1
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Li YJ, Guo Q, Ye MS, Cai G, Xiao WF, Deng S, Xiao Y. YBX1 promotes type H vessel-dependent bone formation in an m5C-dependent manner. JCI Insight 2024; 9:e172345. [PMID: 38385749 PMCID: PMC11143935 DOI: 10.1172/jci.insight.172345] [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: 05/24/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024] Open
Abstract
RNA-binding proteins (RBPs) interact with RNA and ubiquitously regulate RNA transcripts during their life cycle, playing a fundamental role in the progression of angiogenesis-related diseases. In the skeletal system, endothelium-dependent angiogenesis is indispensable for bone formation. However, the role of RBPs in endothelium-dependent bone formation is unclear. Here, we show that RBP-Y-box-binding protein 1 (YBX1) was strongly reduced in the bone vasculature of ovariectomy (OVX) mice. Endothelial cell-specific deletion of Ybx1 impaired CD31-high, endomucin-high (CD31hiEMCNhi) endothelium morphology and resulted in low bone mass whereas Ybx1 overexpression promoted angiogenesis-dependent osteogenesis and ameliorated bone loss. Mechanistically, YBX1 deletion disrupted CD31, EMCN, and bone morphogenetic protein 4 (BMP4) stability in an m5C-dependent manner and blocked endothelium-derived BMP4 release, thereby inhibiting osteogenic differentiation of bone mesenchymal stromal cells. Administration of recombinant BMP4 protein restored impaired bone formation in Ybx1 deletion mice. Tail vein injection of CD31-modified polyethylene glycol-poly (lactic-co-glycolic acid) carrying sciadopitysin, a natural YBX1 agonist, pharmacologically partially reversed CD31hiEMCNhi vessels' decline and improved bone mass in both OVX and aging animals. These findings demonstrated the role of RBP-YBX1 in angiogenesis-dependent bone formation and provided a therapeutic approach for ameliorating osteoporosis.
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Affiliation(s)
- Yu-Jue Li
- Department of Endocrinology, Endocrinology Research Center
| | - Qi Guo
- Department of Endocrinology, Endocrinology Research Center
| | - Ming-Sheng Ye
- Department of Endocrinology, Endocrinology Research Center
| | - GuangPing Cai
- Department of Endocrinology, Endocrinology Research Center
| | | | - Sheng Deng
- Department of Pharmacy, Xiangya Hospital of Central South University, Changsha, China
| | - Ye Xiao
- Department of Endocrinology, Endocrinology Research Center
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2
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Martinelli M, Aguilar G, Lee DS, Kromer A, Nguyen N, Wilkins BJ, Akimova T, Beier UH, Ghanem LR. The poly(C)-binding protein Pcbp2 is essential for CD4 + T cell activation and proliferation. iScience 2022; 26:105860. [PMID: 36632062 PMCID: PMC9826892 DOI: 10.1016/j.isci.2022.105860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA-binding protein Pcbp2 is widely expressed in the innate and adaptive immune systems and is essential for mouse development. To determine whether Pcbp2 is required for CD4+ T cell development and function, we derived mice with conditional Pcbp2 deletion in CD4+ T cells and assessed their overall phenotype and proliferative responses to activating stimuli. We found that Pcbp2 is essential for T conventional cell (Tconv) proliferation, working through regulation of co-stimulatory signaling. Pcbp2 deficiency in the CD4+ lineage did not impact Treg abundance in vivo or function in vitro. In addition, our data demonstrate a clear association between Pcbp2 control of Runx1 exon 6 splicing in CD4+ T cells and a specific role for Pcbp2 in the maintenance of peripheral CD4+ lymphocyte population size. Last, we show that Pcbp2 function is required for optimal in vivo Tconv cell activation in a T cell adoptive transfer colitis model system.
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Affiliation(s)
- Massimo Martinelli
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Translational Medical Science, Section of Pediatrics, University of Naples “Federico II”, Naples 80131, Italy
| | - Gabrielle Aguilar
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David S.M. Lee
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Kromer
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nhu Nguyen
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Benjamin J. Wilkins
- Division of Anatomic Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tatiana Akimova
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ulf H. Beier
- Division of Nephrology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Louis R. Ghanem
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding author
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3
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RNA-Binding Proteins PCBP1 and PCBP2 Are Critical Determinants of Murine Erythropoiesis. Mol Cell Biol 2021; 41:e0066820. [PMID: 34180713 PMCID: PMC8384066 DOI: 10.1128/mcb.00668-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We previously demonstrated that the two paralogous RNA-binding proteins PCBP1 and PCBP2 are individually essential for mouse development: Pcbp1-null embryos are peri-implantation lethal, while Pcbp2-null embryos lose viability at midgestation. Midgestation Pcbp2-/- embryos revealed a complex phenotype that included loss of certain hematopoietic determinants. Whether PCBP2 directly contributes to erythropoietic differentiation and whether PCBP1 has a role in this process remained undetermined. Here, we selectively inactivated the genes encoding these two RNA-binding proteins during differentiation of the erythroid lineage in the developing mouse embryo. Individual inactivation of either locus failed to impact viability or blood formation. However, combined inactivation of the two loci resulted in midgestational repression of erythroid/hematopoietic gene expression, loss of blood formation, and fetal demise. Orthogonal ex vivo analyses of primary erythroid progenitors selectively depleted of these two RNA-binding proteins revealed that they mediate a combination of overlapping and isoform-specific impacts on hematopoietic lineage transcriptome, impacting both mRNA representation and exon splicing. These data lead us to conclude that PCBP1 and PCBP2 mediate functions critical to differentiation of the erythroid lineage.
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4
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Beckham SA, Matak MY, Belousoff MJ, Venugopal H, Shah N, Vankadari N, Elmlund H, Nguyen JHC, Semler BL, Wilce MCJ, Wilce JA. Structure of the PCBP2/stem-loop IV complex underlying translation initiation mediated by the poliovirus type I IRES. Nucleic Acids Res 2020; 48:8006-8021. [PMID: 32556302 PMCID: PMC7641305 DOI: 10.1093/nar/gkaa519] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/15/2020] [Accepted: 06/06/2020] [Indexed: 02/02/2023] Open
Abstract
The poliovirus type I IRES is able to recruit ribosomal machinery only in the presence of host factor PCBP2 that binds to stem-loop IV of the IRES. When PCBP2 is cleaved in its linker region by viral proteinase 3CD, translation initiation ceases allowing the next stage of replication to commence. Here, we investigate the interaction of PCBP2 with the apical region of stem-loop IV (SLIVm) of poliovirus RNA in its full-length and truncated form. CryoEM structure reconstruction of the full-length PCBP2 in complex with SLIVm solved to 6.1 Å resolution reveals a compact globular complex of PCBP2 interacting with the cruciform RNA via KH domains and featuring a prominent GNRA tetraloop. SEC-SAXS, SHAPE and hydroxyl-radical cleavage establish that PCBP2 stabilizes the SLIVm structure, but upon cleavage in the linker domain the complex becomes more flexible and base accessible. Limited proteolysis and REMSA demonstrate the accessibility of the linker region in the PCBP2/SLIVm complex and consequent loss of affinity of PCBP2 for the SLIVm upon cleavage. Together this study sheds light on the structural features of the PCBP2/SLIV complex vital for ribosomal docking, and the way in which this key functional interaction is regulated following translation of the poliovirus genome.
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Affiliation(s)
- Simone A Beckham
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Mehdi Y Matak
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Matthew J Belousoff
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Hariprasad Venugopal
- The Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Victoria 3800, Australia
| | - Neelam Shah
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Naveen Vankadari
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Hans Elmlund
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Joseph H C Nguyen
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697-4025, USA
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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5
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Wu Y, Chen H, Chen Y, Qu L, Zhang E, Wang Z, Wu Y, Yang R, Mao R, Lu C, Fan Y. HPV shapes tumor transcriptome by globally modifying the pool of RNA binding protein-binding motif. Aging (Albany NY) 2020; 11:2430-2446. [PMID: 31039132 PMCID: PMC6520004 DOI: 10.18632/aging.101927] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/19/2019] [Indexed: 12/15/2022]
Abstract
Human papillomavirus (HPV) positive head and neck cancer displayed specific transcription landscape but the underlying molecular mechanisms are not fully determined. Here, we interestingly found that HPV infection could globally elongate the 3’-untranslated regions (3’UTRs) in the majority of alternative polyadenylation (APA)-containing genes. Counterintuitively, the 3’UTR elongation does not affect their resident gene expression. Rather, they significantly increase the number of binding sites for RNA-binding proteins (RBPs) and subsequently upregulate a group of oncogenic genes by absorbing RBPs. A significant fraction of HPV affected genes are regulated through such mechanism that is 3’UTR-mediated recruitment of RBPs. As an example, we observed that HPV infection increases the length of 3’UTR of RBM25 transcript and hence recruits much more RNA binding protein including FUS and DGCR8. Consequently, in the absence of FUS and DGCR8 regulation, PD-1 was rescued and up-regulated after HPV infection. Taken together, our findings not only suggest a novel paradigm of how oncogenic viruses shape tumor transcriptome by modifying the 3’UTR, but also present a previously unrecognized layer of APA—RBP interplay in this molecular hierarchy. Modification of the pool of RBP-binding motif might expand our understandings into virus-associated carcinogenesis.
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Affiliation(s)
- Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Hao Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Yuyan Chen
- Department of Surgery, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Lishuai Qu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Erhao Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Zhou Wang
- School of Life Sciences, Nantong University, Jiangsu 226001, China
| | - Yuanyuan Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Riyun Yang
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Cuihua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China.,Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
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6
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α-Globin pre-mRNA splicing, revisited. Blood 2019; 133:2250-2251. [DOI: 10.1182/blood-2019-03-901108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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7
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A cytosine-rich splice regulatory determinant enforces functional processing of the human α-globin gene transcript. Blood 2019; 133:2338-2347. [PMID: 30833414 DOI: 10.1182/blood-2018-12-891408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/26/2019] [Indexed: 01/28/2023] Open
Abstract
The establishment of efficient and stable splicing patterns in terminally differentiated cells is critical to maintenance of specific functions throughout the lifespan of an organism. The human α-globin (hα-globin) gene contains 3 exons separated by 2 short introns. Naturally occurring α-thalassemia mutations that trigger aberrant splicing have revealed the presence of cryptic splice sites within the hα-globin gene transcript. How cognate (functional) splice sites are selectively used in lieu of these cryptic sites has remained unexplored. Here we demonstrate that the preferential selection of a cognate splice donor essential to functional splicing of the hα-globin transcript is dependent on the actions of an intronic cytosine (C)-rich splice regulatory determinant and its interacting polyC-binding proteins. Inactivation of this determinant by mutation of the C-rich element or by depletion of polyC-binding proteins triggers a dramatic shift in splice donor activity to an upstream, out-of-frame, cryptic donor. The essential role of the C-rich element in hα-globin gene expression is supported by its coevolution with the cryptic donor site in primate species. These data lead us to conclude that an intronic C-rich determinant enforces functional splicing of the hα-globin transcript, thus acting as an obligate determinant of hα-globin gene expression.
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8
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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9
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Ghanem LR, Kromer A, Silverman IM, Ji X, Gazzara M, Nguyen N, Aguilar G, Martinelli M, Barash Y, Liebhaber SA. Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript. Mol Cell Biol 2018; 38:e00175-18. [PMID: 29866654 PMCID: PMC6066754 DOI: 10.1128/mcb.00175-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/10/2018] [Accepted: 05/26/2018] [Indexed: 12/14/2022] Open
Abstract
Formation of the mammalian hematopoietic system is under a complex set of developmental controls. Here, we report that mouse embryos lacking the KH domain poly(C) binding protein, Pcbp2, are selectively deficient in the definitive erythroid lineage. Compared to wild-type controls, transcript splicing analysis of the Pcbp2-/- embryonic liver reveals accentuated exclusion of an exon (exon 6) that encodes a highly conserved transcriptional control segment of the hematopoietic master regulator, Runx1. Embryos rendered homozygous for a Runx1 locus lacking this cassette exon (Runx1ΔE6) effectively phenocopy the loss of the definitive erythroid lineage in Pcbp2-/- embryos. These data support a model in which enhancement of Runx1 cassette exon 6 inclusion by Pcbp2 serves a critical role in development of hematopoietic progenitors and constitutes a critical step in the developmental pathway of the definitive erythropoietic lineage.
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Affiliation(s)
- Louis R Ghanem
- Gastroenterology, Hepatology and Nutrition Division, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew Kromer
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian M Silverman
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xinjun Ji
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew Gazzara
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nhu Nguyen
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gabrielle Aguilar
- Gastroenterology, Hepatology and Nutrition Division, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Massimo Martinelli
- Gastroenterology, Hepatology and Nutrition Division, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen A Liebhaber
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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10
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Ji X, Humenik J, Yang D, Liebhaber SA. PolyC-binding proteins enhance expression of the CDK2 cell cycle regulatory protein via alternative splicing. Nucleic Acids Res 2018; 46:2030-2044. [PMID: 29253178 PMCID: PMC5829739 DOI: 10.1093/nar/gkx1255] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/01/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Abstract
The PolyC binding proteins (PCBPs) impact alternative splicing of a subset of mammalian genes that are enriched in basic cellular functions. Here, we focus our analysis on PCBP-controlled cassette exon-splicing within the cell cycle control regulator cyclin-dependent kinase-2 (CDK2) transcript. We demonstrate that PCBP binding to a C-rich polypyrimidine tract (PPT) preceding exon 5 of the CDK2 transcript enhances cassette exon inclusion. This splice enhancement is U2AF65-independent and predominantly reflects actions of the PCBP1 isoform. Remarkably, PCBPs' control of CDK2 ex5 splicing has evolved subsequent to mammalian divergence via conversion of constitutive exon 5 inclusion in the mouse CDK2 transcript to PCBP-responsive exon 5 alternative splicing in humans. Importantly, exclusion of exon 5 from the hCDK2 transcript dramatically represses the expression of CDK2 protein with a corresponding perturbation in cell cycle kinetics. These data highlight a recently evolved post-transcriptional pathway in primate species with the potential to modulate cell cycle control.
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Affiliation(s)
- Xinjun Ji
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jesse Humenik
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daphne Yang
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen A Liebhaber
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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11
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Howley BV, Howe PH. TGF-beta signaling in cancer: post-transcriptional regulation of EMT via hnRNP E1. Cytokine 2018; 118:19-26. [PMID: 29396052 DOI: 10.1016/j.cyto.2017.12.032] [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] [Received: 12/20/2017] [Accepted: 12/29/2017] [Indexed: 12/12/2022]
Abstract
The TGFβ signaling pathway is a critical regulator of cancer progression in part through induction of the epithelial to mesenchymal transition (EMT). This process is aberrantly activated in cancer cells, facilitating invasion of the basement membrane, survival in the circulatory system, and dissemination to distant organs. The mechanisms through which epithelial cells transition to a mesenchymal state involve coordinated transcriptional and post-transcriptional control of gene expression. One such mechanism of control is through the RNA binding protein hnRNP E1, which regulates splicing and translation of a cohort of EMT and stemness-associated transcripts. A growing body of evidence indicates a major role for hnRNP E1 in the control of epithelial cell plasticity, especially in the context of carcinoma progression. Here, we review the multiple mechanisms through which hnRNP E1 functions to control EMT and metastatic progression.
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Affiliation(s)
- Breege V Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
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12
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Moradi S, Sharifi-Zarchi A, Ahmadi A, Mollamohammadi S, Stubenvoll A, Günther S, Salekdeh GH, Asgari S, Braun T, Baharvand H. Small RNA Sequencing Reveals Dlk1-Dio3 Locus-Embedded MicroRNAs as Major Drivers of Ground-State Pluripotency. Stem Cell Reports 2017; 9:2081-2096. [PMID: 29129685 PMCID: PMC5785679 DOI: 10.1016/j.stemcr.2017.10.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 10/11/2017] [Accepted: 10/11/2017] [Indexed: 11/26/2022] Open
Abstract
Ground-state pluripotency is a cell state in which pluripotency is established and maintained through efficient repression of endogenous differentiation pathways. Self-renewal and pluripotency of embryonic stem cells (ESCs) are influenced by ESC-associated microRNAs (miRNAs). Here, we provide a comprehensive assessment of the “miRNome” of ESCs cultured under conditions favoring ground-state pluripotency. We found that ground-state ESCs express a distinct set of miRNAs compared with ESCs grown in serum. Interestingly, most “ground-state miRNAs” are encoded by an imprinted region on chromosome 12 within the Dlk1-Dio3 locus. Functional analysis revealed that ground-state miRNAs embedded in the Dlk1-Dio3 locus (miR-541-5p, miR-410-3p, and miR-381-3p) promoted pluripotency via inhibition of multi-lineage differentiation and stimulation of self-renewal. Overall, our results demonstrate that ground-state pluripotency is associated with a unique miRNA signature, which supports ground-state self-renewal by suppressing differentiation. Ground-state pluripotency is associated with a unique miRNA signature Dlk1-Dio3 locus on 12qF1 encodes the majority of ground-state miRNAs Dlk1-Dio3 locus is hypomethylated in ground-state ESCs Ground-state miRNAs promote ESC self-renewal and inhibit differentiation
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Affiliation(s)
- Sharif Moradi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran 1665659911, Iran; Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran 1665659911, Iran; Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Amirhossein Ahmadi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran 1665659911, Iran
| | - Sepideh Mollamohammadi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran 1665659911, Iran
| | - Alexander Stubenvoll
- Max-Planck Institute for Heart and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
| | - Stefan Günther
- Max-Planck Institute for Heart and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstrasse 43, 61231 Bad Nauheim, Germany
| | - Ghasem Hosseini Salekdeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran 1665659911, Iran
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Thomas Braun
- Max-Planck Institute for Heart and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstrasse 43, 61231 Bad Nauheim, Germany.
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem Square, Banihashem Street, Ressalat Highway, Tehran 1665659911, Iran; Department of Developmental Biology, University of Science and Culture, Tehran, Iran.
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13
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Mendoza-Viveros L, Bouchard-Cannon P, Hegazi S, Cheng AH, Pastore S, Cheng HYM. Molecular modulators of the circadian clock: lessons from flies and mice. Cell Mol Life Sci 2017; 74:1035-1059. [PMID: 27689221 PMCID: PMC11107503 DOI: 10.1007/s00018-016-2378-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/03/2016] [Accepted: 09/22/2016] [Indexed: 12/16/2022]
Abstract
Circadian timekeeping is a ubiquitous mechanism that enables organisms to maintain temporal coordination between internal biological processes and time of the local environment. The molecular basis of circadian rhythms lies in a set of transcription-translation feedback loops (TTFLs) that drives the rhythmic transcription of core clock genes, whose level and phase of expression serve as the marker of circadian time. However, it has become increasingly evident that additional regulatory mechanisms impinge upon the TTFLs to govern the properties and behavior of the circadian clock. Such mechanisms include changes in chromatin architecture, interactions with other transcription factor networks, post-transcriptional control by RNA modifications, alternative splicing and microRNAs, and post-translational regulation of subcellular trafficking and protein degradation. In this review, we will summarize the current knowledge of circadian clock regulation-from transcriptional to post-translational-drawing from literature pertaining to the Drosophila and murine circadian systems.
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Affiliation(s)
- Lucia Mendoza-Viveros
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Pascale Bouchard-Cannon
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Sara Hegazi
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Arthur H Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Stephen Pastore
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON, L5L 1C6, Canada.
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada.
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Ji X, Park JW, Bahrami-Samani E, Lin L, Duncan-Lewis C, Pherribo G, Xing Y, Liebhaber SA. αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome. Nucleic Acids Res 2016; 44:2283-97. [PMID: 26896798 PMCID: PMC4797308 DOI: 10.1093/nar/gkw088] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 02/03/2016] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS) is a robust generator of mammalian transcriptome complexity. Splice site specification is controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. These interactions are frequently localized to the intronic U-rich polypyrimidine tracts (PPT) located 5′ to the majority of splice acceptor junctions. αCPs (also referred to as polyC-binding proteins (PCBPs) and hnRNPEs) comprise a subset of KH-domain proteins with high affinity and specificity for C-rich polypyrimidine motifs. Here, we demonstrate that αCPs promote the splicing of a defined subset of cassette exons via binding to a C-rich subset of polypyrimidine tracts located 5′ to the αCP-enhanced exonic segments. This enhancement of splice acceptor activity is linked to interactions of αCPs with the U2 snRNP complex and may be mediated by cooperative interactions with the canonical polypyrimidine tract binding protein, U2AF65. Analysis of αCP-targeted exons predicts a substantial impact on fundamental cell functions. These findings lead us to conclude that the αCPs play a direct and global role in modulating the splicing activity and inclusion of an array of cassette exons, thus driving a novel pathway of splice site regulation within the mammalian transcriptome.
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Affiliation(s)
- Xinjun Ji
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lan Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher Duncan-Lewis
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gordon Pherribo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen A Liebhaber
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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15
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The Poly(C) Binding Protein Pcbp2 and Its Retrotransposed Derivative Pcbp1 Are Independently Essential to Mouse Development. Mol Cell Biol 2015; 36:304-19. [PMID: 26527618 DOI: 10.1128/mcb.00936-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 10/28/2015] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins participate in a complex array of posttranscriptional controls essential to cell type specification and somatic development. Despite their detailed biochemical characterizations, the degree to which each RNA-binding protein impacts mammalian embryonic development remains incompletely defined, and the level of functional redundancy among subsets of these proteins remains open to question. The poly(C) binding proteins, PCBPs (αCPs and hnRNP E proteins), are encoded by a highly conserved and broadly expressed gene family. The two major Pcbp isoforms, Pcbp2 and Pcbp1, are robustly expressed in a wide range of tissues and exert both nuclear and cytoplasmic controls over gene expression. Here, we report that Pcbp1-null embryos are rendered nonviable in the peri-implantation stage. In contrast, Pcbp2-null embryos undergo normal development until midgestation (12.5 to 13.5 days postcoitum), at which time they undergo a dramatic loss in viability associated with combined cardiovascular and hematopoietic abnormalities. Mice heterozygous for either Pcbp1 or Pcbp2 null alleles display a mild and nondisruptive defect in initial postpartum weight gain. These data reveal that Pcbp1 and Pcbp2 are individually essential for mouse embryonic development and have distinct impacts on embryonic viability and that Pcpb2 has a nonredundant in vivo role in hematopoiesis. These data further provide direct evidence that Pcbp1, a retrotransposed derivative of Pcpb2, has evolved an essential function(s) in the mammalian genome.
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16
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Grabek KR, Diniz Behn C, Barsh GS, Hesselberth JR, Martin SL. Enhanced stability and polyadenylation of select mRNAs support rapid thermogenesis in the brown fat of a hibernator. eLife 2015; 4. [PMID: 25626169 PMCID: PMC4383249 DOI: 10.7554/elife.04517] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/23/2014] [Indexed: 12/21/2022] Open
Abstract
During hibernation, animals cycle between torpor and arousal. These cycles involve
dramatic but poorly understood mechanisms of dynamic physiological regulation at the
level of gene expression. Each cycle, Brown Adipose Tissue (BAT) drives periodic
arousal from torpor by generating essential heat. We applied digital transcriptome
analysis to precisely timed samples to identify molecular pathways that underlie the
intense activity cycles of hibernator BAT. A cohort of transcripts increased during
torpor, paradoxical because transcription effectively ceases at these low
temperatures. We show that this increase occurs not by elevated transcription but
rather by enhanced stabilization associated with maintenance and/or extension of long
poly(A) tails. Mathematical modeling further supports a temperature-sensitive
mechanism to protect a subset of transcripts from ongoing bulk degradation instead of
increased transcription. This subset was enriched in a C-rich motif and genes
required for BAT activation, suggesting a model and mechanism to prioritize
translation of key proteins for thermogenesis. DOI:http://dx.doi.org/10.7554/eLife.04517.001 Many mammals hibernate to avoid food scarcity and harsh conditions during winter.
Hibernation involves entering a state called torpor, which drastically reduces the
amount of energy used by the body. During torpor, body temperature also decreases.
This is particularly exemplified in ground squirrels, whose body temperature can
hover at just above or even below the point of freezing. However, hibernating mammals
cannot remain in this state continuously over the months of hibernation but instead
cycle between bouts of torpor lasting for 1–3 weeks and brief periods of
‘arousal’ lasting between 12–24 hr, during which their body
rapidly warms up. The heat required to start warming up the hibernator is generated from a specialized
form of fat called brown adipose tissue. Normally, the bursts of metabolic activity
that are required to create this heat depend on certain proteins being produced.
Making a protein involves ‘translating’ its sequence from template
molecules called messenger RNA (mRNA), which are ‘transcribed’ from the
gene that encodes the protein. During the low body temperatures experienced during
torpor, both of these processes stop. So how is the hibernator able to quickly and
efficiently heat itself up during the arousal periods of hibernation? Grabek et al. investigated this by analyzing the relative levels of mRNA in the brown
adipose tissue of hibernating 13-lined ground squirrels. Using a special technique to
sample and sequence small fragments of mRNA taken from brown adipose tissue, Grabek
et al. compiled a profile of the mRNA molecules present at different points in the
torpor–arousal cycle and compared this with a similar profile taken from
squirrels that were not hibernating. From this analysis, Grabek et al. detected that a particular group of mRNA molecules
that are required for producing heat increase in abundance during torpor, even though
body temperature is low enough to stop gene transcription. This increased abundance
does not occur because more of the mRNA molecules are made; instead, the mRNA
molecules are modified to become more stable and long lasting. Once the animal warms
up during arousal, gene transcription is reactivated and more new mRNA molecules are
made. Grabek et al. suggest that the key mRNAs required for brown adipose tissue function
are selectively stabilized during torpor through a temperature-dependent protective
mechanism. These mRNAs are then preferentially translated into proteins during
arousal to rapidly and efficiently heat the hibernator. Most other mRNA molecules
degrade throughout torpor, and so their numbers decline as replacements are not
transcribed until body temperature briefly recovers during arousal. Whether this
protective mechanism is also used in other tissues during torpor remains a question
for future work. DOI:http://dx.doi.org/10.7554/eLife.04517.002
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Affiliation(s)
- Katharine R Grabek
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Cecilia Diniz Behn
- Department of Applied Math and Statistics, Colorado School of Mines, Golden, United States
| | - Gregory S Barsh
- Department of Research, HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - Jay R Hesselberth
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Sandra L Martin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
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17
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An improved poly(A) motifs recognition method based on decision level fusion. Comput Biol Chem 2014; 54:49-56. [PMID: 25594576 DOI: 10.1016/j.compbiolchem.2014.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/27/2014] [Accepted: 12/27/2014] [Indexed: 01/07/2023]
Abstract
Polyadenylation is the process of addition of poly(A) tail to mRNA 3' ends. Identification of motifs controlling polyadenylation plays an essential role in improving genome annotation accuracy and better understanding of the mechanisms governing gene regulation. The bioinformatics methods used for poly(A) motifs recognition have demonstrated that information extracted from sequences surrounding the candidate motifs can differentiate true motifs from the false ones greatly. However, these methods depend on either domain features or string kernels. To date, methods combining information from different sources have not been found yet. Here, we proposed an improved poly(A) motifs recognition method by combing different sources based on decision level fusion. First of all, two novel prediction methods was proposed based on support vector machine (SVM): one method is achieved by using the domain-specific features and principle component analysis (PCA) method to eliminate the redundancy (PCA-SVM); the other method is based on Oligo string kernel (Oligo-SVM). Then we proposed a novel machine-learning method for poly(A) motif prediction by marrying four poly(A) motifs recognition methods, including two state-of-the-art methods (Random Forest (RF) and HMM-SVM), and two novel proposed methods (PCA-SVM and Oligo-SVM). A decision level information fusion method was employed to combine the decision values of different classifiers by applying the DS evidence theory. We evaluated our method on a comprehensive poly(A) dataset that consists of 14,740 samples on 12 variants of poly(A) motifs and 2750 samples containing none of these motifs. Our method has achieved accuracy up to 86.13%. Compared with the four classifiers, our evidence theory based method reduces the average error rate by about 30%, 27%, 26% and 16%, respectively. The experimental results suggest that the proposed method is more effective for poly(A) motif recognition.
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18
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Cui Z, Xu Q, Wang X. Regulation of the circadian clock through pre-mRNA splicing in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1973-80. [PMID: 24604736 DOI: 10.1093/jxb/eru085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Alternative splicing plays an important role in regulating gene functions and enhancing the diversity of the proteome in plants. Most of the genes are interrupted by introns in Arabidopsis. More than half of the intron-split genes involved in multiple biological processes including the circadian clock are alternatively spliced. In this review, we focus on the involvement of alternative splicing in the regulation of the circadian clock.
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Affiliation(s)
- Zhibo Cui
- Rice Research Institute; Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture; Key Laboratory of Northern Japonica Super Rice Breeding, Ministry of Education; Shenyang Agricultural University, Shenyang 110866, China
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19
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Specific enrichment of the RNA-binding proteins PCBP1 and PCBP2 in chief cells of the murine gastric mucosa. Gene Expr Patterns 2014; 14:78-87. [PMID: 24480778 DOI: 10.1016/j.gep.2014.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 12/31/2013] [Accepted: 01/20/2014] [Indexed: 01/05/2023]
Abstract
RNA-binding proteins and corresponding post-transcriptional controls play critical roles in gene expression. The poly-(C) binding proteins, PCBPs (αCPs, hnRNPEs), comprise a well-characterized family of abundant RNA-binding proteins that impact on RNA processing in the nucleus as well as mRNA stability and translation in the cytoplasm. Here we demonstrate that PCBP1 and PCBP2 are abundantly expressed in the gastric epithelium with prominent enrichment in specific cell types within the gastric glandular mucosa. The spatial and intracellular patterns of PCBP1 and PCBP2 expression in these regions are highly correlated. Remarkably, we observe that these proteins are present in the nuclear and cytoplasmic compartments of zymogenic chief cells while they are restricted to the nuclear compartment in acid-secreting parietal cells and poorly expressed in pit cells that line the gland exit. This specificity of expression patterns and subcellular localization of PCBP1 and PCBP2, along with their appearance in the precursor tissues of the gastric epithelium during early postnatal development, suggests these RNA-binding proteins play specific roles in cell differentiation and organismal development within the gastric glandular epithelium.
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20
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Bebee TW, Cieply BW, Carstens RP. Genome-wide activities of RNA binding proteins that regulate cellular changes in the epithelial to mesenchymal transition (EMT). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:267-302. [PMID: 25201109 DOI: 10.1007/978-1-4939-1221-6_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The epithelial to mesenchymal transition (EMT) and reverse mesenchymal to epithelial transition (MET) are developmentally conserved processes that are essential for patterning of developing embryos and organs. The EMT/MET are further utilized in wound healing, but they can also be hijacked by cancer cells to promote tumor progression and metastasis. The molecular pathways governing these processes have historically focused on the transcriptional regulation and networks that control them. Indeed, global profiling of transcriptional changes has provided a wealth of information into how these networks are regulated, the downstream targets, and functional consequence of alterations to the global transcriptome. However, recent evidence has revealed that the posttranscriptional landscape of the cell is also dramatically altered during the EMT/MET and contributes to changes in cell behavior and phenotypes. While studies of this aspect of EMT biology are still in their infancy, recent progress has been achieved by the identification of several RNA binding proteins (RBPs) that regulate splicing, polyadenylation, mRNA stability, and translational control during EMT. This chapter focuses on the global impact of RBPs that regulate mRNA maturation as well as outlines the functional impact of several key posttranscriptional changes during the EMT. The growing evidence of RBP involvement in the cellular transformation during EMT underscores that a coordinated regulation of both transcriptional and posttranscriptional changes is essential for EMT. Furthermore, new discoveries into these events will paint a more detailed picture of the transcriptome during the EMT/MET and provide novel molecular targets for treatment of human diseases.
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Affiliation(s)
- Thomas W Bebee
- Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
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21
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Zheng D, Tian B. RNA-binding proteins in regulation of alternative cleavage and polyadenylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:97-127. [PMID: 25201104 DOI: 10.1007/978-1-4939-1221-6_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Almost all eukaryotic pre-mRNAs are processed at the 3' end by the cleavage and polyadenylation (C/P) reaction, which preludes termination of transcription and gives rise to the poly(A) tail of mature mRNA. Genomic studies in recent years have indicated that most eukaryotic mRNA genes have multiple cleavage and polyadenylation sites (pAs), leading to alternative cleavage and polyadenylation (APA) products. APA isoforms generally differ in their 3' untranslated regions (3' UTRs), but can also have different coding sequences (CDSs). APA expands the repertoire of transcripts expressed from the genome, and is highly regulated under various physiological and pathological conditions. Growing lines of evidence have shown that RNA-binding proteins (RBPs) play important roles in regulation of APA. Some RBPs are part of the machinery for C/P; others influence pA choice through binding to adjacent regions. In this chapter, we review cis elements and trans factors involved in C/P, the significance of APA, and increasingly elucidated roles of RBPs in APA regulation. We also discuss analysis of APA using transcriptome-wide techniques as well as molecular biology approaches.
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Affiliation(s)
- Dinghai Zheng
- Department of Biochemistry and Molecular Biology, University of Medicine and Dentistry of New Jersey (UMDNJ)-New Jersey Medical School, 185 South Orange Ave., Newark, NJ, 07103, USA
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22
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Tuck AC, Tollervey D. A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 2013; 154:996-1009. [PMID: 23993093 PMCID: PMC3778888 DOI: 10.1016/j.cell.2013.07.047] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/25/2013] [Accepted: 07/31/2013] [Indexed: 01/30/2023]
Abstract
Eukaryotic genomes generate a heterogeneous ensemble of mRNAs and long noncoding RNAs (lncRNAs). LncRNAs and mRNAs are both transcribed by Pol II and acquire 5′ caps and poly(A) tails, but only mRNAs are translated into proteins. To address how these classes are distinguished, we identified the transcriptome-wide targets of 13 RNA processing, export, and turnover factors in budding yeast. Comparing the maturation pathways of mRNAs and lncRNAs revealed that transcript fate is largely determined during 3′ end formation. Most lncRNAs are targeted for nuclear RNA surveillance, but a subset with 3′ cleavage and polyadenylation features resembling the mRNA consensus can be exported to the cytoplasm. The Hrp1 and Nab2 proteins act at this decision point, with dual roles in mRNA cleavage/polyadenylation and lncRNA surveillance. Our data also reveal the dynamic and heterogeneous nature of mRNA maturation, and highlight a subset of “lncRNA-like” mRNAs regulated by the nuclear surveillance machinery. Transcriptome-wide analysis shows dynamic assembly of ribonucleoprotein particles LncRNA and mRNA subclasses undergo distinct maturation and turnover pathways Transcript fate is determined during 3′ end formation Transcript classes overlap, with many “mRNA-like” lncRNAs and “lncRNA-like” mRNAs
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Affiliation(s)
- Alex Charles Tuck
- The University of Edinburgh, Wellcome Trust Centre for Cell Biology, Michael Swann Building, Kings Buildings, Edinburgh EH9 3JR, UK
| | - David Tollervey
- The University of Edinburgh, Wellcome Trust Centre for Cell Biology, Michael Swann Building, Kings Buildings, Edinburgh EH9 3JR, UK.
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23
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Functions of heterogeneous nuclear ribonucleoproteins in stem cell potency and differentiation. BIOMED RESEARCH INTERNATIONAL 2013; 2013:623978. [PMID: 23984388 PMCID: PMC3745930 DOI: 10.1155/2013/623978] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 12/26/2022]
Abstract
Stem cells possess huge importance in developmental biology, disease modelling, cell replacement therapy, and tissue engineering in regenerative medicine because they have the remarkable potential for self-renewal and to differentiate into almost all the cell types in the human body. Elucidation of molecular mechanisms regulating stem cell potency and differentiation is essential and critical for extensive application. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are modular proteins consisting of RNA-binding motifs and auxiliary domains characterized by extensive and divergent functions in nucleic acid metabolism. Multiple roles of hnRNPs in transcriptional and posttranscriptional regulation enable them to be effective gene expression regulators. More recent findings show that hnRNP proteins are crucial factors implicated in maintenance of stem cell self-renewal and pluripotency and cell differentiation. The hnRNPs interact with certain sequences in target gene promoter regions to initiate transcription. In addition, they recognize 3′UTR or 5′UTR of specific gene mRNA forming mRNP complex to regulate mRNA stability and translation. Both of these regulatory pathways lead to modulation of gene expression that is associated with stem cell proliferation, cell cycle control, pluripotency, and committed differentiation.
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24
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αCP Poly(C) binding proteins act as global regulators of alternative polyadenylation. Mol Cell Biol 2013; 33:2560-73. [PMID: 23629627 DOI: 10.1128/mcb.01380-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We have previously demonstrated that the KH-domain protein αCP binds to a 3' untranslated region (3'UTR) C-rich motif of the nascent human alpha-globin (hα-globin) transcript and enhances the efficiency of 3' processing. Here we assess the genome-wide impact of αCP RNA-protein (RNP) complexes on 3' processing with a specific focus on its role in alternative polyadenylation (APA) site utilization. The major isoforms of αCP were acutely depleted from a human hematopoietic cell line, and the impact on mRNA representation and poly(A) site utilization was determined by direct RNA sequencing (DRS). Bioinformatic analysis revealed 357 significant alterations in poly(A) site utilization that could be specifically linked to the αCP depletion. These APA events correlated strongly with the presence of C-rich sequences in close proximity to the impacted poly(A) addition sites. The most significant linkage was the presence of a C-rich motif within a window 30 to 40 bases 5' to poly(A) signals (AAUAAA) that were repressed upon αCP depletion. This linkage is consistent with a general role for αCPs as enhancers of 3' processing. These findings predict a role for αCPs in posttranscriptional control pathways that can alter the coding potential and/or levels of expression of subsets of mRNAs in the mammalian transcriptome.
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25
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Sendler E, Johnson GD, Mao S, Goodrich RJ, Diamond MP, Hauser R, Krawetz SA. Stability, delivery and functions of human sperm RNAs at fertilization. Nucleic Acids Res 2013; 41:4104-17. [PMID: 23471003 PMCID: PMC3627604 DOI: 10.1093/nar/gkt132] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Increasing attention has focused on the significance of RNA in sperm, in light of its contribution to the birth and long-term health of a child, role in sperm function and diagnostic potential. As the composition of sperm RNA is in flux, assigning specific roles to individual RNAs presents a significant challenge. For the first time RNA-seq was used to characterize the population of coding and non-coding transcripts in human sperm. Examining RNA representation as a function of multiple methods of library preparation revealed unique features indicative of very specific and stage-dependent maturation and regulation of sperm RNA, illuminating their various transitional roles. Correlation of sperm transcript abundance with epigenetic marks suggested roles for these elements in the pre- and post-fertilization genome. Several classes of non-coding RNAs including lncRNAs, CARs, pri-miRNAs, novel elements and mRNAs have been identified which, based on factors including relative abundance, integrity in sperm, available knockout data of embryonic effect and presence or absence in the unfertilized human oocyte, are likely to be essential male factors critical to early post-fertilization development. The diverse and unique attributes of sperm transcripts that were revealed provides the first detailed analysis of the biology and anticipated clinical significance of spermatozoal RNAs.
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Affiliation(s)
- Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
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26
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Papic N, Maxwell CI, Delker DA, Liu S, Heale BSE, Hagedorn CH. RNA-sequencing analysis of 5' capped RNAs identifies many new differentially expressed genes in acute hepatitis C virus infection. Viruses 2012; 4:581-612. [PMID: 22590687 PMCID: PMC3347324 DOI: 10.3390/v4040581] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/31/2012] [Accepted: 04/03/2012] [Indexed: 12/28/2022] Open
Abstract
We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. We identified 100, 684, and 1,844 significantly differentially expressed annotated genes in acutely infected proliferative Huh 7.5 cells at 6, 48, and 72 hours, respectively (fold change ≥ 1.5 and Bonferroni adjusted p-values < 0.05). Most of the differentially expressed genes (>80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. These genes are critical components of host immune, inflammatory and oncogenic pathways and provide new information regarding changes that may benefit the virus or mediate HCV induced pathology. RNAi knockdown studies of newly identified highly upregulated FUT1 and KLHDC7B genes provide evidence that their gene products regulate and facilitate HCV replication in hepatocytes. Our approach also identified novel Pol II unannotated transcripts that were upregulated. Results further identify new pathways that regulate HCV replication in hepatocytes and suggest that our approach will have general applications in studying viral-host interactions in model systems and clinical biospecimens.
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Affiliation(s)
- Neven Papic
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Christopher I. Maxwell
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
- Huntsman Cancer Institute, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
| | - Don A. Delker
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Shuanghu Liu
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Bret S. E. Heale
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Curt H. Hagedorn
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
- Department of Experimental Pathology, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-801-587-4619; Fax: +1-801-585-0187
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Yoga YMK, Traore DAK, Sidiqi M, Szeto C, Pendini NR, Barker A, Leedman PJ, Wilce JA, Wilce MCJ. Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides. Nucleic Acids Res 2012; 40:5101-14. [PMID: 22344691 PMCID: PMC3367169 DOI: 10.1093/nar/gks058] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, we analyse the contributions of individual αCP1 KH domains to binding C-rich oligonucleotides using biophysical and structural methods. Using surface plasmon resonance (SPR), we demonstrate that KH1 makes the most stable interactions with both RNA and DNA, KH3 binds with intermediate affinity and KH2 only interacts detectibly with DNA. The crystal structure of KH1 bound to a 5′-CCCTCCCT-3′ DNA sequence shows a 2:1 protein:DNA stoichiometry and demonstrates a molecular arrangement of KH domains bound to immediately adjacent oligonucleotide target sites. SPR experiments, with a series of poly-C-sequences reveals that cytosine is preferred at all four positions in the oligonucleotide binding cleft and that a C-tetrad binds KH1 with 10 times higher affinity than a C-triplet. The basis for this high affinity interaction is finally detailed with the structure determination of a KH1.W.C54S mutant bound to 5′-ACCCCA-3′ DNA sequence. Together, these data establish the lead role of KH1 in oligonucleotide binding by αCP1 and reveal the molecular basis of its specificity for a C-rich tetrad.
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Affiliation(s)
- Yano M K Yoga
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia
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28
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Di Giammartino DC, Nishida K, Manley JL. Mechanisms and consequences of alternative polyadenylation. Mol Cell 2011; 43:853-66. [PMID: 21925375 DOI: 10.1016/j.molcel.2011.08.017] [Citation(s) in RCA: 544] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/02/2011] [Accepted: 08/09/2011] [Indexed: 12/11/2022]
Abstract
Alternative polyadenylation (APA) is emerging as a widespread mechanism used to control gene expression. Like alternative splicing, usage of alternative poly(A) sites allows a single gene to encode multiple mRNA transcripts. In some cases, this changes the mRNA coding potential; in other cases, the code remains unchanged but the 3' UTR length is altered, influencing the fate of mRNAs in several ways, for example, by altering the availability of RNA binding protein sites and microRNA binding sites. The mechanisms governing both global and gene-specific APA are only starting to be deciphered. Here we review what is known about these mechanisms and the functional consequences of alternative polyadenylation.
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