAs that their expression was inversely correlated to the CFIm25, overexpressed in MDA-MB-231 cell line, and their effect on proliferation and migration monitored via MTT and wound healing assays, respectively. Fourth, interaction of miRNAs of interest with 3′-UTR of CFIm25 confirmed via luciferase assay and western blot. Our results indicate that CFIm25 considerably down-regulates in human breast cancer tissue. qRT-PCR assay, luciferase test, and western blotting confirm that CFIm25 itself could be directly regulated by oncomiRs such as miR-23, -24, -27, -135, -182 and -374. Besides, according to MTT and wound healing assays of cell lines, CFIm25 knockdown intensifies cell growth, proliferation and migration. Our results also confirm indirect impact of CFIm25 on regulation of mRNA’s 3′–UTR length, which then control corresponding miRNAs’ action. miRNAs directly control CFIm25 expression level, which then tunes expression of the oncogenes and tumor proliferation. Therefore, regulation of CFIm25 expression level via miRNAs is expected to improve treatment responses in breast cancer.
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Affiliation(s)
- Mona Tamaddon
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | - Gelareh Shokri
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | | | - Iman Rad
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran
| | - Àmirnader Emami Razavi
- Ìran National Tumor Bank, Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Kouhkan
- Stem Cell Technology Research Center, No. 9, East 2nd, St., Farhang Blvd., Saadat Abad St., Tehran, 1997775555, Iran.
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17
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Lee CH, Grey F. Systems Virology and Human Cytomegalovirus: Using High Throughput Approaches to Identify Novel Host-Virus Interactions During Lytic Infection. Front Cell Infect Microbiol 2020; 10:280. [PMID: 32587832 PMCID: PMC7298070 DOI: 10.3389/fcimb.2020.00280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
Human Cytomegalovirus (HCMV) is a highly prevalent herpesvirus, persistently infecting between 30 and 100% of the population, depending on socio-economic status (Fields et al., 2013). HCMV remains an important clinical pathogen accounting for more than 60% of complications associated with solid organ transplant patients (Kotton, 2013; Kowalsky et al., 2013; Bruminhent and Razonable, 2014). It is also the leading cause of infectious congenital birth defects and has been linked to chronic inflammation and immune aging (Ballard et al., 1979; Griffith et al., 2016; Jergovic et al., 2019). There is currently no effective vaccine and HCMV antivirals have significant side effects. As current antivirals target viral genes, the virus can develop resistance, reducing drug efficacy. There is therefore an urgent need for new antiviral agents that are effective against HCMV, have better toxicity profiles and are less vulnerable to the emergence of resistant strains. Targeting of host factors that are critical to virus replication is a potential strategy for the development of novel antivirals that circumvent the development of viral resistance. Systematic high throughput approaches provide powerful methods for the identification of novel host-virus interactions. As well as contributing to our basic understanding of virus and cell biology, such studies provide potential targets for the development of novel antiviral agents. High-throughput studies, such as RNA sequencing, proteomics, and RNA interference screens, are useful tools to identify HCMV-induced global changes in host mRNA and protein expression levels and host factors important for virus replication. Here, we summarize new findings on HCMV lytic infection from high-throughput studies since 2014 and how screening approaches have evolved.
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Affiliation(s)
- Chen-Hsuin Lee
- Division of Infection and Immunity, Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Finn Grey
- Division of Infection and Immunity, Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
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18
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Conesa CM, Saez A, Navarro-Neila S, de Lorenzo L, Hunt AG, Sepúlveda EB, Baigorri R, Garcia-Mina JM, Zamarreño AM, Sacristán S, del Pozo JC. Alternative Polyadenylation and Salicylic Acid Modulate Root Responses to Low Nitrogen Availability. PLANTS (BASEL, SWITZERLAND) 2020; 9:E251. [PMID: 32079121 PMCID: PMC7076428 DOI: 10.3390/plants9020251] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023]
Abstract
Nitrogen (N) is probably the most important macronutrient and its scarcity limits plant growth, development and fitness. N starvation response has been largely studied by transcriptomic analyses, but little is known about the role of alternative polyadenylation (APA) in such response. In this work, we show that N starvation modifies poly(A) usage in a large number of transcripts, some of them mediated by FIP1, a component of the polyadenylation machinery. Interestingly, the number of mRNAs isoforms with poly(A) tags located in protein-coding regions or 5'-UTRs significantly increases in response to N starvation. The set of genes affected by APA in response to N deficiency is enriched in N-metabolism, oxidation-reduction processes, response to stresses, and hormone responses, among others. A hormone profile analysis shows that the levels of salicylic acid (SA), a phytohormone that reduces nitrate accumulation and root growth, increase significantly upon N starvation. Meta-analyses of APA-affected and fip1-2-deregulated genes indicate a connection between the nitrogen starvation response and salicylic acid (SA) signaling. Genetic analyses show that SA may be important for preventing the overgrowth of the root system in low N environments. This work provides new insights on how plants interconnect different pathways, such as defense-related hormonal signaling and the regulation of genomic information by APA, to fine-tune the response to low N availability.
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Affiliation(s)
- Carlos M. Conesa
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (C.M.C.); (S.N.-N.)
- Centro de Biotecnología y Genómica de Plantas (CBGP) and Escuela Técnica Superior de Ingeniería Agronómica, Agroambiental y de Biosistemas (ETSIAAB), Universidad Polictécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain;
| | - Angela Saez
- DTD Development and Technical Department, Timac Agro Spain, 31580 Lodosa, Navarra, Spain; (A.S.); (R.B.)
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (C.M.C.); (S.N.-N.)
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA; (L.d.L.); (A.G.H.)
| | - Arthur G. Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, USA; (L.d.L.); (A.G.H.)
| | - Edgar B. Sepúlveda
- Departamento de Biotecnología y Bioingeniería CINVESTAV Instituto Politécnico Nacional, 07360 Ciudad de Mexico, Mexico;
| | - Roberto Baigorri
- DTD Development and Technical Department, Timac Agro Spain, 31580 Lodosa, Navarra, Spain; (A.S.); (R.B.)
| | - Jose M. Garcia-Mina
- Environmental Biology Department, University of Navarra, 31008 Navarra, Spain; (J.M.G.-M.); (A.M.Z.)
| | - Angel M. Zamarreño
- Environmental Biology Department, University of Navarra, 31008 Navarra, Spain; (J.M.G.-M.); (A.M.Z.)
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (CBGP) and Escuela Técnica Superior de Ingeniería Agronómica, Agroambiental y de Biosistemas (ETSIAAB), Universidad Polictécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain;
| | - Juan C. del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (C.M.C.); (S.N.-N.)
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19
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Wang PH, Kumar S, Zeng J, McEwan R, Wright TR, Gupta M. Transcription Terminator-Mediated Enhancement in Transgene Expression in Maize: Preponderance of the AUGAAU Motif Overlapping With Poly(A) Signals. FRONTIERS IN PLANT SCIENCE 2020; 11:570778. [PMID: 33178242 PMCID: PMC7591816 DOI: 10.3389/fpls.2020.570778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/11/2020] [Indexed: 05/08/2023]
Abstract
The selection of transcription terminators (TTs) for pairing with high expressing constitutive promoters in chimeric constructs is crucial to deliver optimal transgene expression in plants. In this study, the use of the native combinations of four polyubiquitin gene promoters and corresponding TTs resulted in up to >3-fold increase in transgene expression in maize. Of the eight polyubiquitin promoter and TT regulatory elements utilized, seven were novel and identified from the polyubiquitin genes of Brachypodium distachyon, Setaria italica, and Zea mays. Furthermore, gene expression driven by the Cassava mosaic virus promoter was studied by pairing the promoter with distinct TTs derived from the high expressing genes of Arabidopsis. Of the three TTs studied, the polyubiquitin10 gene TT produced the highest transgene expression in maize. Polyadenylation patterns and mRNA abundance from eight distinct TTs were analyzed using 3'-RACE and next-generation sequencing. The results exhibited one to three unique polyadenylation sites in the TTs. The poly(A) site patterns for the StPinII TT were consistent when the same TT was deployed in chimeric constructs irrespective of the reporter gene and promoter used. Distal to the poly(A) sites, putative polyadenylation signals were identified in the near-upstream regions of the TTs based on previously reported mutagenesis and bioinformatics studies in rice and Arabidopsis. The putative polyadenylation signals were 9 to 11 nucleotides in length. Six of the eight TTs contained the putative polyadenylation signals that were overlaps of either canonical AAUAAA or AAUAAA-like polyadenylation signals and AUGAAU, a top-ranking-hexamer of rice and Arabidopsis gene near-upstream regions. Three of the polyubiquitin gene TTs contained the identical 9-nucleotide overlap, AUGAAUAAG, underscoring the functional significance of such overlaps in mRNA 3' end processing. In addition to identifying new combinations of regulatory elements for high constitutive trait gene expression in maize, this study demonstrated the importance of TTs for optimizing gene expression in plants. Learning from this study could be applied to other dicotyledonous and monocotyledonous plant species for transgene expression. Research on TTs is not limited to transgene expression but could be extended to the introduction of appropriate mutations into TTs via genome editing, paving the way for expression modulation of endogenous genes.
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Affiliation(s)
- Po-Hao Wang
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Sandeep Kumar
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
- *Correspondence: Sandeep Kumar,
| | - Jia Zeng
- Data Science & Informatics, Corteva Agriscience, Indianapolis, IN, United States
| | - Robert McEwan
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Terry R. Wright
- Trait Discovery, Corteva Agriscience, Indianapolis, IN, United States
| | - Manju Gupta
- Trait Product Development, Dow Agrosciences, Indianapolis, IN, United States
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20
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Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
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21
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Vainberg Slutskin I, Weinberger A, Segal E. Sequence determinants of polyadenylation-mediated regulation. Genome Res 2019; 29:1635-1647. [PMID: 31530582 PMCID: PMC6771402 DOI: 10.1101/gr.247312.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 08/13/2019] [Indexed: 12/31/2022]
Abstract
The cleavage and polyadenylation reaction is a crucial step in transcription termination and pre-mRNA maturation in human cells. Despite extensive research, the encoding of polyadenylation-mediated regulation of gene expression within the DNA sequence is not well understood. Here, we utilized a massively parallel reporter assay to inspect the effect of over 12,000 rationally designed polyadenylation sequences (PASs) on reporter gene expression and cleavage efficiency. We find that the PAS sequence can modulate gene expression by over five orders of magnitude. By using a uniquely designed scanning mutagenesis data set, we gain mechanistic insight into various modes of action by which the cleavage efficiency affects the sensitivity or robustness of the PAS to mutation. Furthermore, we employ motif discovery to identify both known and novel sequence motifs associated with PAS-mediated regulation. By leveraging the large scale of our data, we train a deep learning model for the highly accurate prediction of RNA levels from DNA sequence alone (R = 0.83). Moreover, we devise unique approaches for predicting exact cleavage sites for our reporter constructs and for endogenous transcripts. Taken together, our results expand our understanding of PAS-mediated regulation, and provide an unprecedented resource for analyzing and predicting PAS for regulatory genomics applications.
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Affiliation(s)
- Ilya Vainberg Slutskin
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 7610001, Israel.,Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
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22
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Téllez-Robledo B, Manzano C, Saez A, Navarro-Neila S, Silva-Navas J, de Lorenzo L, González-García MP, Toribio R, Hunt AG, Baigorri R, Casimiro I, Brady SM, Castellano MM, Del Pozo JC. The polyadenylation factor FIP1 is important for plant development and root responses to abiotic stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1203-1219. [PMID: 31111599 DOI: 10.1111/tpj.14416] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 05/28/2023]
Abstract
Root development and its response to environmental changes is crucial for whole plant adaptation. These responses include changes in transcript levels. Here, we show that the alternative polyadenylation (APA) of mRNA is important for root development and responses. Mutations in FIP1, a component of polyadenylation machinery, affects plant development, cell division and elongation, and response to different abiotic stresses. Salt treatment increases the amount of poly(A) site usage within the coding region and 5' untranslated regions (5'-UTRs), and the lack of FIP1 activity reduces the poly(A) site usage within these non-canonical sites. Gene ontology analyses of transcripts displaying APA in response to salt show an enrichment in ABA signaling, and in the response to stresses such as salt or cadmium (Cd), among others. Root growth assays show that fip1-2 is more tolerant to salt but is hypersensitive to ABA or Cd. Our data indicate that FIP1-mediated alternative polyadenylation is important for plant development and stress responses.
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Affiliation(s)
- Barbara Téllez-Robledo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Concepcion Manzano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Angela Saez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
- DTD, Timac Agro Spain, Lodosa, 31580, Navarra, Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Javier Silva-Navas
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | - Mary-Paz González-García
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - René Toribio
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546-0312, USA
| | | | - Ilda Casimiro
- Facultad de Ciencias, Department de Anatomía, Biología Celular y Zoología, Universidad de Extremadura, 06006, Badajoz, Spain
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, 1 Shields Avenue, Davis, CA, 95616, USA
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - J Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (CBGP), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
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Cell Cycle Kinase Polo Is Controlled by a Widespread 3' Untranslated Region Regulatory Sequence in Drosophila melanogaster. Mol Cell Biol 2019; 39:MCB.00581-18. [PMID: 31085682 DOI: 10.1128/mcb.00581-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/04/2019] [Indexed: 01/06/2023] Open
Abstract
Alternative polyadenylation generates transcriptomic diversity, although the physiological impact and regulatory mechanisms involved are still poorly understood. The cell cycle kinase Polo is controlled by alternative polyadenylation in the 3' untranslated region (3'UTR), with critical physiological consequences. Here, we characterized the molecular mechanisms required for polo alternative polyadenylation. We identified a conserved upstream sequence element (USE) close to the polo proximal poly(A) signal. Transgenic flies without this sequence show incorrect selection of polo poly(A) signals with consequent downregulation of Polo expression levels and insufficient/defective activation of Polo kinetochore targets Mps1 and Aurora B. Deletion of the USE results in abnormal mitoses in neuroblasts, revealing a role for this sequence in vivo We found that Hephaestus binds to the USE RNA and that hephaestus mutants display defects in polo alternative polyadenylation concomitant with a striking reduction in Polo protein levels, leading to mitotic errors and aneuploidy. Bioinformatic analyses show that the USE is preferentially localized upstream of noncanonical polyadenylation signals in Drosophila melanogaster genes. Taken together, our results revealed the molecular mechanisms involved in polo alternative polyadenylation, with remarkable physiological functions in Polo expression and activity at the kinetochores, and disclosed a new in vivo function for USEs in Drosophila melanogaster.
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Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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25
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MacDonald CC. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1526. [PMID: 30816016 PMCID: PMC6617714 DOI: 10.1002/wrna.1526] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Alternative polyadenylation (APA) is how genes choose different sites for 3′ end formation for mRNAs during transcription. APA often occurs in a tissue‐ or developmental stage‐specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue‐specific gene expression, only a few examples have been characterized mechanistically. In this 2018 update to our 2010 review, we examine mechanisms for the control of APA and update our understanding of the older mechanisms since 2010. We once postulated the existence of tissue‐specific factors in APA. However, while a few tissue‐specific polyadenylation factors are known, the emerging conclusion is that the majority of APA is accomplished by altering levels of core polyadenylation proteins. Examples of those core proteins include CSTF2, CPSF1, and subunits of mammalian cleavage factor I. But despite support for these mechanisms, no one has yet documented any of these proteins changing in either a tissue‐specific or developmental manner. Given the profound effect that APA can have on gene expression and human health, improved understanding of tissue‐specific APA could lead to numerous advances in gene activity control. This article is categorized under:RNA Processing > 3′ End Processing RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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26
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Bilyk KT, Zhuang X, Murphy KR, Cheng CHC. A tale of two genes: divergent evolutionary fate of haptoglobin and hemopexin in hemoglobinless antarctic icefishes. J Exp Biol 2019; 222:jeb.188573. [DOI: 10.1242/jeb.188573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/06/2019] [Indexed: 12/31/2022]
Abstract
Evolution of Antarctic notothenioid fishes in the isolated freezing Southern Ocean have led to remarkable trait gains and losses. One of the most extraordinary was the loss of the major oxygen carrier hemoglobin (Hb) in the icefishes (family Channichthyidae). While the mechanisms of this loss and the resulting compensatory changes have been well studied, the impact of Hb loss on the network of genes that once supported its recycling and disposal has remained unexplored. Here we report the functional fate and underlying molecular changes of two such key Hb-supporting proteins across the icefish family - haptoglobin (Hp) and hemopexin (Hx), crucial in removing cytotoxic free Hb and heme respectively. Hp plays a critical role in binding free Hb for intracellular recycling and absent its primary client, icefish Hp transcription is now vanishingly little and translation into a functional protein is nearly silenced. Hp genotype degeneration has manifested in separate lineages of the icefish phylogeny with three distinct nonsense mutations and a deletion-frameshift, as well as mutated polyadenylation signal sequences. Thus, Hb loss appears to have diminished selective constraint on Hp maintenance, resulting in its stochastic, co-evolutionary drift towards extinction. Hx binds free heme for iron recycling in hepatocytes. In contrast to Hp, Hx genotype integrity is preserved in the icefishes and transcription occurs at comparable levels to the red-blooded notothenioids. The persistence of Hx likely owes to continued selective pressure for its function from mitochondrial and non-Hb cellular hemoproteins.
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Affiliation(s)
- Kevin T. Bilyk
- Department of Biology, Western Kentucky University, USA
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
| | - Xuan Zhuang
- Department of Ecology & Evolution, University of Chicago, USA
| | - Katherine R. Murphy
- Department of Animal Biology, University of Illinois, Urbana Champaign, USA
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, USA
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Guvenek A, Tian B. Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data. QUANTITATIVE BIOLOGY 2018; 6:253-266. [PMID: 31380142 DOI: 10.1007/s40484-018-0148-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Most eukaryotic protein-coding genes exhibit alternative cleavage and polyadenylation (APA), resulting in mRNA isoforms with different 3' untranslated regions (3' UTRs). Studies have shown that brain cells tend to express long 3' UTR isoforms using distal cleavage and polyadenylation sites (PASs). Methods Using our recently developed, comprehensive PAS database PolyA_DB, we developed an efficient method to examine APA, named Significance Analysis of Alternative Polyadenylation using RNA-seq (SAAP-RS). We applied this method to study APA in brain cells and neurogenesis. Results We found that neurons globally express longer 3' UTRs than other cell types in brain, and microglia and endothelial cells express substantially shorter 3' UTRs. We show that the 3' UTR diversity across brain cells can be corroborated with single cell sequencing data. Further analysis of APA regulation of 3' UTRs during differentiation of embryonic stem cells into neurons indicates that a large fraction of the APA events regulated in neurogenesis are similarly modulated in myogenesis, but to a much greater extent. Conclusion Together, our data delineate APA profiles in different brain cells and indicate that APA regulation in neurogenesis is largely an augmented process taking place in other types of cell differentiation.
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Affiliation(s)
- Aysegul Guvenek
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.,Rutgers School of Graduate Studies, Newark, NJ 07103, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.,Rutgers Cancer Institute of New Jersey, Newark, NJ 07103, USA.,Rutgers Brain Health Institute, Newark, NJ 07103, USA
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Characterization of mRNA polyadenylation in the apicomplexa. PLoS One 2018; 13:e0203317. [PMID: 30161237 PMCID: PMC6117058 DOI: 10.1371/journal.pone.0203317] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/18/2018] [Indexed: 11/19/2022] Open
Abstract
Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the AAUAAA polyadenylation signal (PAS) were not immediately obvious, a computational analysis of sequences adjacent to experimentally-determined apicomplexan poly(A) sites was conducted. The results of this study showed that there exists in apicomplexans an A-rich region that corresponds in position to the AAUAAA PAS. The set of experimentally-determined sites in one species, Sarcocystis neurona, was further analyzed to evaluate the extent and significance of alternative poly(A) site choice in this organism. The results showed that almost 80% of S. neurona genes possess more than one poly(A) site, and that more than 780 sites showed differential usage in the two developmental stages–extracellular merozoites and intracellular schizonts–studied. These sites affected more than 450 genes, and included a disproportionate number of genes that encode membrane transporters and ribosomal proteins. Taken together, these results reveal that apicomplexan species seem to possess a poly(A) signal analogous to AAUAAA even though genes that may encode obvious counterparts of the AAUAAA-recognizing proteins are absent in these organisms. They also indicate that, as is the case in other eukaryotes, alternative polyadenylation is a widespread phenomenon in S. neurona that has the potential to impact growth and development.
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Genome-wide atlas of alternative polyadenylation in the forage legume red clover. Sci Rep 2018; 8:11379. [PMID: 30054540 PMCID: PMC6063945 DOI: 10.1038/s41598-018-29699-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
Studies on prevalence and significance of alternative polyadenylation (APA) in plants have been so far limited mostly to the model plants. Here, a genome-wide analysis of APA was carried out in different tissue types in the non-model forage legume red clover (Trifolium pratense L). A profile of poly(A) sites in different tissue types was generated using so-called 'poly(A)-tag sequencing' (PATseq) approach. Our analysis revealed tissue-wise dynamics of usage of poly(A) sites located at different genomic locations. We also identified poly(A) sites and underlying genes displaying APA in different tissues. Functional categories enriched in groups of genes manifesting APA between tissue types were determined. Analysis of spatial expression of genes encoding different poly(A) factors showed significant differential expression of genes encoding orthologs of FIP1(V) and PCFS4, suggesting that these two factors may play a role in regulating spatial APA in red clover. Our analysis also revealed a high degree of conservation in diverse plant species of APA events in mRNAs encoding two key polyadenylation factors, CPSF30 and FIP1(V). Together with our previously reported study of spatial gene expression in red clover, this study will provide a comprehensive account of transcriptome dynamics in this non-model forage legume.
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31
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Chen LF, Han XL, Li FX, Yao YY, Fang JP, Liu XJ, Li XC, Wu K, Liu M, Chen XG. Comparative studies of Toxoplasma gondii transcriptomes: insights into stage conversion based on gene expression profiling and alternative splicing. Parasit Vectors 2018; 11:402. [PMID: 29996885 PMCID: PMC6042387 DOI: 10.1186/s13071-018-2983-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/27/2018] [Indexed: 11/19/2022] Open
Abstract
Background Toxoplasma gondii is one of the most important apicomplexan parasites and infects one-third of the human population worldwide. Transformation between the tachyzoite and bradyzoite stages in the intermediate host is central to chronic infection and life-long risk. There have been some transcriptome studies on T. gondii; however, we are still early in our understanding of the kinds and levels of gene expression that occur during the conversion between stages. Results We used high-throughput RNA-sequencing data to assemble transcripts using genome-based and de novo strategies. The expression-level analysis of 6996 T. gondii genes showed that over half (3986) were significantly differentially expressed during stage conversion, whereas 2205 genes were upregulated, and 1778 genes were downregulated in tachyzoites compared with bradyzoites. Several important gene families were expressed at relatively high levels. Comprehensive functional annotation and gene ontology analysis revealed that stress response-related genes are important for survival of bradyzoites in immune-competent hosts. We compared Trinity-based de novo and genome-based strategies, and found that the de novo assembly strategy compensated for the defects of the genome-based strategy by filtering out several transcripts with low expression or those unannotated on the genome. We also found some inaccuracies in the ToxoDB gene models. In addition, our analysis revealed that alternative splicing can be differentially regulated in response to life-cycle change. In depth analysis revealed a 20-nt, AG-rich sequence, alternative splicing locus from alt_acceptor motif search in tachyzoite. Conclusion This study represents the first large-scale effort to sequence the transcriptome of bradyzoites from T. gondii tissue cysts. Our data provide a comparative view of the tachyzoite and bradyzoite transcriptomes to allow a more complete dissection of all the molecular regulation mechanisms during stage conversions. A better understanding of the processes regulating stage conversion may guide targeted interventions to disrupt the transmission of T. gondii. Electronic supplementary material The online version of this article (10.1186/s13071-018-2983-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Long-Fei Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Xiao-Long Han
- Department of Bioinformatics, School of Basic Medicine School of Basic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Fen-Xiang Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Yun-Ying Yao
- Epidemiology and Infection Control Branch, Shenzhen Guangming District Center for Disease Control and Prevention, Shenzhen, 518106, Guangdong, China
| | - Jin-Ping Fang
- First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiao-Ju Liu
- First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiao-Cong Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Kun Wu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China
| | - Min Liu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China.
| | - Xiao-Guang Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou North Avenue No.1838, Guangzhou, 510515, Guangdong, China.
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Fontes MM, Guvenek A, Kawaguchi R, Zheng D, Huang A, Ho VM, Chen PB, Liu X, O'Dell TJ, Coppola G, Tian B, Martin KC. Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation. Sci Rep 2017; 7:17377. [PMID: 29234016 PMCID: PMC5727029 DOI: 10.1038/s41598-017-17407-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
Long-lasting forms of synaptic plasticity that underlie learning and memory require new transcription and translation for their persistence. The remarkable polarity and compartmentalization of neurons raises questions about the spatial and temporal regulation of gene expression within neurons. Alternative cleavage and polyadenylation (APA) generates mRNA isoforms with different 3' untranslated regions (3'UTRs) and/or coding sequences. Changes in the 3'UTR composition of mRNAs can alter gene expression by regulating transcript localization, stability and/or translation, while changes in the coding sequences lead to mRNAs encoding distinct proteins. Using specialized 3' end deep sequencing methods, we undertook a comprehensive analysis of APA following induction of long-term potentiation (LTP) of mouse hippocampal CA3-CA1 synapses. We identified extensive LTP-induced APA changes, including a general trend of 3'UTR shortening and activation of intronic APA isoforms. Comparison with transcriptome profiling indicated that most APA regulatory events were uncoupled from changes in transcript abundance. We further show that specific APA regulatory events can impact expression of two molecules with known functions during LTP, including 3'UTR APA of Notch1 and intronic APA of Creb1. Together, our results reveal that activity-dependent APA provides an important layer of gene regulation during learning and memory.
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Affiliation(s)
- Mariana M Fontes
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Graduate Program in Areas of Basic and Applied Biology, University of Porto, Porto, Portugal
| | - Aysegul Guvenek
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Riki Kawaguchi
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Alden Huang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Victoria M Ho
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Interdepartmental Graduate Program in Neuroscience, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrick B Chen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Interdepartmental Graduate Program in Neuroscience, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Thomas J O'Dell
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA.
| | - Kelsey C Martin
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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Liu X, Freitas J, Zheng D, Oliveira MS, Hoque M, Martins T, Henriques T, Tian B, Moreira A. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster. RNA (NEW YORK, N.Y.) 2017; 23:1807-1816. [PMID: 28851752 PMCID: PMC5689002 DOI: 10.1261/rna.062661.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/18/2017] [Indexed: 06/07/2023]
Abstract
Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here, using 3' region extraction and deep sequencing (3'READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in Drosophila melanogaster, expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. Cis-element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in Drosophila melanogaster undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3'UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the RpII215C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3'UTRs and in introns, consistent with the "first come, first served" model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for Drosophila melanogaster and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate.
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Affiliation(s)
- Xiaochuan Liu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Jaime Freitas
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Marta S Oliveira
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Torcato Martins
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Telmo Henriques
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Alexandra Moreira
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-013 Porto, Portugal
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Li Z, Wang R, Gao Y, Wang C, Zhao L, Xu N, Chen KE, Qi S, Zhang M, Tsay YF, Crawford NM, Wang Y. The Arabidopsis CPSF30-L gene plays an essential role in nitrate signaling and regulates the nitrate transceptor gene NRT1.1. THE NEW PHYTOLOGIST 2017; 216:1205-1222. [PMID: 28850721 DOI: 10.1111/nph.14743] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/04/2017] [Indexed: 05/20/2023]
Abstract
Plants have evolved sophisticated mechanisms to adapt to fluctuating environmental nitrogen availability. However, more underlying genes regulating the response to nitrate have yet to be characterized. We report here the identification of a nitrate regulatory mutant whose mutation mapped to the Cleavage and Polyadenylation Specificity Factor 30 gene (CPSF30-L). In the mutant, induction of nitrate-responsive genes was inhibited independent of the ammonium conditions and was restored by expression of the wild-type 65 kDa encoded by CPSF30-L. Molecular and genetic evidence suggests that CPSF30-L works upstream of NRT1.1 and independently of NLP7 in response to nitrate. Analysis of the 3'-UTR of NRT1.1 showed that the pattern of polyadenylation sites was altered in the cpsf30 mutant. Transcriptome analysis revealed that four nitrogen-related clusters were enriched in the differentially expressed genes of the cpsf30 mutant. Nitrate uptake was decreased in the mutant along with reduced expression of the nitrate transporter/sensor gene NRT1.1, while nitrate reduction and amino acid content were enhanced in roots along with increased expression of several nitrate assimilatory genes. These findings indicate that the 65 kDa protein encoded by CPSF30-L mediates nitrate signaling in part by regulating NRT1.1 expression, thus adding an important component to the nitrate signaling network.
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Affiliation(s)
- Zehui Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Rongchen Wang
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Chao Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Lufei Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Na Xu
- School of Biological Science, Jining Medical University, Rizhao, Shandong, 276826, China
| | - Kuo-En Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Shengdong Qi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Min Zhang
- College of Resources and Environment, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093-0116, USA
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Wohlfarth C, Schmitteckert S, Härtle JD, Houghton LA, Dweep H, Fortea M, Assadi G, Braun A, Mederer T, Pöhner S, Becker PP, Fischer C, Granzow M, Mönnikes H, Mayer EA, Sayuk G, Boeckxstaens G, Wouters MM, Simrén M, Lindberg G, Ohlsson B, Schmidt PT, Dlugosz A, Agreus L, Andreasson A, D'Amato M, Burwinkel B, Bermejo JL, Röth R, Lasitschka F, Vicario M, Metzger M, Santos J, Rappold GA, Martinez C, Niesler B. miR-16 and miR-103 impact 5-HT 4 receptor signalling and correlate with symptom profile in irritable bowel syndrome. Sci Rep 2017; 7:14680. [PMID: 29089619 PMCID: PMC5665867 DOI: 10.1038/s41598-017-13982-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/04/2017] [Indexed: 12/19/2022] Open
Abstract
Irritable bowel syndrome (IBS) is a gut-brain disorder involving alterations in intestinal sensitivity and motility. Serotonin 5-HT4 receptors are promising candidates in IBS pathophysiology since they regulate gut motor function and stool consistency, and targeted 5-HT4R selective drug intervention has been proven beneficial in subgroups of patients. We identified a single nucleotide polymorphism (SNP) (rs201253747) c.*61 T > C within the 5-HT4 receptor gene HTR4 to be predominantly present in diarrhoea-IBS patients (IBS-D). It affects a binding site for the miR-16 family and miR-103/miR-107 within the isoforms HTR4b/i and putatively impairs HTR4 expression. Subsequent miRNA-profiling revealed downregulation of miR-16 and miR-103 in the jejunum of IBS-D patients correlating with symptoms. In vitro assays confirmed expression regulation via three 3'UTR binding sites. The novel isoform HTR4b_2 lacking two of the three miRNA binding sites escapes miR-16/103/107 regulation in SNP carriers. We provide the first evidence that HTR4 expression is fine-tuned by miRNAs, and that this regulation is impaired either by the SNP c.*61 T > C or by diminished levels of miR-16 and miR-103 suggesting that HTR4 might be involved in the development of IBS-D.
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Affiliation(s)
- Carolin Wohlfarth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Stefanie Schmitteckert
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Janina D Härtle
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Lesley A Houghton
- University of Leeds, St. James's University Hospital, LS97TF, Leeds, UK
- Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Harsh Dweep
- Medical Research Centre, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, 68167, Germany
- Division of Bioinformatics and Biostatistics, National Centre for Toxicological Research, U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, USA
| | - Marina Fortea
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Ghazaleh Assadi
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Alexander Braun
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Tanja Mederer
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Sarina Pöhner
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Philip P Becker
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Christine Fischer
- Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Martin Granzow
- Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | | | - Emeran A Mayer
- Oppenheimer Centre for Neurobiology of Stress, Division of Digestive Diseases, University of California, Los Angeles, CA 90095-7378, USA
| | - Gregory Sayuk
- Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Mira M Wouters
- TARGID, University Hospital Leuven, 3000, Leuven, Belgium
| | - Magnus Simrén
- Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden
| | - Greger Lindberg
- Department of Medicine, Division of Gastroenterology and Hepatology, Karolinska University Hospital, Karolinska Institutet, Huddinge, 17176, Stockholm, Sweden
| | - Bodil Ohlsson
- Department of Clinical Sciences, Division of Internal Medicine, Skåne University Hospital, Malmö, Lund University, 22241, Lund, Sweden
| | - Peter Thelin Schmidt
- Department of Medicine, Division of Gastroenterology and Hepatology, Karolinska University Hospital, Karolinska Institutet, 14186, Stockholm, Sweden
| | - Aldona Dlugosz
- Department of Medicine, Division of Gastroenterology and Hepatology, Karolinska University Hospital, Karolinska Institutet, Huddinge, 17176, Stockholm, Sweden
| | - Lars Agreus
- Division for Family Medicine and Primary Care, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Anna Andreasson
- Department of Medicine, Solna, Karolinska Institutet, 171 76, Solna, Sweden
- Stress Research Institute, Stockholm University, 10691, Stockholm, Sweden
| | - Mauro D'Amato
- Unit of Clinical Epidemiology, Department of Medicine, Karolinska Institutet, 171 76, Stockholm, Sweden
- BioDonostia Health Research Institute, San Sebastian and Ikerbasque, Basque Science Foundation, 48013, Bilbao, Spain
| | - Barbara Burwinkel
- Molecular Epidemiology Group, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Division of Molecular Biology of Breast Cancer, Department of Gynaecology and Obstetrics, University Women's Clinic, University of Heidelberg, 69120, Heidelberg, Germany
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Ralph Röth
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
- nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Felix Lasitschka
- Institute of Pathology, University of Heidelberg, 69120, Heidelberg, Germany
| | - Maria Vicario
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Marco Metzger
- Department Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, 97082, Wuerzburg, Germany
- Translational Centre 'Regenerative Therapies for Oncology and Musculoskeletal Diseases' (TZKME), Branch of the Fraunhofer Institute Interfacial Engineering and Biotechnology (IGB) Wuerzburg, 97082, Wuerzburg, Germany
| | - Javier Santos
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
| | - Cristina Martinez
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany
- Digestive System Research Unit, Institut de Recerca Vall d'Hebron, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), 08035, Barcelona, Spain
| | - Beate Niesler
- Department of Human Molecular Genetics, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany.
- nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, 69120, Heidelberg, Germany.
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36
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Li W, Li W, Laishram RS, Hoque M, Ji Z, Tian B, Anderson RA. Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases. Nucleic Acids Res 2017; 45:8930-8942. [PMID: 28911096 PMCID: PMC5587728 DOI: 10.1093/nar/gkx560] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/23/2017] [Indexed: 12/14/2022] Open
Abstract
Polyadenylation of nascent RNA by poly(A) polymerase (PAP) is important for 3′ end maturation of almost all eukaryotic mRNAs. Most mammalian genes harbor multiple polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms with distinct functions. How poly(A) polymerases may regulate PAS usage and hence gene expression is poorly understood. Here, we show that the nuclear canonical (PAPα and PAPγ) and non-canonical (Star-PAP) PAPs play diverse roles in PAS selection and gene expression. Deficiencies in the PAPs resulted in perturbations of gene expression, with Star-PAP impacting lowly expressed mRNAs and long-noncoding RNAs to the greatest extent. Importantly, different PASs of a gene are distinctly regulated by different PAPs, leading to widespread relative expression changes of APA isoforms. The location and surrounding sequence motifs of a PAS appear to differentiate its regulation by the PAPs. We show Star-PAP-specific PAS usage regulates the expression of the eukaryotic translation initiation factor EIF4A1, the tumor suppressor gene PTEN and the long non-coding RNA NEAT1. The Star-PAP-mediated APA of PTEN is essential for DNA damage-induced increase of PTEN protein levels. Together, our results reveal a PAS-guided and PAP-mediated paradigm for gene expression in response to cellular signaling cues.
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Affiliation(s)
- Weimin Li
- University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA.,Washington State University, Elson S. Floyd College of Medicine, Department of Biomedical Sciences, Spokane, WA 99202, USA
| | - Wencheng Li
- Rutgers New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Newark, NJ 07103, USA
| | - Rakesh S Laishram
- University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
| | - Mainul Hoque
- Rutgers New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Newark, NJ 07103, USA
| | - Zhe Ji
- Rutgers New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Newark, NJ 07103, USA
| | - Bin Tian
- Rutgers New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Newark, NJ 07103, USA
| | - Richard A Anderson
- University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53706, USA
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Abstract
BACKGROUND Mitogenome diversity is staggering among early branching animals with respect to size, gene density, content and order, and number of tRNA genes, especially in cnidarians. This last point is of special interest as tRNA cleavage drives the maturation of mitochondrial mRNAs and is a primary mechanism for mt-RNA processing in animals. Mitochondrial RNA processing in non-bilaterian metazoans, some of which possess a single tRNA gene in their mitogenomes, is essentially unstudied despite its importance in understanding the evolution of mitochondrial transcription in animals. RESULTS We characterized the mature mitochondrial mRNA transcripts in a species of the octocoral genus Sinularia (Alcyoniidae: Octocorallia), and defined precise boundaries of transcription units using different molecular methods. Most mt-mRNAs were polycistronic units containing two or three genes and 5' and/or 3' untranslated regions of varied length. The octocoral specific, mtDNA-encoded mismatch repair gene, the mtMutS, was found to undergo alternative polyadenylation, and exhibited differential expression of alternate transcripts suggesting a unique regulatory mechanism for this gene. In addition, a long noncoding RNA complementary to the ATP6 gene (lncATP6) potentially involved in antisense regulation was detected. CONCLUSIONS Mt-mRNA processing in octocorals possessing a single mt-tRNA is complex. Considering the variety of mitogenome arrangements known in cnidarians, and in general among non-bilaterian metazoans, our findings provide a first glimpse into the complex mtDNA transcription, mt-mRNA processing, and regulation among early branching animals and represent a first step towards understanding its functional and evolutionary implications.
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Expression of Rac1 alternative 3′ UTRs is a cell specific mechanism with a function in dendrite outgrowth in cortical neurons. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:685-694. [DOI: 10.1016/j.bbagrm.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 01/24/2023]
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Hu W, Li S, Park JY, Boppana S, Ni T, Li M, Zhu J, Tian B, Xie Z, Xiang M. Dynamic landscape of alternative polyadenylation during retinal development. Cell Mol Life Sci 2016; 74:1721-1739. [PMID: 27990575 DOI: 10.1007/s00018-016-2429-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 10/20/2022]
Abstract
The development of the central nervous system (CNS) is a complex process that must be exquisitely controlled at multiple levels to ensure the production of appropriate types and quantity of neurons. RNA alternative polyadenylation (APA) contributes to transcriptome diversity and gene regulation, and has recently been shown to be widespread in the CNS. However, the previous studies have been primarily focused on the tissue specificity of APA and developmental APA change of whole model organisms; a systematic survey of APA usage is lacking during CNS development. Here, we conducted global analysis of APA during mouse retinal development, and identified stage-specific polyadenylation (pA) sites that are enriched for genes critical for retinal development and visual perception. Moreover, we demonstrated 3'UTR (untranslated region) lengthening and increased usage of intronic pA sites over development that would result in gaining many different RBP (RNA-binding protein) and miRNA target sites. Furthermore, we showed that a considerable number of polyadenylated lncRNAs are co-expressed with protein-coding genes involved in retinal development and functions. Together, our data indicate that APA is highly and dynamically regulated during retinal development and maturation, suggesting that APA may serve as a crucial mechanism of gene regulation underlying the delicate process of CNS development.
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Affiliation(s)
- Wenyan Hu
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 500040, China
| | - Shengguo Li
- Center for Advanced Biotechnology and Medicine and Department of Pediatrics, Rutgers University-Robert Wood Johnson Medical School, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Ji Yeon Park
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07101, USA
| | - Sridhar Boppana
- Center for Advanced Biotechnology and Medicine and Department of Pediatrics, Rutgers University-Robert Wood Johnson Medical School, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Ting Ni
- State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Miaoxin Li
- Department of Medical Genetics, Center for Genome Research, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, 07101, USA
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 500040, China.
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 500040, China. .,Center for Advanced Biotechnology and Medicine and Department of Pediatrics, Rutgers University-Robert Wood Johnson Medical School, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
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40
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The Cstf2t Polyadenylation Gene Plays a Sex-Specific Role in Learning Behaviors in Mice. PLoS One 2016; 11:e0165976. [PMID: 27812195 PMCID: PMC5094787 DOI: 10.1371/journal.pone.0165976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
Polyadenylation is an essential mechanism for the processing of mRNA 3′ ends. CstF-64 (the 64,000 Mr subunit of the cleavage stimulation factor; gene symbol Cstf2) is an RNA-binding protein that regulates mRNA polyadenylation site usage. We discovered a paralogous form of CstF-64 called τCstF-64 (Cstf2t). The Cstf2t gene is conserved in all eutherian mammals including mice and humans, but the τCstF-64 protein is expressed only in a subset of mammalian tissues, mostly testis and brain. Male mice that lack Cstf2t (Cstf2t-/- mice) experience disruption of spermatogenesis and are infertile, although female fertility is unaffected. However, a role for τCstF-64 in the brain has not yet been determined. Given the importance of RNA polyadenylation and splicing in neuronal gene expression, we chose to test the hypothesis that τCstF-64 is important for brain function. Male and female 185-day old wild type and Cstf2t-/- mice were examined for motor function, general activity, learning, and memory using rotarod, open field activity, 8-arm radial arm maze, and Morris water maze tasks. Male wild type and Cstf2t-/- mice did not show differences in learning and memory. However, female Cstf2t-/- mice showed significantly better retention of learned maze tasks than did female wild type mice. These results suggest that τCstf-64 is important in memory function in female mice. Interestingly, male Cstf2t-/- mice displayed less thigmotactic behavior than did wild type mice, suggesting that Cstf2t may play a role in anxiety in males. Taken together, our studies highlight the importance of mRNA processing in cognition and behavior as well as their established functions in reproduction.
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Chen CYA, Shyu AB. Emerging Themes in Regulation of Global mRNA Turnover in cis. Trends Biochem Sci 2016; 42:16-27. [PMID: 27647213 DOI: 10.1016/j.tibs.2016.08.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 11/25/2022]
Abstract
mRNA is the molecule that conveys genetic information from DNA to the translation apparatus. mRNAs in all organisms display a wide range of stability, and mechanisms have evolved to selectively and differentially regulate individual mRNA stability in response to intracellular and extracellular cues. In recent years, three seemingly distinct aspects of RNA biology-mRNA N6-methyladenosine (m6A) modification, alternative 3' end processing and polyadenylation (APA), and mRNA codon usage-have been linked to mRNA turnover, and all three aspects function to regulate global mRNA stability in cis. Here, we discuss the discovery and molecular dissection of these mechanisms in relation to how they impact the intrinsic decay rate of mRNA in eukaryotes, leading to transcriptome reprogramming.
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Affiliation(s)
- Chyi-Ying A Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ann-Bin Shyu
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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Hudson SW, McNally LM, McNally MT. Evidence that a threshold of serine/arginine-rich (SR) proteins recruits CFIm to promote rous sarcoma virus mRNA 3' end formation. Virology 2016; 498:181-191. [PMID: 27596537 DOI: 10.1016/j.virol.2016.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 11/24/2022]
Abstract
The weak polyadenylation site (PAS) of Rous sarcoma virus (RSV) is activated by the juxtaposition of SR protein binding sites within the spatially separate negative regulator of splicing (NRS) element and the env RNA splicing enhancer (Env enhancer), which are far upstream of the PAS. Juxtaposition occurs by formation of the NRS - 3' ss splicing regulatory complex and is thought to provide a threshold of SR proteins that facilitate long-range stimulation of the PAS. We provide evidence for the threshold model by showing that greater than three synthetic SR protein binding sites are needed to substitute for the Env enhancer, that either the NRS or Env enhancer alone promotes polyadenylation when the distance to the PAS is decreased, and that SR protein binding sites promote binding of the polyadenylation factor cleavage factor I (CFIm) to the weak PAS. These observations may be relevant for cellular PASs.
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Affiliation(s)
- Stephen W Hudson
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Lisa M McNally
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
| | - Mark T McNally
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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43
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Zhang Y, Rataj K, Simpson GG, Tong L. Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA. PLoS One 2016; 11:e0160694. [PMID: 27513867 PMCID: PMC4981400 DOI: 10.1371/journal.pone.0160694] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/23/2016] [Indexed: 11/18/2022] Open
Abstract
The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain.
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Affiliation(s)
- Yinglu Zhang
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
| | - Katarzyna Rataj
- Division Plant Sciences & Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Gordon G. Simpson
- Division Plant Sciences & Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
- Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, United Kingdom
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
- * E-mail:
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Genome-Wide Identification of Alternative Polyadenylation Events Using 3'T-Fill. Methods Mol Biol 2016; 1358:295-302. [PMID: 26463391 DOI: 10.1007/978-1-4939-3067-8_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Due to the increasing appreciation of the impact of alternative polyadenylation on cellular biology, our straightforward, scalable method is of interest to any researcher studying eukaryotic transcription. In addition to high quality gene expression measurements, it precisely maps poly(A) sites and thereby permits the distinction between differential 3'UTR isoforms. As sequencing through long homopolymer stretches is not possible on the Illumina platform, we developed a method that fills up the poly(A) stretch with dTTPs before the sequencing reaction starts.
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45
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Intronic cleavage and polyadenylation regulates gene expression during DNA damage response through U1 snRNA. Cell Discov 2016; 2:16013. [PMID: 27462460 PMCID: PMC4906801 DOI: 10.1038/celldisc.2016.13] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
The DNA damage response involves coordinated control of gene expression and DNA repair. Using deep sequencing, we found widespread changes of alternative cleavage and polyadenylation site usage on ultraviolet-treatment in mammalian cells. Alternative cleavage and polyadenylation regulation in the 3ʹ untranslated region is substantial, leading to both shortening and lengthening of 3ʹ untranslated regions of genes. Interestingly, a strong activation of intronic alternative cleavage and polyadenylation sites is detected, resulting in widespread expression of truncated transcripts. Intronic alternative cleavage and polyadenylation events are biased to the 5ʹ end of genes and affect gene groups with important functions in DNA damage response and cancer. Moreover, intronic alternative cleavage and polyadenylation site activation during DNA damage response correlates with a decrease in U1 snRNA levels, and is reversible by U1 snRNA overexpression. Importantly, U1 snRNA overexpression mitigates ultraviolet-induced apoptosis. Together, these data reveal a significant gene regulatory scheme in DNA damage response where U1 snRNA impacts gene expression via the U1-alternative cleavage and polyadenylation axis.
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Domingues RG, Lago-Baldaia I, Pereira-Castro I, Fachini JM, Oliveira L, Drpic D, Lopes N, Henriques T, Neilson JR, Carmo AM, Moreira A. CD5 expression is regulated during human T-cell activation by alternative polyadenylation, PTBP1, and miR-204. Eur J Immunol 2016; 46:1490-503. [PMID: 27005442 DOI: 10.1002/eji.201545663] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 02/17/2016] [Accepted: 03/16/2016] [Indexed: 01/29/2023]
Abstract
T lymphocytes stimulated through their antigen receptor (TCR) preferentially express mRNA isoforms with shorter 3´ untranslated regions (3´-UTRs) derived from alternative pre-mRNA cleavage and polyadenylation (APA). However, the physiological relevance of APA programs remains poorly understood. CD5 is a T-cell surface glycoprotein that negatively regulates TCR signaling from the onset of T-cell activation. CD5 plays a pivotal role in mediating outcomes of cell survival or apoptosis, and may prevent both autoimmunity and cancer. In human primary T lymphocytes and Jurkat cells we found three distinct mRNA isoforms encoding CD5, each derived from distinct poly(A) signals (PASs). Upon T-cell activation, there is an overall increase in CD5 mRNAs with a specific increase in the relative expression of the shorter isoforms. 3´-UTRs derived from these shorter isoforms confer higher reporter expression in activated T cells relative to the longer isoform. We further show that polypyrimidine tract binding protein (PTB/PTBP1) directly binds to the proximal PAS and PTB siRNA depletion causes a decrease in mRNA derived from this PAS, suggesting an effect on stability or poly(A) site selection to circumvent targeting of the longer CD5 mRNA isoform by miR-204. These mechanisms fine-tune CD5 expression levels and thus ultimately T-cell responses.
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Affiliation(s)
- Rita G Domingues
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Inês Lago-Baldaia
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Isabel Pereira-Castro
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Joseph M Fachini
- Department of Molecular Physiology and Biophysics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Liliana Oliveira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Cell Activation and Gene Expression Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Danica Drpic
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Nair Lopes
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Telmo Henriques
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Alexandre M Carmo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,Cell Activation and Gene Expression Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation Group, IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Portugal.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
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47
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Erson-Bensan AE, Can T. Alternative Polyadenylation: Another Foe in Cancer. Mol Cancer Res 2016; 14:507-17. [PMID: 27075335 DOI: 10.1158/1541-7786.mcr-15-0489] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/30/2016] [Indexed: 11/16/2022]
Abstract
Advancements in sequencing and transcriptome analysis methods have led to seminal discoveries that have begun to unravel the complexity of cancer. These studies are paving the way toward the development of improved diagnostics, prognostic predictions, and targeted treatment options. However, it is clear that pieces of the cancer puzzle are still missing. In an effort to have a more comprehensive understanding of the development and progression of cancer, we have come to appreciate the value of the noncoding regions of our genomes, partly due to the discovery of miRNAs and their significance in gene regulation. Interestingly, the miRNA-mRNA interactions are not solely dependent on variations in miRNA levels. Instead, the majority of genes harbor multiple polyadenylation signals on their 3' UTRs (untranslated regions) that can be differentially selected on the basis of the physiologic state of cells, resulting in alternative 3' UTR isoforms. Deregulation of alternative polyadenylation (APA) has increasing interest in cancer research, because APA generates mRNA 3' UTR isoforms with potentially different stabilities, subcellular localizations, translation efficiencies, and functions. This review focuses on the link between APA and cancer and discusses the mechanisms as well as the tools available for investigating APA events in cancer. Overall, detection of deregulated APA-generated isoforms in cancer may implicate some proto-oncogene activation cases of unknown causes and may help the discovery of novel cases; thus, contributing to a better understanding of molecular mechanisms of cancer. Mol Cancer Res; 14(6); 507-17. ©2016 AACR.
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Affiliation(s)
- Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University (METU) (ODTU), Ankara, Turkey.
| | - Tolga Can
- Department of Computer Engineering, Middle East Technical University (METU) (ODTU), Ankara, Turkey
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48
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Lamas-Maceiras M, Singh BN, Hampsey M, Freire-Picos MA. Promoter-Terminator Gene Loops Affect Alternative 3'-End Processing in Yeast. J Biol Chem 2016; 291:8960-8. [PMID: 26929407 DOI: 10.1074/jbc.m115.687491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Indexed: 11/06/2022] Open
Abstract
Many eukaryotic genes undergo alternative 3'-end poly(A)-site selection producing transcript isoforms with 3'-UTRs of different lengths and post-transcriptional fates. Gene loops are dynamic structures that juxtapose the 3'-ends of genes with their promoters. Several functions have been attributed to looping, including memory of recent transcriptional activity and polarity of transcription initiation. In this study, we investigated the relationship between gene loops and alternative poly(A)-site. Using the KlCYC1 gene of the yeast Kluyveromyces lactis, which includes a single promoter and two poly(A) sites separated by 394 nucleotides, we demonstrate in two yeast species the formation of alternative gene loops (L1 and L2) that juxtapose the KlCYC1 promoter with either proximal or distal 3'-end processing sites, resulting in the synthesis of short and long forms of KlCYC1 mRNA. Furthermore, synthesis of short and long mRNAs and formation of the L1 and L2 loops are growth phase-dependent. Chromatin immunoprecipitation experiments revealed that the Ssu72 RNA polymerase II carboxyl-terminal domain phosphatase, a critical determinant of looping, peaks in early log phase at the proximal poly(A) site, but as growth phase advances, it extends to the distal site. These results define a cause-and-effect relationship between gene loops and alternative poly(A) site selection that responds to different physiological signals manifested by RNA polymerase II carboxyl-terminal domain phosphorylation status.
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Affiliation(s)
- Mónica Lamas-Maceiras
- From the Departamento de Biología Celular e Molecular, Facultad de Ciencias, Universidade da Coruña, Campus de A Coruña, Rúa da Fraga 10, 15008 A Coruña, Spain and
| | - Badri Nath Singh
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Michael Hampsey
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - María A Freire-Picos
- From the Departamento de Biología Celular e Molecular, Facultad de Ciencias, Universidade da Coruña, Campus de A Coruña, Rúa da Fraga 10, 15008 A Coruña, Spain and
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49
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Redis RS, Vela LE, Lu W, Ferreira de Oliveira J, Ivan C, Rodriguez-Aguayo C, Adamoski D, Pasculli B, Taguchi A, Chen Y, Fernandez AF, Valledor L, Van Roosbroeck K, Chang S, Shah M, Kinnebrew G, Han L, Atlasi Y, Cheung LH, Huang GY, Monroig P, Ramirez MS, Catela Ivkovic T, Van L, Ling H, Gafà R, Kapitanovic S, Lanza G, Bankson JA, Huang P, Lai SY, Bast RC, Rosenblum MG, Radovich M, Ivan M, Bartholomeusz G, Liang H, Fraga MF, Widger WR, Hanash S, Berindan-Neagoe I, Lopez-Berestein G, Ambrosio ALB, Gomes Dias SM, Calin GA. Allele-Specific Reprogramming of Cancer Metabolism by the Long Non-coding RNA CCAT2. Mol Cell 2016; 61:520-534. [PMID: 26853146 DOI: 10.1016/j.molcel.2016.01.015] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 10/23/2015] [Accepted: 01/08/2016] [Indexed: 12/31/2022]
Abstract
Altered energy metabolism is a cancer hallmark as malignant cells tailor their metabolic pathways to meet their energy requirements. Glucose and glutamine are the major nutrients that fuel cellular metabolism, and the pathways utilizing these nutrients are often altered in cancer. Here, we show that the long ncRNA CCAT2, located at the 8q24 amplicon on cancer risk-associated rs6983267 SNP, regulates cancer metabolism in vitro and in vivo in an allele-specific manner by binding the Cleavage Factor I (CFIm) complex with distinct affinities for the two subunits (CFIm25 and CFIm68). The CCAT2 interaction with the CFIm complex fine-tunes the alternative splicing of Glutaminase (GLS) by selecting the poly(A) site in intron 14 of the precursor mRNA. These findings uncover a complex, allele-specific regulatory mechanism of cancer metabolism orchestrated by the two alleles of a long ncRNA.
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Affiliation(s)
- Roxana S Redis
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luz E Vela
- Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Weiqin Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juliana Ferreira de Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-100, Brazil
| | - Cristina Ivan
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Douglas Adamoski
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-100, Brazil
| | - Barbara Pasculli
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yunyun Chen
- Department of Head & Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Agustin F Fernandez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo 33006, Spain
| | - Luis Valledor
- Department of Organisms and Systems Biology, University of Oviedo, Ovideo 33006, Spain
| | - Katrien Van Roosbroeck
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel Chang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maitri Shah
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Garrett Kinnebrew
- Department of Surgery, Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA
| | - Yaser Atlasi
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center, Rotterdam 3015, the Netherlands
| | - Lawrence H Cheung
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gilbert Y Huang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Paloma Monroig
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marc S Ramirez
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tina Catela Ivkovic
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Laboratory for Personalized Medicine, Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb 10000, Croatia
| | - Long Van
- Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roberta Gafà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara 44121, Italy
| | - Sanja Kapitanovic
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb 10000, Croatia
| | - Giovanni Lanza
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara 44121, Italy
| | - James A Bankson
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Huang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen Y Lai
- Department of Head & Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert C Bast
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael G Rosenblum
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Milan Radovich
- Department of Surgery, Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mircea Ivan
- Department of Medicine, Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Geoffrey Bartholomeusz
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Asturias 33424, Spain
| | - William R Widger
- Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ioana Berindan-Neagoe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, Cluj-Napoca 400012, Romania; Department of Functional Genomics, The Oncology Institute, Cluj-Napoca 400015, Romania
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andre L B Ambrosio
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-100, Brazil
| | - Sandra M Gomes Dias
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas 13083-100, Brazil
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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50
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Zong X, Nakagawa S, Freier SM, Fei J, Ha T, Prasanth SG, Prasanth KV. Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. Nucleic Acids Res 2016; 44:2898-908. [PMID: 26826711 PMCID: PMC4824109 DOI: 10.1093/nar/gkw047] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/17/2016] [Indexed: 01/09/2023] Open
Abstract
The RNase P-mediated endonucleolytic cleavage plays a crucial role in the 3′ end processing and cellular accumulation of MALAT1, a nuclear-retained long noncoding RNA that promotes malignancy. The regulation of this cleavage event is largely undetermined. Here we characterize a broadly expressed natural antisense transcript at the MALAT1 locus, designated as TALAM1, that positively regulates MALAT1 levels by promoting the 3′ end cleavage and maturation of MALAT1 RNA. TALAM1 RNA preferentially localizes at the site of transcription, and also interacts with MALAT1 RNA. Depletion of TALAM1 leads to defects in the 3′ end cleavage reaction and compromises cellular accumulation of MALAT1. Conversely, overexpression of TALAM1 facilitates the cleavage reaction in trans. Interestingly, TALAM1 is also positively regulated by MALAT1 at the level of both transcription and RNA stability. Together, our data demonstrate a novel feed-forward positive regulatory loop that is established to maintain the high cellular levels of MALAT1, and also unravel the existence of sense-antisense mediated regulatory mechanism for cellular lncRNAs that display RNase P-mediated 3′ end processing.
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Affiliation(s)
- Xinying Zong
- Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan
| | | | - Jingyi Fei
- Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA
| | - Taekjip Ha
- Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA
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