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Gorjifard S, Jores T, Tonnies J, Mueth NA, Bubb K, Wrightsman T, Buckler ES, Fields S, Cuperus JT, Queitsch C. Arabidopsis and Maize Terminator Strength is Determined by GC Content, Polyadenylation Motifs and Cleavage Probability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.16.545379. [PMID: 37398426 PMCID: PMC10312805 DOI: 10.1101/2023.06.16.545379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The 3' end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.
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Affiliation(s)
- Sayeh Gorjifard
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Graduate Program in Biology, University of Washington, Seattle, WA 98195
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Kerry Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
- Department of Medicine, University of Washington, Seattle, WA 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195
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Masoumzadeh E, Grozdanov PN, Jetly A, MacDonald CC, Latham MP. Electrostatic Interactions between CSTF2 and pre-mRNA Drive Cleavage and Polyadenylation. Biophys J 2022; 121:607-619. [PMID: 35090899 PMCID: PMC8873925 DOI: 10.1016/j.bpj.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 11/25/2022] Open
Abstract
Nascent pre-mRNA 3'-end cleavage and polyadenylation (C/P) involves numerous proteins that recognize multiple RNA elements. Human CSTF2 binds to a downstream U- or G/U-rich sequence through its RNA recognition motif (RRM) regulating C/P. We previously reported the only known disease-related CSTF2 RRM mutant (CSTF2D50A) and showed that it changed the on-rate of RNA binding, leading to alternative polyadenylation in brains of mice carrying the same mutation. In this study, we further investigated the role of electrostatic interactions in the thermodynamics and kinetics of RNA binding for the CSTF2 RRM and the downstream consequences for regulation of C/P. By combining mutagenesis with NMR spectroscopy and biophysical assays, we confirmed that electrostatic attraction is the dominant factor in RRM binding to a naturally occurring U-rich RNA sequence. Moreover, we demonstrate that RNA binding is accompanied by an enthalpy-entropy compensation mechanism that is supported by changes in pico-to-nanosecond timescale RRM protein dynamics. We suggest that the dynamic binding of the RRM to U-rich RNA supports the diversity of sequences it encounters in the nucleus. Lastly, in vivo C/P assays demonstrate a competition between fast, high affinity RNA binding and efficient, correct C/P. These results highlight the importance of the surface charge of the RRM in RNA binding and the balance between nascent mRNA binding and C/P in vivo.
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Alternative polyadenylation: An untapped source for prostate cancer biomarkers and therapeutic targets? Asian J Urol 2021; 8:407-415. [PMID: 34765448 PMCID: PMC8566364 DOI: 10.1016/j.ajur.2021.05.014] [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: 11/10/2020] [Revised: 03/20/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
Objective To review alternative polyadenylation (APA) as a mechanism of gene regulation and consider potential roles for APA in prostate cancer (PCa) biology and treatment. Methods An extensive review of mRNA polyadenylation, APA, and PCa literature was performed. This review article introduces APA and its association with human disease, outlines the mechanisms and components of APA, reviews APA in cancer biology, and considers whether APA may contribute to PCa progression and/or produce novel biomarkers and therapeutic targets for PCa. Results Eukaryotic mRNA 3′-end cleavage and polyadenylation play a critical role in gene expression. Most human genes encode more than one polyadenylation signal, and produce more than one transcript isoform, through APA. Polyadenylation can occur throughout the gene body to generate transcripts with differing 3′-termini and coding sequence. Differences in 3′-untranslated regions length can modify post-transcriptional gene regulation by microRNAs and RNA binding proteins, and alter mRNA stability, translation efficiency, and subcellular localization. Distinctive APA patterns are associated with human diseases, tissue origins, and changes in cellular proliferation rate and differentiation state. APA events may therefore generate unique mRNA biomarkers or therapeutic targets in certain cancer types or phenotypic states. Conclusions The full extent of cancer-associated and tissue-specific APA events have yet to be defined, and the mechanisms and functional consequences of APA in cancer remain incompletely understood. There is evidence that APA is active in PCa, and that it may be an untapped resource for PCa biomarkers or therapeutic targets.
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Yang W, Hsu PL, Yang F, Song JE, Varani G. Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals. Nucleic Acids Res 2019; 46:493-503. [PMID: 29186539 PMCID: PMC5778602 DOI: 10.1093/nar/gkx1177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/13/2017] [Indexed: 01/18/2023] Open
Abstract
Cleavage stimulation factor (CstF) is a highly conserved protein complex composed of three subunits that recognizes G/U-rich sequences downstream of the polyadenylation signal of eukaryotic mRNAs. While CstF has been identified over 25 years ago, the architecture and contribution of each subunit to RNA recognition have not been fully understood. In this study, we provide a structural basis for the recruitment of CstF-50 to CstF via interaction with CstF-77 and establish that the hexameric assembly of CstF creates a high affinity platform to target various G/U-rich sequences. We further demonstrate that CstF-77 boosts the affinity of the CstF-64 RRM to the RNA targets and CstF-50 fine tunes the ability of the complex to recognize G/U sequences of certain lengths and content.
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Affiliation(s)
- Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Peter L Hsu
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Jae-Eun Song
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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Schäfer P, Tüting C, Schönemann L, Kühn U, Treiber T, Treiber N, Ihling C, Graber A, Keller W, Meister G, Sinz A, Wahle E. Reconstitution of mammalian cleavage factor II involved in 3' processing of mRNA precursors. RNA (NEW YORK, N.Y.) 2018; 24:1721-1737. [PMID: 30139799 PMCID: PMC6239180 DOI: 10.1261/rna.068056.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/17/2018] [Indexed: 05/05/2023]
Abstract
Cleavage factor II (CF II) is a poorly characterized component of the multiprotein complex catalyzing 3' cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5' kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage. CF II binds RNA with nanomolar affinity. Binding is mediated mostly by the two zinc fingers in the C-terminal region of hPcf11. RNA is bound without pronounced sequence-specificity, but extended G-rich sequences appear to be preferred. We discuss the possibility that CF II contributes to the recognition of cleavage/polyadenylation substrates through interaction with G-rich far-downstream sequence elements.
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Affiliation(s)
- Peter Schäfer
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christian Tüting
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Lars Schönemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Uwe Kühn
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Christian Ihling
- Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Anne Graber
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Walter Keller
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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Khleborodova A, Pan X, Nagre NN, Ryan K. An investigation into the role of ATP in the mammalian pre-mRNA 3' cleavage reaction. Biochimie 2016; 125:213-22. [PMID: 27060432 DOI: 10.1016/j.biochi.2016.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/04/2016] [Indexed: 01/05/2023]
Abstract
RNA Polymerase II transcribes beyond what later becomes the 3' end of a mature messenger RNA (mRNA). The formation of most mRNA 3' ends results from pre-mRNA cleavage followed by polyadenylation. In vitro studies have shown that low concentrations of ATP stimulate the 3' cleavage reaction while high concentrations inhibit it, but the origin of these ATP effects is unknown. ATP might enable a cleavage factor kinase or activate a cleavage factor directly. To distinguish between these possibilities, we tested several ATP structural analogs in a pre-mRNA 3' cleavage reaction reconstituted from DEAE-fractionated cleavage factors. We found that adenosine 5'-(β,γ-methylene)triphosphate (AMP-PCP) is an effective in vitro 3' cleavage inhibitor with an IC50 of ∼300 μM, but that most other ATP analogs, including adenosine 5'-(β,γ-imido)triphosphate, which cannot serve as a protein kinase substrate, promoted 3' cleavage but less efficiently than ATP. In combination with previous literature data, our results do not support ATP stimulation of 3' cleavage through cleavage factor phosphorylation in vitro. Instead, the more likely mechanism is that ATP stimulates cleavage factor activity through direct cleavage factor binding. The mammalian 3' cleavage factors known to bind ATP include the cleavage factor II (CF IIm) Clp1 subunit, the CF Im25 subunit and poly(A) polymerase alpha (PAP). The yeast homolog of the CF IIm complex also binds ATP through yClp1. To investigate the mammalian complex, we used a cell-line expressing FLAG-tagged Clp1 to co-immunoprecipitate Pcf11 as a function of ATP concentration. FLAG-Clp1 co-precipitated Pcf11 with or without ATP and the complex was not affected by AMP-PCP. Diadenosine tetraphosphate (Ap4A), an ATP analog that binds the Nudix domain of the CF Im25 subunit with higher affinity than ATP, neither stimulated 3' cleavage in place of ATP nor antagonized ATP-stimulated 3' cleavage. The ATP-binding site of PAP was disrupted by site directed mutagenesis but a reconstituted 3' cleavage reaction containing a mutant PAP unable to bind ATP nevertheless underwent ATP-stimulated 3' cleavage. Fluctuating ATP levels might contribute to the regulation of pre-mRNA 3' cleavage, but the three subunits investigated here do not appear to be responsible for the ATP-stimulation of pre-mRNA cleavage.
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Affiliation(s)
- Asya Khleborodova
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA; Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA
| | - Xiaozhou Pan
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA
| | - Nagaraja N Nagre
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA
| | - Kevin Ryan
- Department of Chemistry and Biochemistry, The City College of New York, The City University, New York, NY 10031, USA; Biochemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA; Chemistry Ph.D. Program, The City University of New York Graduate Center, New York, NY 10016, USA.
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Kandala DT, Mohan N, A V, A P S, G R, Laishram RS. CstF-64 and 3'-UTR cis-element determine Star-PAP specificity for target mRNA selection by excluding PAPα. Nucleic Acids Res 2015; 44:811-23. [PMID: 26496945 PMCID: PMC4737136 DOI: 10.1093/nar/gkv1074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/06/2015] [Indexed: 01/02/2023] Open
Abstract
Almost all eukaryotic mRNAs have a poly (A) tail at the 3′-end. Canonical PAPs (PAPα/γ) polyadenylate nuclear pre-mRNAs. The recent identification of the non-canonical Star-PAP revealed specificity of nuclear PAPs for pre-mRNAs, yet the mechanism how Star-PAP selects mRNA targets is still elusive. Moreover, how Star-PAP target mRNAs having canonical AAUAAA signal are not regulated by PAPα is unclear. We investigate specificity mechanisms of Star-PAP that selects pre-mRNA targets for polyadenylation. Star-PAP assembles distinct 3′-end processing complex and controls pre-mRNAs independent of PAPα. We identified a Star-PAP recognition nucleotide motif and showed that suboptimal DSE on Star-PAP target pre-mRNA 3′-UTRs inhibit CstF-64 binding, thus preventing PAPα recruitment onto it. Altering 3′-UTR cis-elements on a Star-PAP target pre-mRNA can switch the regulatory PAP from Star-PAP to PAPα. Our results suggest a mechanism of poly (A) site selection that has potential implication on the regulation of alternative polyadenylation.
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Affiliation(s)
- Divya T Kandala
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Nimmy Mohan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Vivekanand A
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Sudheesh A P
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Reshmi G
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
| | - Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India
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Cao XL, Chen JJ, Cao Y, Nie GX, Wan QY, Wang LF, Su JG. Identification and expression of the laboratory of genetics and physiology 2 gene in common carp Cyprinus carpio. JOURNAL OF FISH BIOLOGY 2015; 86:74-91. [PMID: 25359511 DOI: 10.1111/jfb.12541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 09/09/2014] [Indexed: 06/04/2023]
Abstract
In this study, a laboratory of genetics and physiology 2 gene (lgp2) from common carp Cyprinus carpio was isolated and characterized. The full-length complementary (c)DNA of lgp2 was 3061 bp and encoded a polypeptide of 680 amino acids, with an estimated molecular mass of 77 341·2 Da and a predicted isoelectric point of 6·53. The predicted protein included four main overlapping structural domains: a conserved restriction domain of bacterial type III restriction enzyme, a DEAD-DEAH box helicase domain, a helicase super family C-terminal domain and a regulatory domain. Real-time quantitative polymerase chain reaction (PCR) showed widespread expression of lgp2, mitochondrial antiviral signalling protein (mavs) and interferon transcription factor 3 (irf3) in tissues of nine organs. lgp2, mavs and irf3 expression levels were significantly induced in all examined organs by infection with koi herpesvirus (KHV). lgp2, mavs and irf3 messenger (m)RNA levels were significantly up-regulated in vivo after KHV infection, and lgp2 transcripts were also significantly enhanced in vitro after stimulation with synthetic, double-stranded RNA polyinosinic polycytidylic [poly(I:C)]. These findings suggest that lgp2 is an inducible protein involved in the innate immune defence against KHV in C. carpio. These results provide the basis for further research into the role and mechanisms of lgp2 in fishes.
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Affiliation(s)
- X L Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, People's Republic of China; College of Fisheries, Henan Normal University, Xinxiang 453007, People's Republic of China
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9
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Li XQ, Du D. Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals. BMC Evol Biol 2014; 14:162. [PMID: 25052519 PMCID: PMC4360255 DOI: 10.1186/s12862-014-0162-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
Background The polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mRNA polyadenylation [poly(A)] sites are still uncharacterized in most species. The evolutionary tendency for poly(A) site selection is still largely unknown. Results We analyzed the poly(A) site regions of 31 species or phyla. Different groups of species showed different poly(A) signal motifs: UUACUU at the poly(A) site in the parasite Trypanosoma cruzi; UGUAAC (approximately 13 bases upstream of the site) in the alga Chlamydomonas reinhardtii; UGUUUG (or UGUUUGUU) at mainly the fourth base downstream of the poly(A) site in the parasite Blastocystis hominis; and AAUAAA at approximately 16 bases and approximately 19 bases upstream of the poly(A) site in animals and plants, respectively. Polyadenylation signal motifs are usually several hundred times more abundant around poly(A) sites than in whole genomes. These predominant motifs usually had very specific locations, whether upstream of, at, or downstream of poly(A) sites, depending on the species or phylum. The poly(A) site was usually an adenosine (A) in all analyzed species except for B. hominis, and there was weak A predominance in C. reinhardtii. Fungi, animals, plants, and the protist Phytophthora infestans shared a general base abundance pattern (or base composition pattern) of “U-rich—A-rich—U-rich—Poly(A) site—U-rich regions”, or U-A-U-A-U for short, with some variation for each kingdom or subkingdom. Conclusion This study identified the poly(A) signal motifs, motif locations, and base composition patterns around mRNA poly(A) sites in protists, fungi, plants, and animals and provided insight into poly(A) site evolution.
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Affiliation(s)
- Xiu-Qing Li
- Molecular Genetics Laboratory, Potato Research Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada.
| | - Donglei Du
- Quantitative Methods Research Group, Faculty of Business Administration, University of New Brunswick, 7 Macaulay Lane, Fredericton, NB, E3B 5A3, Canada.
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10
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Laishram RS. Poly(A) polymerase (PAP) diversity in gene expression--star-PAP vs canonical PAP. FEBS Lett 2014; 588:2185-97. [PMID: 24873880 PMCID: PMC6309179 DOI: 10.1016/j.febslet.2014.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 01/09/2023]
Abstract
Almost all eukaryotic mRNAs acquire a poly(A) tail at the 3'-end by a concerted RNA processing event: cleavage and polyadenylation. The canonical PAP, PAPα, was considered the only nuclear PAP involved in general polyadenylation of mRNAs. A phosphoinositide-modulated nuclear PAP, Star-PAP, was then reported to regulate a select set of mRNAs in the cell. In addition, several non-canonical PAPs have been identified with diverse cellular functions. Further, canonical PAP itself exists in multiple isoforms thus illustrating the diversity of PAPs. In this review, we compare two nuclear PAPs, Star-PAP and PAPα with a general overview of PAP diversity in the cell. Emerging evidence suggests distinct niches of target pre-mRNAs for the two PAPs and that modulation of these PAPs regulates distinct cellular functions.
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Affiliation(s)
- Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
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11
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Gruber AR, Martin G, Keller W, Zavolan M. Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:183-96. [PMID: 24243805 PMCID: PMC4282565 DOI: 10.1002/wrna.1206] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/16/2013] [Accepted: 10/18/2013] [Indexed: 12/24/2022]
Abstract
Expression of mature messenger RNAs (mRNAs) requires appropriate transcription initiation and termination, as well as pre-mRNA processing by capping, splicing, cleavage, and polyadenylation. A core 3'-end processing complex carries out the cleavage and polyadenylation reactions, but many proteins have been implicated in the selection of polyadenylation sites among the multiple alternatives that eukaryotic genes typically have. In recent years, high-throughput approaches to map both the 3'-end processing sites as well as the binding sites of proteins that are involved in the selection of cleavage sites and in the processing reactions have been developed. Here, we review these approaches as well as the insights into the mechanisms of polyadenylation that emerged from genome-wide studies of polyadenylation across a range of cell types and states.
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Affiliation(s)
- Andreas R Gruber
- Computational and Systems Biology, Biozentrum, University of Basel, Basel, Switzerland
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12
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Prasad MK, Bhalla K, Pan ZH, O’Connell JR, Weder AB, Chakravarti A, Tian B, Chang YPC. A polymorphic 3'UTR element in ATP1B1 regulates alternative polyadenylation and is associated with blood pressure. PLoS One 2013; 8:e76290. [PMID: 24098465 PMCID: PMC3788127 DOI: 10.1371/journal.pone.0076290] [Citation(s) in RCA: 16] [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: 05/28/2013] [Accepted: 08/22/2013] [Indexed: 12/31/2022] Open
Abstract
Although variants in many genes have previously been shown to be associated with blood pressure (BP) levels, the molecular mechanism underlying these associations are mostly unknown. We identified a multi-allelic T-rich sequence (TRS) in the 3’UTR of ATP1B1 that varies in length and sequence composition (T22-27 and T12GT 3GT6). The 3’UTR of ATP1B1 contains 2 functional polyadenylation signals and the TRS is downstream of the proximal polyadenylation site (A2). Therefore, we hypothesized that alleles of this TRS might influence ATP1B1 expression by regulating alternative polyadenylation. In vitro, the T12GT 3GT6 allele increases polyadenylation at the A2 polyadenylation site as compared to the T23 allele. Consistent with our hypothesis, the relative abundance of the A2-polyadenylated ATP1B1 mRNA was higher in human kidneys with at least one copy of the T12GT 3GT6 allele than in those lacking this allele. The T12GT 3GT6 allele is also associated with higher systolic BP (beta = 3.3 mmHg, p = 0.014) and diastolic BP (beta = 2.4 mmHg, p = 0.003) in a European-American population. Therefore, we have identified a novel multi-allelic TRS in the 3’UTR of ATP1B1 that is associated with higher BP and may mediate its effect by regulating the polyadenylation of the ATP1B1 mRNA.
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Affiliation(s)
- Megana K. Prasad
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Kavita Bhalla
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Zhen Hua Pan
- Department of Biochemistry & Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Jeffrey R. O’Connell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alan B. Weder
- Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Bin Tian
- Department of Biochemistry & Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Yen-Pei C. Chang
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Wang L, Dowell RD, Yi R. Genome-wide maps of polyadenylation reveal dynamic mRNA 3'-end formation in mammalian cell lineages. RNA (NEW YORK, N.Y.) 2013; 19:413-25. [PMID: 23325109 PMCID: PMC3677251 DOI: 10.1261/rna.035360.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 11/27/2012] [Indexed: 05/24/2023]
Abstract
Post-transcriptional regulation, often mediated by miRNAs and RNA-binding proteins at the 3' untranslated regions (UTRs) of mRNAs, is implicated in important roles in the output of transcriptome. To decipher this layer of gene regulation, it is essential to measure global mRNA expression quantitatively in a 3'-UTR-specific manner. Here we establish an experimental and bioinformatics pipeline that simultaneously determines 3'-end formation by leveraging local nucleotide composition and quantitatively measures mRNA expression by sequencing polyadenylated transcripts. When applied to purified mouse embryonic skin stem cells and their daughter lineages, we identify 18,060 3' UTRs representing 12,739 distinct mRNAs that are abundantly expressed in the skin. We determine that ∼78% of UTRs are formed by using canonical A[A/U]UAAA polyadenylation signals, whereas ∼22% of UTRs use alternative signals. By comparing to relative and absolute mRNA abundance determined by qPCR, our RNA-seq approach can precisely measure mRNA fold-change and accurately determine the expression of mRNAs over four orders of magnitude. Surprisingly, only 829 out of 12,739 genes show differential 3'-end usage between embryonic skin stem cells and their immediate daughter cells, whereas the numbers increase to 933 genes when comparing embryonic skin stem cells with the more remotely related hair follicle cells. This suggests an evolving diversity instead of switch-like dynamics in 3'-end formation during development. Finally, core components of the miRNA pathway including Dicer, Dgcr8, Xpo5, and Argonautes show dynamic 3'-UTR formation patterns, indicating a self-regulatory mechanism. Together, our quantitative analysis reveals a dynamic picture of mRNA 3'-end formation in tissue stem cell lineages in vivo.
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Affiliation(s)
- Li Wang
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Robin D. Dowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, Colorado 80309, USA
| | - Rui Yi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
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Martin G, Gruber AR, Keller W, Zavolan M. Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell Rep 2012; 1:753-63. [PMID: 22813749 DOI: 10.1016/j.celrep.2012.05.003] [Citation(s) in RCA: 269] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/10/2012] [Accepted: 05/07/2012] [Indexed: 11/16/2022] Open
Abstract
Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we performed transcriptome-wide mapping of both binding sites of 3' end processing factors CPSF-160, CPSF-100, CPSF-73, CPSF-30, Fip1, CstF-64, CstF-64τ, CF I(m)25, CF I(m)59, and CF I(m)68 and 3' end processing sites in HEK293 cells. We found that although binding sites of these factors generally cluster around the poly(A) sites most frequently used in cleavage, CstF-64/CstF-64τ and CFI(m) proteins have much higher positional specificity compared to CPSF components. Knockdown of CF I(m)68 induced a systematic use of proximal polyadenylation sites, indicating that changes in relative abundance of a single 3' end processing factor can modulate the length of 3' untranslated regions across the transcriptome and suggesting a mechanism behind the previously observed increase in tumor cell invasiveness upon CF I(m)68 knockdown.
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Affiliation(s)
- Georges Martin
- Computational and Systems Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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15
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Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:385-96. [PMID: 22012871 DOI: 10.1002/wrna.116] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pre-mRNA cleavage and polyadenylation is an essential step for 3' end formation of almost all protein-coding transcripts in eukaryotes. The reaction, involving cleavage of nascent mRNA followed by addition of a polyadenylate or poly(A) tail, is controlled by cis-acting elements in the pre-mRNA surrounding the cleavage site. Experimental and bioinformatic studies in the past three decades have elucidated conserved and divergent elements across eukaryotes, from yeast to human. Here we review histories and current models of these elements in a broad range of species.
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Affiliation(s)
- Bin Tian
- UMDNJ-New Jersey Medical School, Newark, NJ, USA.
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16
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Yang Q, Doublié S. Structural biology of poly(A) site definition. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:732-47. [PMID: 21823232 DOI: 10.1002/wrna.88] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
3' processing is an essential step in the maturation of all messenger RNAs (mRNAs) and is a tightly coupled two-step reaction: endonucleolytic cleavage at the poly(A) site is followed by the addition of a poly(A) tail, except for metazoan histone mRNAs, which are cleaved but not polyadenylated. The recognition of a poly(A) site is coordinated by the sequence elements in the mRNA 3' UTR and associated protein factors. In mammalian cells, three well-studied sequence elements, UGUA, AAUAAA, and GU-rich, are recognized by three multisubunit factors: cleavage factor I(m) (CFI(m) ), cleavage and polyadenylation specificity factor (CPSF), and cleavage stimulation factor (CstF), respectively. In the yeast Saccharomyces cerevisiae, UA repeats and A-rich sequence elements are recognized by Hrp1p and cleavage factor IA. Structural studies of protein-RNA complexes have helped decipher the mechanisms underlying sequence recognition and shed light on the role of protein factors in poly(A) site selection and 3' processing machinery assembly. In this review we focus on the interactions between the mRNA cis-elements and the protein factors (CFI(m) , CPSF, CstF, and homologous factors from yeast and other eukaryotes) that define the poly(A) site. WIREs RNA 2011 2 732-747 DOI: 10.1002/wrna.88 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Qin Yang
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, USA
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17
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Hockert KJ, Martincic K, Mendis-Handagama SMLC, Borghesi LA, Milcarek C, Dass B, MacDonald CC. Spermatogenetic but not immunological defects in mice lacking the τCstF-64 polyadenylation protein. J Reprod Immunol 2011; 89:26-37. [PMID: 21489638 DOI: 10.1016/j.jri.2011.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/07/2011] [Accepted: 01/16/2011] [Indexed: 12/31/2022]
Abstract
Alternative polyadenylation controls expression of genes in many tissues including immune cells and male germ cells. The τCstF-64 polyadenylation protein is expressed in both cell types, and we previously showed that Cstf2t, the gene encoding τCstF-64 was necessary for spermatogenesis and fertilization. Here we examine consequences of τCstF-64 loss in both germ cells and immune cells. Spermatozoa from Cstf2t null mutant (Cstf2t(-/-)) mice of ages ranging from 60 to 108 days postpartum exhibited severe defects in motility and morphology that were correlated with a decrease in numbers of round spermatids. Spermatozoa in these mice also displayed severe morphological defects at every age, especially in the head and midpiece. In the testicular epithelium, we saw normal numbers of cells in earlier stages of spermatogenesis, but reduced numbers of round spermatids in Cstf2t(-/-) mice. Although Leydig cell numbers were normal, we did observe reduced levels of plasma testosterone in the knockout animals, suggesting that reduced androgen might also be contributing to the Cstf2t(-/-) phenotype. Finally, while τCstF-64 was expressed in a variety of immune cell types in wild type mice, we did not find differences in secreted IgG or IgM or changes in immune cell populations in Cstf2t(-/-) mice, suggesting that τCstF-64 function in immune cells is either redundant or vestigial. Together, these data show that τCstF-64 function is primarily to support spermatogenesis, but only incidentally to support immune cell function.
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Affiliation(s)
- Kathy Jo Hockert
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Texas, Lubbock, TX 79430, USA
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18
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Yang L, Liu J, Liu M, Qian M, Zhang M, Hu H. Identification of fatty acid synthase from the Pacific white shrimp, Litopenaeus vannamei and its specific expression profiles during white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2011; 30:744-749. [PMID: 21199673 DOI: 10.1016/j.fsi.2010.12.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/24/2010] [Accepted: 12/24/2010] [Indexed: 05/30/2023]
Abstract
Fatty acid synthase (FAS) in animal tissues consists of two identical monomers and is known to be a complex multi-functional enzyme that plays an important role in energy homeostasis. However, there are few reports of studies focused on the relationship between FAS and virus infection in invertebrates. In the present study, we cloned the FAS gene from an economically important invertebrate, the Pacific white shrimp Litopenaeus vannamei. The full-length FAS cDNA is 8268 bp, including a 5'-terminal untranslated region of 137 bp, a 3'-terminal untranslated region of 601 bp and an open reading frame of 7530 bp. FAS cDNA encodes a polypeptide of 2509 amino acid residues that contains a typical β-ketoacyl synthase (KS) domain at the N-terminus, next to a malonyl/acetyltransferase (MAT) domain, a dehydrase domain, an enoyl reductase domain, a ketoacyl reductase domain, a phosphopantetheine attachment site domain and a thioesterase domain at the C-terminus. Quantitative real-time RT-PCR revealed the up-regulated expression of FAS in L. vannamei hepatopancreas and muscle after white spot syndrome virus (WSSV) infection. The expression of FAS in muscle was 13.03-fold greater than that in the control (p<0.05) and 2.93-fold greater in hepatopancreas (p>0.05). Meanwhile, expression of the fatty acid-binding protein (FABP), another important factor in lipid metabolism, was increased in muscle to 19.20-fold greater than that in the control (p<0.05) but only 0.76-fold in hepatopancreas (p>0.05). These results implied that WSSV infected body surface tissues, but there was very little infection of internal organs. We suggest that the increase of FAS expression is induced in WSSV-infected shrimps, and the virus changes the lipid metabolism of the host, which directly affects virus assembly or defense against virus infection.
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Affiliation(s)
- Ling Yang
- College of Life Sciences, China Jiliang University, 258 Xueyuan Street, Xiasha, HangZhou, ZheJiang, China
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The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Lett 2010; 584:1449-54. [PMID: 20214900 DOI: 10.1016/j.febslet.2010.03.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 02/23/2010] [Accepted: 03/03/2010] [Indexed: 01/27/2023]
Abstract
The 77 kDa subunit of the polyadenylation cleavage stimulation factor (CstF77) is important in messenger RNA 3' end processing. Previously, we demonstrated that AtCstF77 interacts with AtCPSF30, the Arabidopsis ortholog of the 30 kDa subunit of the Cleavage and Polyadenylation Specificity Factor. In further dissecting this interaction, it was found that the C-terminus of AtCstF77 interacts with AtCPSF30. Remarkably, we also found that the C-terminal domain of AtCstF77 possesses RNA-binding ability. These studies therefore reveal AtCstF77 to be an RNA-binding protein, adding yet another RNA-binding activity to the plant polyadenylation complex. This raises interesting questions as to the means by which RNAs are recognized during mRNA 3' end formation in plants.
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20
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Pancevac C, Goldstone DC, Ramos A, Taylor IA. Structure of the Rna15 RRM-RNA complex reveals the molecular basis of GU specificity in transcriptional 3'-end processing factors. Nucleic Acids Res 2010; 38:3119-32. [PMID: 20097654 PMCID: PMC2875009 DOI: 10.1093/nar/gkq002] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Rna15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3′-end processing factor from Saccharomyces cerevisiae. CFIA is required for polyA site selection/cleavage targeting RNA sequences that surround polyadenylation sites in the 3′-UTR of RNA polymerase-II transcripts. RNA recognition by CFIA is mediated by an RNA recognition motif (RRM) contained in the Rna15 subunit of the complex. We show here that Rna15 has a strong and unexpected preference for GU containing RNAs and reveal the molecular basis for a base selectivity mechanism that accommodates G or U but discriminates against C and A bases. This mode of base selectivity is rather different to that observed in other RRM-RNA structures and is structurally conserved in CstF64, the mammalian counterpart of Rna15. Our observations provide evidence for a highly conserved mechanism of base recognition amongst the 3′-end processing complexes that interact with the U-rich or U/G-rich elements at 3′-end cleavage/polyadenylation sites.
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Affiliation(s)
- Christina Pancevac
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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21
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Chatterjee A, Dutta S, Mukherjee S, Mukherjee N, Chandra S, Mukherjee A, Sinha S, Panda CK, Chaudhuri K, Mukhopadyay K. Differential allelic distribution of V-ets erythroblastosis virus E26 oncogene homolog2 (ETS2) functional polymorphisms in different group of patients. Gene Expr 2010; 15:61-73. [PMID: 21526717 PMCID: PMC6043833 DOI: 10.3727/105221611x12973615737541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
V-ets erythroblastosis virus E26 oncogene homolog2 (ETS2), located at chromosome 21 and overexpressed in Down's syndrome (DS), has known cancer regulatory functions. Because leukemia is of common occurrence in DS subjects while solid tumors are rare, we have explored the role of ETS2 functional genetic polymorphisms in this differential oncological development. In silico methods were used for identifying deleterious SNPs, tagged SNPs, and linkage disequilibrium followed by genotyping of 14 SNPs in Indo-Caucasoid individuals (N=668). Significantly different allelic frequencies for rs457705, rs1051420, and rs1051425 were observed in Indian controls (N=149) compared to other ethnic groups. A heterozygous "T" insertion, between chromosomal contig positions 40195541 and 40195542, was observed in DS subjects and their parents. rs461155 showed significant allelic and genotypic association in breast and oral cancer patients. Significantly higher occurrence of G-C haplotype (rs461155-rs1051425) was also observed in these patients compared to DS and leukemic patients. This is the first report on this type of allelic discrimination pattern of ETS2 under different disease conditions. From the data obtained it may be proposed that allelic discrimination of deleterious SNPs in ETS2 may play a regulatory role in the differential development of malignancy in DS subjects.
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Affiliation(s)
- Arpita Chatterjee
- Manovikas Biomedical Research and Diagnostic Centre, MRIH, Kolkata, India
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22
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Hockert JA, Yeh HJ, MacDonald CC. The hinge domain of the cleavage stimulation factor protein CstF-64 is essential for CstF-77 interaction, nuclear localization, and polyadenylation. J Biol Chem 2009; 285:695-704. [PMID: 19887456 DOI: 10.1074/jbc.m109.061705] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Because polyadenylation is essential for cell growth, in vivo examination of polyadenylation protein function has been difficult. Here we describe a new in vivo assay that allows structure-function assays on CstF-64, a protein that binds to pre-mRNAs downstream of the cleavage site for accurate and efficient polyadenylation. In this assay (the stem-loop luciferase assay for polyadenylation, SLAP), expression of a luciferase pre-mRNA with a modified downstream sequence element was made dependent upon co-expression of an MS2-CstF-64 fusion protein. We show here that SLAP accurately reflects CstF-64-dependent polyadenylation, confirming the validity of this assay. Using SLAP, we determined that CstF-64 domains involved in RNA binding, interaction with CstF-77 (the "Hinge" domain), and coupling to transcription are critical for polyadenylation. Further, we showed that the Hinge domain is necessary for CstF-64 interaction with CstF-77 and consequent nuclear localization, suggesting that nuclear import of a preformed CstF complex is an essential step in polyadenylation.
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Affiliation(s)
- J Andrew Hockert
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430-6540, USA
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23
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Rao S, Dinkins RD, Hunt AG. Distinctive interactions of the Arabidopsis homolog of the 30 kD subunit of the cleavage and polyadenylation specificity factor (AtCPSF30) with other polyadenylation factor subunits. BMC Cell Biol 2009; 10:51. [PMID: 19573236 PMCID: PMC2712457 DOI: 10.1186/1471-2121-10-51] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 07/02/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Arabidopsis ortholog of the 30 kD subunit of the mammalian Cleavage and Polyadenylation Specificity Factor (AtCPSF30) is an RNA-binding endonuclease that is associated with other Arabidopsis CPSF subunits (orthologs of the 160, 100, and 73 kD subunits of CPSF). In order to further explore the functions of AtCPSF30, the subcellular distribution of the protein was examined by over-expressing fusion proteins containing fluorescent reporters linked to different CPSF subunits. RESULTS It was found that AtCPSF30 by itself localizes, not to the nucleus, but to the cytoplasm. AtCPSF30 could be found in the nucleus when co-expressed with AtCPSF160 or AtCPSF73(I), one of the two Arabidopsis orthologs of CPSF73. This re-directing of AtCPSF30 indicates that AtCPSF30 is retained in the nucleus via interactions with either or both of these other CPSF subunits. Co-expression of AtCSPF30 with AtCPSF100 altered the location, not of AtCPSF30, but rather of AtCPSF100, with these proteins residing in the cytoplasm. Deletion of plant-specific N- or C-terminal domains of AtCPSF30 abolished various of the interactions between AtCPSF30 and other CPSF subunits, suggesting that the plant CPSF complex assembles via novel protein-protein interactions. CONCLUSION These results suggest that the nuclear CPSF complex in plants is a dynamic one, and that the interactions between AtCPSF30 and other CPSF subunits are different from those existing in other eukaryotes.
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Affiliation(s)
- Suryadevara Rao
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
| | - Randy D Dinkins
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
- USDA-ARS, FAPRU, Lexington, KY 40546-0091 USA
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312 USA
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Prediction of non-canonical polyadenylation signals in human genomic sequences based on a novel algorithm using a fuzzy membership function. J Biosci Bioeng 2009; 107:569-78. [DOI: 10.1016/j.jbiosc.2009.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2008] [Revised: 01/05/2009] [Accepted: 01/05/2009] [Indexed: 11/23/2022]
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Graber JH, Salisbury J, Hutchins LN, Blumenthal T. C. elegans sequences that control trans-splicing and operon pre-mRNA processing. RNA (NEW YORK, N.Y.) 2007; 13:1409-26. [PMID: 17630324 PMCID: PMC1950753 DOI: 10.1261/rna.596707] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 05/17/2007] [Indexed: 05/04/2023]
Abstract
Many mRNAs in Caenorhabditis elegans are generated through a trans-splicing reaction that adds one of two classes of spliced leader RNA to an independently transcribed pre-mRNA. SL1 leaders are spliced mostly to pre-mRNAs from genes with outrons, intron-like sequences at the 5'-ends of the pre-mRNAs. In contrast, SL2 leaders are nearly exclusively trans-spliced to genes that occur downstream in polycistronic pre-mRNAs produced from operons. Operon pre-mRNA processing requires separation into individual transcripts, which is accomplished by 3'-processing of upstream genes and spliced leader trans-splicing to the downstream genes. We used a novel computational analysis, based on nonnegative matrix factorization, to identify and characterize significant differences in the cis-acting sequence elements that differentiate various types of functional site, including internal versus terminal 3'-processing sites, and SL1 versus SL2 trans-splicing sites. We describe several key elements, including the U-rich (Ur) element that couples 3'-processing with SL2 trans-splicing, and a novel outron (Ou) element that occurs upstream of SL1 trans-splicing sites. Finally, we present models of the distinct classes of trans-splicing reaction, including SL1 trans-splicing at the outron, SL2 trans-splicing in standard operons, competitive SL1-SL2 trans-splicing in operons with large intergenic separation, and SL1 trans-splicing in SL1-type operons, which have no intergenic separation.
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Legrand P, Pinaud N, Minvielle-Sébastia L, Fribourg S. The structure of the CstF-77 homodimer provides insights into CstF assembly. Nucleic Acids Res 2007; 35:4515-22. [PMID: 17584787 PMCID: PMC1935011 DOI: 10.1093/nar/gkm458] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The cleavage stimulation factor (CstF) is essential for the first step of poly(A) tail formation at the 3' ends of mRNAs. This heterotrimeric complex is built around the 77-kDa protein bridging both CstF-64 and CstF-50 subunits. We have solved the crystal structure of the 77-kDa protein from Encephalitozoon cuniculi at a resolution of 2 Å. The structure folds around 11 Half-a-TPR repeats defining two domains. The crystal structure reveals a tight homodimer exposing phylogenetically conserved areas for interaction with protein partners. Mapping experiments identify the C-terminal region of Rna14p, the yeast counterpart of CstF-77, as the docking domain for Rna15p, the yeast CstF-64 homologue.
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Affiliation(s)
- Pierre Legrand
- Institut Européen de Chimie et Biologie, INSERM U869, 2 rue Robert Escarpit Pessac, F-33607, Université Victor Segalen, Bordeaux 2, 146 rue Léo Saignat, F-33076, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, and Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1 rue Camille Saint-Saëns, F-33077 Bordeaux cedex
| | - Noël Pinaud
- Institut Européen de Chimie et Biologie, INSERM U869, 2 rue Robert Escarpit Pessac, F-33607, Université Victor Segalen, Bordeaux 2, 146 rue Léo Saignat, F-33076, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, and Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1 rue Camille Saint-Saëns, F-33077 Bordeaux cedex
| | - Lionel Minvielle-Sébastia
- Institut Européen de Chimie et Biologie, INSERM U869, 2 rue Robert Escarpit Pessac, F-33607, Université Victor Segalen, Bordeaux 2, 146 rue Léo Saignat, F-33076, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, and Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1 rue Camille Saint-Saëns, F-33077 Bordeaux cedex
| | - Sébastien Fribourg
- Institut Européen de Chimie et Biologie, INSERM U869, 2 rue Robert Escarpit Pessac, F-33607, Université Victor Segalen, Bordeaux 2, 146 rue Léo Saignat, F-33076, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, B.P. 48, 91192 Gif-sur-Yvette Cedex, and Institut de Biochimie et Génétique Cellulaires, CNRS UMR 5095, 1 rue Camille Saint-Saëns, F-33077 Bordeaux cedex
- *To whom correspondence should be addressed. 00 33 (0)5 40 00 30 6300 33 (0)5 40 00 30 68
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Uitte de Willige S, Rietveld IM, De Visser MCH, Vos HL, Bertina RM. Polymorphism 10034C>T is located in a region regulating polyadenylation of FGG transcripts and influences the fibrinogen gamma'/gammaA mRNA ratio. J Thromb Haemost 2007; 5:1243-9. [PMID: 17403086 DOI: 10.1111/j.1538-7836.2007.02566.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Fibrinogen gamma haplotype 2 (FGG-H2) is associated with reduced fibrinogen gamma' levels and fibrinogen gamma'/total fibrinogen ratios and with an increased deep-venous thrombosis (DVT) risk. Two FGG-H2 tagging single nucleotide polymorphisms (SNPs), 9615C>T and 10034C>T, are located in the region of alternative FGG pre-mRNA processing. 10034C>T is located in a GT-rich downstream sequence element (DSE) that comprises a putative cleavage stimulation factor (CstF) binding site. OBJECTIVES To investigate the functionality of SNPs 9615C>T and 10034C>T, and the importance of the DSE containing 10034C>T. METHODS Different minigene constructs containing FGG exon 9, intron 9, exon 10 and the 3' region were transiently transfected into HepG2 cells and quantitative real-time polymerase chain reaction was used to measure relative polyadenylation (pA) signal usage (pA1/pA2 ratio). RESULTS Compared with the reference construct CC (9615C-10034C; FGG-H1; pA1/pA2 ratio set at 100%), the pA1/pA2 ratio of construct TT (9615T-10034T; FGG-H2) was 1.4-fold decreased (71.5%, P = 0.015). The pA1/pA2 ratio of construct CT (9615C-10034T) was almost 1.2-fold decreased (85.3%, P = 0.001), whereas the pA1/pA2 ratio of construct TC (9615T-10034C) did not differ significantly from the reference construct (101.6%, P = 0.890). Functionality of the putative CstF binding site was confirmed using constructs in which this site was deleted or its sequence altered by point mutations. CONCLUSIONS SNP 10034C>T is located in a GT-rich DSE involved in regulating the usage of the pA2 signal of FGG, which may represent a CstF binding site. We propose that the 10034C>T change is the functional variation in FGG-H2 that is responsible for the reduction in the fibrinogen gamma'/total fibrinogen ratio and the increased DVT risk.
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Affiliation(s)
- S Uitte de Willige
- Department of Hematology, Hemostasis and Thrombosis Research Center, Leiden University Medical Center, Leiden, The Netherlands
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Bai Y, Auperin TC, Chou CY, Chang GG, Manley JL, Tong L. Crystal structure of murine CstF-77: dimeric association and implications for polyadenylation of mRNA precursors. Mol Cell 2007; 25:863-75. [PMID: 17386263 DOI: 10.1016/j.molcel.2007.01.034] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 12/20/2006] [Accepted: 01/22/2007] [Indexed: 01/25/2023]
Abstract
Cleavage stimulation factor (CstF) is a heterotrimeric protein complex essential for polyadenylation of mRNA precursors. The 77 kDa subunit, CstF-77, is known to mediate interactions with the other two subunits of CstF as well as with other components of the polyadenylation machinery. We report here the crystal structure of the HAT (half a TPR) domain of murine CstF-77, as well as its C-terminal subdomain. Structural and biochemical studies show that the HAT domain consists of two subdomains, HAT-N and HAT-C domains, with drastically different orientations of their helical motifs. The structures reveal a highly elongated dimer, spanning 165 A, with the dimerization mediated by the HAT-C domain. Light-scattering studies, yeast two-hybrid assays, and analytical ultracentrifugation measurements confirm this self-association. The mode of dimerization and the relative arrangement of the HAT-N and HAT-C domains are unique to CstF-77. Our data support a role for CstF dimerization in pre-mRNA 3' end processing.
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Affiliation(s)
- Yun Bai
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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Monarez RR, MacDonald CC, Dass B. Polyadenylation proteins CstF-64 and tauCstF-64 exhibit differential binding affinities for RNA polymers. Biochem J 2007; 401:651-8. [PMID: 17029590 PMCID: PMC1770853 DOI: 10.1042/bj20061097] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
CstF-64 (cleavage stimulation factor-64), a major regulatory protein of polyadenylation, is absent during male meiosis. Therefore a paralogous variant, tauCstF-64 is expressed in male germ cells to maintain normal spermatogenesis. Based on sequence differences between tauCstF-64 and CstF-64, and on the high incidence of alternative polyadenylation in testes, we hypothesized that the RBDs (RNA-binding domains) of tauCstF-64 and CstF-64 have different affinities for RNA elements. We quantified K(d) values of CstF-64 and tauCstF-64 RBDs for various ribopolymers using an RNA cross-linking assay. The two RBDs had similar affinities for poly(G)18, poly(A)18 or poly(C)18, with affinity for poly(C)18 being the lowest. However, CstF-64 had a higher affinity for poly(U)18 than tauCstF-64, whereas it had a lower affinity for poly(GU)9. Changing Pro-41 to a serine residue in the CstF-64 RBD did not affect its affinity for poly(U)18, but changes in amino acids downstream of the C-terminal alpha-helical region decreased affinity towards poly(U)18. Thus we show that the two CstF-64 paralogues differ in their affinities for specific RNA sequences, and that the region C-terminal to the RBD is mportant in RNA sequence recognition. This supports the hypothesis that tauCstF-64 promotes germ-cell-specific patterns of polyadenylation by binding to different downstream sequence elements.
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Affiliation(s)
- Roberto R Monarez
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430, USA
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Al-Zoghaibi F, Ashour T, Al-Ahmadi W, Abulleef H, Demirkaya O, Khabar KSA. Bioinformatics and experimental derivation of an efficient hybrid 3' untranslated region and use in expression active linear DNA with minimum poly(A) region. Gene 2006; 391:130-9. [PMID: 17258873 DOI: 10.1016/j.gene.2006.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2006] [Revised: 12/11/2006] [Accepted: 12/15/2006] [Indexed: 11/25/2022]
Abstract
Untranslated regions at the 3' end of the messenger RNA (3' UTR) contain regulatory elements that affect mRNA stability and translation and subsequently the protein levels. In this report, we performed bioinformatics analysis on housekeeping genes with putative stable mRNAs in comparison with Class II AU-rich elements (ARE)-containing mRNAs, a group of mRNAs known to represent many labile transcripts. We have found that ARE-mRNAs are less abundant and had longer 3' UTR than stable housekeeping mRNAs. As a result of the analysis, we evaluated the use of a 3' UTR derived from the abundant elongation factor 1 alpha 1 (EEF1A1) mRNA, in expression vectors. Due to the excellent consequence of the modified 3' UTR, we were able to produce expression active linear DNA generated by cloning-free PCR. We have also applied this approach to study the in vivo minimum requirement of poly(A) signal context that allows efficient protein synthesis. The efficient 3' UTR may find use in enhanced recombinant protein production and also provide a simplified tool for generation of expression active linear DNA.
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Affiliation(s)
- Fahad Al-Zoghaibi
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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Liu D, Brockman JM, Dass B, Hutchins LN, Singh P, McCarrey JR, MacDonald CC, Graber JH. Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. Nucleic Acids Res 2006; 35:234-46. [PMID: 17158511 PMCID: PMC1802579 DOI: 10.1093/nar/gkl919] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Gene expression and processing during mouse male germ cell maturation (spermatogenesis) is highly specialized. Previous reports have suggested that there is a high incidence of alternative 3′-processing in male germ cell mRNAs, including reduced usage of the canonical polyadenylation signal, AAUAAA. We used EST libraries generated from mouse testicular cells to identify 3′-processing sites used at various stages of spermatogenesis (spermatogonia, spermatocytes and round spermatids) and testicular somatic Sertoli cells. We assessed differences in 3′-processing characteristics in the testicular samples, compared to control sets of widely used 3′-processing sites. Using a new method for comparison of degenerate regulatory elements between sequence samples, we identified significant changes in the use of putative 3′-processing regulatory sequence elements in all spermatogenic cell types. In addition, we observed a trend towards truncated 3′-untranslated regions (3′-UTRs), with the most significant differences apparent in round spermatids. In contrast, Sertoli cells displayed a much smaller trend towards 3′-UTR truncation and no significant difference in 3′-processing regulatory sequences. Finally, we identified a number of genes encoding mRNAs that were specifically subject to alternative 3′-processing during meiosis and postmeiotic development. Our results highlight developmental differences in polyadenylation site choice and in the elements that likely control them during spermatogenesis.
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Affiliation(s)
- Donglin Liu
- The Jackson Laboratory, 600 Main StreetBar Harbor, ME 04609, USA
| | - J. Michael Brockman
- The Jackson Laboratory, 600 Main StreetBar Harbor, ME 04609, USA
- Bioinformatics Program, Boston University24 Cummington Street, Boston, MA 02215, USA
| | - Brinda Dass
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, TX 79430, USA
| | | | - Priyam Singh
- The Jackson Laboratory, 600 Main StreetBar Harbor, ME 04609, USA
- Bioinformatics Program, Boston University24 Cummington Street, Boston, MA 02215, USA
| | - John R. McCarrey
- Department of Biology, University of Texas at San AntonioSan Antonio, TX 78249, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbock, TX 79430, USA
| | - Joel H. Graber
- The Jackson Laboratory, 600 Main StreetBar Harbor, ME 04609, USA
- Bioinformatics Program, Boston University24 Cummington Street, Boston, MA 02215, USA
- To whom correspondence should be addressed. Tel: +1 207 288 6847; Fax: +1 207 288 6073;
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Qu X, Perez-Canadillas JM, Agrawal S, De Baecke J, Cheng H, Varani G, Moore C. The C-terminal domains of vertebrate CstF-64 and its yeast orthologue Rna15 form a new structure critical for mRNA 3'-end processing. J Biol Chem 2006; 282:2101-15. [PMID: 17116658 DOI: 10.1074/jbc.m609981200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Yeast Rna15 and its vertebrate orthologue CstF-64 play critical roles in mRNA 3 '-end processing and in transcription termination downstream of poly(A) sites. These proteins contain N-terminal domains that recognize the poly(A) site, but little is known about their highly conserved C-terminal regions. Here we show by NMR that the C-terminal domains of CstF-64 and Rna15 fold into a three-helix bundle with an uncommon topological arrangement. The structure defines a cluster of evolutionary conserved yet exposed residues we show to be essential for the interaction between Pcf11 and Rna15. Furthermore, we demonstrate that this interaction is critical for the function of Rna15 in 3 '-end processing but dispensable for transcription termination. The C-terminal domain of the Rna15 homologue Pti1 contains critical sequence alterations within this region that are predicted to prevent Pcf11 interaction, providing an explanation for the distinct functions of these two closely related proteins in the 3 '-end formation of RNA polymerase II transcripts. These results define the role of the C-terminal half of Rna15 and provide insight into the network of protein/protein interactions responsible for assembly of the 3 '-end processing apparatus.
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Affiliation(s)
- Xiangping Qu
- Department of Molecular Microbiology, Tufts University School of Medicine and the Sackler Graduate School of Biomedical Sciences, Boston, Massachusetts 02111, USA
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Chen JM, Férec C, Cooper DN. A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes I: general principles and overview. Hum Genet 2006; 120:1-21. [PMID: 16645853 DOI: 10.1007/s00439-006-0180-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 03/26/2006] [Indexed: 10/24/2022]
Abstract
The 3' regulatory regions (3' RRs) of human genes play an important role in regulating mRNA 3' end formation, stability/degradation, nuclear export, subcellular localization and translation and are consequently rich in regulatory elements. Although 3' RRs contain only approximately 0.2% of known disease-associated mutations, this is likely to represent a rather conservative estimate of their actual prevalence. In an attempt to catalogue 3' RR-mediated disease and also to gain a greater understanding of the functional role of regulatory elements within 3' RRs, we have performed a systematic analysis of disease-associated 3' RR variants; 121 3' RR variants in 94 human genes were collated. These included 17 mutations in the upstream core polyadenylation signal sequence (UCPAS), 81 in the upstream sequence (USS) between the translational termination codon and the UCPAS, 6 in the left arm of the 'spacer' sequence (LAS) between the UCPAS and the pre-mRNA cleavage site (CS), 3 in the right arm of the 'spacer' sequence (RAS) or downstream core polyadenylation signal sequence (DCPAS) and 7 in the downstream sequence (DSS) of the 3'-flanking region, with 7 further mutations being treated as isolated examples. All the UCPAS mutations and the rather unusual cases of the DMPK, SCA8, FCMD and GLA mutations exert a significant effect on the mRNA phenotype and are usually associated with monogenic disease. By contrast, most of the remaining variants are polymorphisms that exert a comparatively minor influence on mRNA expression, but which may nevertheless predispose to or otherwise modify complex clinical phenotypes. Considerable efforts have been made to validate/elucidate the mechanisms through which the 3' untranslated region (3' UTR) variants affect gene expression. It is hoped that the integrative approach employed here in the study of naturally occurring variants of actual or potential pathological significance will serve to complement ongoing efforts to identify all functional regulatory elements in the human genome.
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Salisbury J, Hutchison KW, Graber JH. A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif. BMC Genomics 2006; 7:55. [PMID: 16542450 PMCID: PMC1539018 DOI: 10.1186/1471-2164-7-55] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Accepted: 03/16/2006] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Cleavage Stimulation Factor (CstF) is a required protein complex for eukaryotic mRNA 3'-processing. CstF interacts with 3'-processing downstream elements (DSEs) through its 64-kDa subunit, CstF-64; however, the exact nature of this interaction has remained unclear. We used EST-to-genome alignments to identify and extract large sets of putative 3'-processing sites for mRNA from ten metazoan species, including Homo sapiens, Canis familiaris, Rattus norvegicus, Mus musculus, Gallus gallus, Danio rerio, Takifugu rubripes, Drosophila melanogaster, Anopheles gambiae, and Caenorhabditis elegans. In order to further delineate the details of the mRNA-protein interaction, we obtained and multiply aligned CstF-64 protein sequences from the same species. RESULTS We characterized the sequence content and specific positioning of putative DSEs across the range of organisms studied. Our analysis characterized the downstream element (DSE) as two distinct parts - a proximal UG-rich element and a distal U-rich element. We find that while the U-rich element is largely conserved in all of the organisms studied, the UG-rich element is not. Multiple alignment of the CstF-64 RNA recognition motif revealed that, while it is highly conserved throughout metazoans, we can identify amino acid changes that correlate with observed variation in the sequence content and positioning of the DSEs. CONCLUSION Our analysis confirms the early reports of separate U- and UG-rich DSEs. The correlated variations in protein sequence and mRNA binding sequences provide novel insights into the interactions between the precursor mRNA and the 3'-processing machinery.
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Affiliation(s)
- Jesse Salisbury
- Functional Genomics Program, The University of Maine, Orono, Maine 04469, USA
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
| | - Keith W Hutchison
- Functional Genomics Program, The University of Maine, Orono, Maine 04469, USA
- Department of Biochemistry, Microbiology and Molecular Biology, The University of Maine, Orono, ME 04469, USA
| | - Joel H Graber
- Functional Genomics Program, The University of Maine, Orono, Maine 04469, USA
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA
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36
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Uitte de Willige S, de Visser MCH, Houwing-Duistermaat JJ, Rosendaal FR, Vos HL, Bertina RM. Genetic variation in the fibrinogen gamma gene increases the risk for deep venous thrombosis by reducing plasma fibrinogen gamma' levels. Blood 2005; 106:4176-83. [PMID: 16144795 DOI: 10.1182/blood-2005-05-2180] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We investigated the association between haplotypes of fibrinogen alpha (FGA), beta (FGB), and gamma (FGG), total fibrinogen levels, fibrinogen gamma' (gammaA/gamma' plus gamma'/gamma') levels, and risk for deep venous thrombosis. In a population-based case-control study, the Leiden Thrombophilia Study, we typed 15 haplotype-tagging single nucleotide polymorphisms (htSNPs) in this gene cluster. None of these haplotypes was associated with total fibrinogen levels. In each gene, one haplotype increased the thrombosis risk approximately 2-fold. After adjustment for linkage disequilibrium between the genes, only FGG-H2 homozygosity remained associated with risk (odds ratio [OR], 2.4; 95% confidence interval [95% CI], 1.5-3.9). FGG-H2 was also associated with reduced fibrinogen gamma' levels and reduced ratios of fibrinogen gamma' to total fibrinogen. Multivariate analysis showed that reduced fibrinogen gamma' levels and elevated total fibrinogen levels were both associated with an increased risk for thrombosis, even after adjustment for FGG-H2. A reduced fibrinogen gamma' to total fibrinogen ratio (less than 0.69) also increased the risk (OR, 2.4; 95% CI, 1.7-3.5). We propose that FGG-H2 influences thrombosis risk through htSNP 10034C/T [rs2066865] by strengthening the consensus of a CstF site and thus favoring the formation of gammaA chain above that of gamma' chain. Fibrinogen gamma' contains a unique high-affinity, nonsubstrate binding site for thrombin, which seems critical for the expression of the antithrombin activity that develops during fibrin formation (antithrombin 1).
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Affiliation(s)
- Shirley Uitte de Willige
- Hemostasis and Thrombosis Research Center, Department of Hematology (C2-R), Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
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Deka P, Rajan PK, Perez-Canadillas JM, Varani G. Protein and RNA Dynamics Play Key Roles in Determining the Specific Recognition of GU-rich Polyadenylation Regulatory Elements by Human Cstf-64 Protein. J Mol Biol 2005; 347:719-33. [PMID: 15769465 DOI: 10.1016/j.jmb.2005.01.046] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Revised: 12/14/2004] [Accepted: 01/21/2005] [Indexed: 12/16/2022]
Abstract
The N-terminal domain of the 64 kDa subunit of the cleavage stimulation factor (CstF-64) recognizes GU-rich elements within the 3'-untranslated region of eukaryotic mRNAs. This interaction is essential for mRNA 3' end processing and transcription termination, and its strength affects the efficiency of utilization of different polyadenylation sites. The structure of the RNA-binding N-terminal domain of CstF-64 showed how the N-terminal RNA recognition motif of CstF-64 recognizes GU-rich RNAs. However, it is still perplexing how this protein can bind selectively to RNAs that are rich in G and U residues regardless of their detailed sequence composition, yet discriminate effectively against non-GU-RNAs. We investigated by NMR the dynamics of the CstF-64 RNA-binding domain, both free and bound to two GU-rich RNA sequences that represent polyadenylation regulatory elements. While the free protein displays the motional properties typical of a well-folded protein domain and is uniformly rigid, the protein-RNA interface acquires significant mobility on the micro- to millisecond time-scale once GU-rich RNAs binds to it. These motional features, we propose, are intrinsic to the functional requirement to bind all GU-rich sequences and yet to discriminate against non-GU-rich RNAs. This behavior may be a general mechanism by which some RNA-binding proteins are able to bind to classes of sequences, as opposed to a well-defined sequence or consensus.
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Affiliation(s)
- Pritilekha Deka
- Department of Biochemistry and Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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38
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Danckwardt S, Gehring NH, Neu-Yilik G, Hundsdoerfer P, Pforsich M, Frede U, Hentze MW, Kulozik AE. The prothrombin 3'end formation signal reveals a unique architecture that is sensitive to thrombophilic gain-of-function mutations. Blood 2004; 104:428-35. [PMID: 15059842 DOI: 10.1182/blood-2003-08-2894] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The functional analysis of the common prothrombin 20210 G>A(F2 20210(*)A) mutation has recently revealed gain of function of 3'end processing as a novel genetic mechanism predisposing to human disease. We now show that the physiologic G at the cleavage site at position 20210 is the functionally least efficient nucleotide to support 3'end processing but has evolved to be physiologically optimal. Furthermore, the F2 3'end processing signal is characterized by a weak downstream cleavage stimulating factor (CstF) binding site with a low uridine density, and the functional efficiency of F2 3'end processing can be enhanced by the introduction of additional uridine residues. The recently identified thrombosis-related mutation (F2 20221(*)T) within the CstF binding site up-regulates F2 3'end processing and prothrombin biosynthesis in vivo. F2 20221(*)T thus represents the first example of a likely pathologically relevant mutation of the putative CstF binding site in the 3'flanking sequence of a human gene. Finally, we show that the low-efficiency F2 cleavage and CstF binding sites are balanced by a stimulatory upstream uridine-rich element in the 3'UTR. The architecture of the F2 3'end processing signal is thus characterized by a delicate balance of positive and negative signals. This balance appears to be highly susceptible to being disturbed by clinically relevant gain-of-function mutations.
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Affiliation(s)
- Sven Danckwardt
- Molecular Medicine Partnership Unit, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany
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Ryan K, Calvo O, Manley JL. Evidence that polyadenylation factor CPSF-73 is the mRNA 3' processing endonuclease. RNA (NEW YORK, N.Y.) 2004; 10:565-73. [PMID: 15037765 PMCID: PMC1370546 DOI: 10.1261/rna.5214404] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Accepted: 12/29/2003] [Indexed: 05/04/2023]
Abstract
Generation of the polyadenylated 3' end of an mRNA requires an endonucleolytic cleavage followed by synthesis of the poly(A) tail. Despite the seeming simplicity of the reaction, more than a dozen polypeptides are required, and nearly all appear to be necessary for the cleavage reaction. Because of this complexity, the identity of the endonuclease has remained a mystery. Here we present evidence that a component of the cleavage-polyadenylation specificity factor CPSF-73 is the long-sought endonuclease. We first show, using site-specific labeling and UV-cross-linking, that a protein with properties of CPSF-73 is one of only two polypeptides in HeLa nuclear extract to contact the cleavage site in an AAUAAA-dependent manner. The recent identification of CPSF-73 as a possible member of the metallo-beta-lactamase family of Zn(2+)-dependent hydrolytic enzymes suggests that this contact may identify CPSF-73 as the nuclease. Supporting the significance of the putative hydrolytic lactamase domain in CPSF-73, we show that mutation of key residues predicted to be required for activity in the yeast CPSF-73 homolog result in lethality. Furthermore, in contrast to long held belief, but consistent with properties of metallo-beta-lactamases, we show that 3' cleavage is metal-dependent, likely reflecting a requirement for tightly protein-bound Zn(2+). Taken together, the available data provide strong evidence that CPSF-73 is the 3' processing endonuclease.
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Affiliation(s)
- Kevin Ryan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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Brown KM, Gilmartin GM. A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im. Mol Cell 2004; 12:1467-76. [PMID: 14690600 DOI: 10.1016/s1097-2765(03)00453-2] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Human cleavage factor I(m) (CFI(m)) is a heterodimeric RNA binding protein complex that functions at an early step in the assembly of the pre-mRNA 3' processing complex. In this report we show that CFI(m) can stimulate both cleavage and poly(A) addition, and can act to suppress poly(A) site cleavage in a sequence-dependent manner. Elevated levels of CFI(m) suppressed cleavage at the primary poly(A) site of the pre-mRNA encoding the 68 kDa subunit of CFI(m). CFI(m)-mediated suppression of poly(A) site cleavage was dependent upon the presence of three copies of an RNA element initially identified by CFI(m)-SELEX. These data provide evidence for a mechanism for the regulation of poly(A) site selection by a basal pre-mRNA 3' processing factor.
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Affiliation(s)
- Kirk M Brown
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
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Su Y, Adair R, Davis CN, DiFronzo NL, Colberg-Poley AM. Convergence of RNA cis elements and cellular polyadenylation factors in the regulation of human cytomegalovirus UL37 exon 1 unspliced RNA production. J Virol 2004; 77:12729-41. [PMID: 14610195 PMCID: PMC262569 DOI: 10.1128/jvi.77.23.12729-12741.2003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The human cytomegalovirus (HCMV) UL36-38 immediate early (IE) locus encodes proteins required for its growth. The UL37 promoter drives production of an unspliced and several alternatively spliced RNAs. The UL37 exon 1 (UL37x1) unspliced RNA is abundant from IE to late times of HCMV infection, whereas the UL37 spliced RNAs are markedly less abundant. Production of the UL37x1 unspliced RNA requires polyadenylation (PA) at nucleotide 50998, which lies within intron 1, upstream of the UL37 exon 2 (UL37x2) acceptor. The physical proximity of its cis elements suggests steric hindrance between PA and splicing machineries for UL37 pre-mRNA. To test this possibility, we generated site-specific mutants in Target 1 PA and RNA splicing cis elements and compared the PA and splicing efficiencies of mutant RNAs with those of wild-type RNA. The mutually exclusive processing events of UL37x1 PA and UL37x1-UL37x2 splicing have been accurately recapitulated in transfected permissive human fibroblasts (HFFs) expressing a Target 1 minigene RNA, which contains the required splicing and PA cis elements. Two mutants in the invariant PA signal dramatically decreased UL37x1 PA as expected and, concomitantly, increased the efficiency of UL37x1-UL37x2 RNA splicing. Consistent with these results, changes to consensus UL37x1 donor and UL37x2 acceptor sites increased the efficiency of UL37x1-UL37x2 RNA splicing but decreased the efficiency of UL37x1 PA. Moreover, HCMV infection of HFFs increased the abundance of the PA cleavage stimulatory factor CstF-64, the potent splicing suppressor PTB, and the hypophosphorylated form of the splicing factor SF2 at 4 h postinfection. Induction of these factors further favors production of the UL37x1 unspliced RNA over that of the spliced RNAs. Taken together, these results suggest that there is a convergence in UL37 RNA regulation by cis elements and cellular proteins which favors production of the UL37x1 unspliced RNA during HCMV infection at the posttranscriptional level.
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Affiliation(s)
- Yan Su
- Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, USA
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Ceelie H, Spaargaren-van Riel CC, Bertina RM, Vos HL. G20210A is a functional mutation in the prothrombin gene; effect on protein levels and 3'-end formation. J Thromb Haemost 2004; 2:119-27. [PMID: 14717975 DOI: 10.1111/j.1538-7836.2003.00493.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND The prothrombin G20210A mutation is associated with increased plasma prothrombin levels and risk of thrombosis. The mechanism by which this mutation leads to increased prothrombin expression is as yet unclear and still the subject of debate. OBJECTIVES The aim of this study was to investigate the effect of the G20210A mutation on mRNA and protein expression. METHODS We made a set of constructs containing the prothrombin 5'-regulatory region, the firefly luciferase reporter gene and the prothrombin 3'-UTR+ downstream region. The latter element contained either the 20210G or A allele and was inserted either as a single unit (constructs G1 and A1) or in tandem (A1A2, G1G2, A1G2, G1A2). Constructs were transiently expressed in HepG2 cells. Expression was evaluated by luciferase assays and reverse transcriptase-polymerase chain reaction (RT-PCR), followed by quantification of the products and determination of the ratio of poly(A)site usage. RT-PCR sequencing was used for determination of the actual site of polyadenylation in mRNAs from constructs G1 and A1 and from endogenous prothrombin mRNAs from HepG2 cells and human liver tissue. RESULTS The A1 constructs expressed 1.2-fold more protein than the G1 constructs. The double constructs expressed 1.4-fold more protein (A1A2 vs. G1G2). Similar results were found in a set of constructs in which an SV40 promoter replaced the prothrombin 5'-regulatory region. Ratios of poly(A) site usage (expressed as ratio poly(A) site 1 and 2) for the tandem constructs were similar for constructs with two Gs or As at both poly(A)sites; 2.92 (95% confidence interval 2.39-3.45) and 2.75 (2.55-2.95). pA1/pA2 ratios were 1.46 (1.11-1.81) for G1A2 and 6.29 (5.48-7.10) for A1G2 constructs with different poly(A) sites, indicating that the poly(A)site with the 20210A variant is favored over the normal site. In 20210G mRNAs, the G at 20210 was the last non-A nucleotide in the majority of mRNAs, whereas in most 20210A mRNAs, the last non-A nucleotide was the C at 20209. Over 70% of the prothrombin 20210G mRNAs from HepG2 cells and human liver tissue is polyadenylated at position 20210. CONCLUSIONS The 20210A variant has a more effective poly(A) site, leading to increased mRNA and protein expression, irrespective of the promoter and gene. It does not affect the position of poly(A) attachment.
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Affiliation(s)
- H Ceelie
- Hemostasis and Thrombosis Research Center, Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands.
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Pérez Cañadillas JM, Varani G. Recognition of GU-rich polyadenylation regulatory elements by human CstF-64 protein. EMBO J 2003; 22:2821-30. [PMID: 12773396 PMCID: PMC156756 DOI: 10.1093/emboj/cdg259] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Vertebrate polyadenylation sites are identified by the AAUAAA signal and by GU-rich sequences downstream of the cleavage site. These are recognized by a heterotrimeric protein complex (CstF) through its 64 kDa subunit (CstF-64); the strength of this interaction affects the efficiency of poly(A) site utilization. We present the structure of the RNA-binding domain of CstF-64 containing an RNA recognition motif (RRM) augmented by N- and C-terminal helices. The C-terminal helix unfolds upon RNA binding and extends into the hinge domain where interactions with factors responsible for assembly of the polyadenylation complex occur. We propose that this conformational change initiates assembly. Consecutive Us are required for a strong CstF-GU interaction and we show how UU dinucleotides are recognized. Contacts outside the UU pocket fine tune the protein-RNA interaction and provide different affinities for distinct GU-rich elements. The protein-RNA interface remains mobile, most likely a requirement to bind many GU-rich sequences and yet discriminate against other RNAs. The structural distinction between sequences that form stable and unstable complexes provides an operational distinction between weakly and strongly processed poly(A) sites.
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res 2003; 31:1375-86. [PMID: 12595544 PMCID: PMC149834 DOI: 10.1093/nar/gkg241] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2002] [Accepted: 01/13/2003] [Indexed: 01/06/2023] Open
Abstract
Primary, secondary and higher-order structures of downstream elements of mammalian pre-mRNA polyadenylation signals [poly(A) signals] are re viewed. We have carried out a detailed analysis on our database of 244 human pre-mRNA poly(A) signals in order to characterize elements in their downstream regions. We suggest that the downstream region of the mammalian pre-mRNA poly(A) signal consists of various simple elements located at different distances from each other. Thus, the downstream region is not described by any precise consensus. Searching our database, we found that approximately 80% of pre-mRNAs with the AAUAAA or AUUAAA core upstream elements contain simple downstream elements, consisting of U-rich and/or 2GU/U tracts, the former occurring approximately 2-fold more often than the latter. Approximately one-third of the pre-mRNAs analyzed here contain sequences that may form G-quadruplexes. A substantial number of these sequences are located immediately downstream of the poly(A) signal. A possible role of G-rich sequences in the polyadenylation process is discussed. A model of the secondary structure of the SV40 late pre-mRNA poly(A) signal downstream region is presented.
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Affiliation(s)
- Margarita I Zarudnaya
- Molecular Biophysics Department, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, vul. Zabolotnoho, Kyiv, 03143, Ukraine.
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Hodges MD, Vieira H, Gregory-Evans K, Gregory-Evans CY. Characterization of the genomic and transcriptional structure of the CRX gene: substantial differences between human and mouse. Genomics 2002; 80:531-42. [PMID: 12408971 DOI: 10.1006/geno.2002.6854] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
UNLABELLED We have previously shown that there is a temporal difference in human CRX: gene expression compared with that of mouse Crx. We have now characterized these genes at the genomic and transcriptional levels and here we expand on this earlier report. Human CRX: spans 25 kb and has six exons, and mouse CRX: spans 15 kb and has four exons. We isolated seven human and two mouse mRNAs generated by alternative splicing of a variable 5' untranslated region. The human and mouse genes share an evolutionarily conserved promoter, which contains OTX/CRX type and SP1/AP2 binding sites and drives expression of two conserved transcripts in both species. Additionally, the human gene has a second human-specific promoter, which has OTX/CRX type binding sites and drives expression of five other transcripts. Band shift assays have shown that six of the seven candidate OTX/CRX elements bind CRX in vitro, possibly implying that the gene can regulate its own expression. These data may account for the differences in temporal expression IN VIVO we have previously reported between these two species.
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Affiliation(s)
- Matthew D Hodges
- Section of Cell and Molecular Biology, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
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Maeda Y, Ito M, Harashima N, Nakatsura T, Hida N, Imai N, Sato Y, Shichijo S, Todo S, Itoh K. Cleavage and polyadenylation specificity factor (CPSF)-derived peptides can induce HLA-A2-restricted and tumor-specific CTLs in the majority of gastrointestinal cancer patients. Int J Cancer 2002; 99:409-17. [PMID: 11992410 DOI: 10.1002/ijc.10377] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
To identify CTL-directed antigens in gastrointestinal cancer, we have investigated antigens recognized by the HLA-A2-restricted CTL line established from T cells infiltrating into colon cancer and report herein cleavage and polyadenylation specificity factor (CPSF) as a potent antigen holding peptides capable of inducing CTLs. Five peptides at amino acid positions 250-258, 392-400, 534-542, 1296-1304 and 1359-1368 of CPSF, which were recognized by the CTL line, were found to have the ability to induce HLA-A2-restricted and tumor-specific CTLs in peripheral blood mononuclear cells of the majority (69%, 11/16) of gastrointestinal cancer patients with different HLA-A2 subtypes. Thus, these peptides might be appropriate molecules for use in the peptide-based specific immunotherapy of HLA-A2(+) patients with gastrointestinal cancers.
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Affiliation(s)
- Yoshiaki Maeda
- Department of Immunology, Kurume University School of Medicine, Kurume, Japan
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Abstract
Polyadenylation is the process by which most eukaryotic mRNAs form their 3' ends. It was long held that polyadenylation required the sequence AAUAAA and that 90% of mRNAs had AAUAAA within 30 nucleotides of the site of poly(A) addition. More recent studies, aided by computer analysis of sequences made available in GenBank and expressed sequence tag (EST) databases, have suggested that the actual incidence of AAUAAA is much lower, perhaps as low as 50-60%. Reproductive biologists have long recognized that a large number of mRNAs in male germ cells of mammals lack AAUAAA but are otherwise normally polyadenylated. Recent research in our laboratory has uncovered a new form of an essential polyadenylation protein, tauCstF-64, that is most highly expressed in male germ cells, and to a smaller extent in the brain, and which we propose plays a significant role in AAUAAA-independent mRNA polyadenylation in germ cells.
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Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry and Southwest Cancer Center at University Medical Center, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock 79430, USA.
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Arhin GK, Boots M, Bagga PS, Milcarek C, Wilusz J. Downstream sequence elements with different affinities for the hnRNP H/H' protein influence the processing efficiency of mammalian polyadenylation signals. Nucleic Acids Res 2002; 30:1842-50. [PMID: 11937639 PMCID: PMC113221 DOI: 10.1093/nar/30.8.1842] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2001] [Revised: 02/21/2002] [Accepted: 02/21/2002] [Indexed: 11/13/2022] Open
Abstract
Auxiliary factors likely play an important role in determining the polyadenylation efficiency of mammalian pre-mRNAs. We previously identified an auxiliary factor, hnRNP H/H', which stimulates 3'-end processing through an interaction with sequences downstream of the core elements of the SV40 late polyadenylation signal. Using in vitro reconstitution assays we have demonstrated that hnRNP H/H' can stimulate processing of two additional model polyadenylation signals by binding at similar relative downstream locations but with significantly different affinities. A short tract of G residues was determined to be a common property of all three hnRNP H/H' binding sites. A survey of mammalian polyadenylation signals identified potential G-rich hnRNP H/H' binding sites at similar downstream locations in approximately 34% of these signals. All of the novel G-rich elements tested were found to bind hnRNP H/H' protein and the processing of selected signals identified in the survey was stimulated by the protein both in vivo and in vitro. Downstream G-rich tracts, therefore, are a common auxiliary element in mammalian polyadenylation signals. Sequences capable of binding hnRNP H protein with varying affinities may play a role in determining the processing efficiency of a significant number of mammalian polyadenylation signals.
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Affiliation(s)
- George K Arhin
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
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Graber JH, McAllister GD, Smith TF. Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites. Nucleic Acids Res 2002; 30:1851-8. [PMID: 11937640 PMCID: PMC113205 DOI: 10.1093/nar/30.8.1851] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a tool for the prediction of mRNA 3'-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3'-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3'-processing sites. Known alternative 3'-processing sites, both within the 3'-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3'-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences.
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Affiliation(s)
- Joel H Graber
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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Gross S, Moore CL. Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3'-end formation. Mol Cell Biol 2001; 21:8045-55. [PMID: 11689695 PMCID: PMC99971 DOI: 10.1128/mcb.21.23.8045-8055.2001] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2001] [Accepted: 08/28/2001] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, four factors [cleavage factor I (CF I), CF II, polyadenylation factor I (PF I), and poly(A) polymerase (PAP)] are required for maturation of the 3' end of the mRNA. CF I and CF II are required for cleavage; a complex of PAP and PF I, which includes CF II subunits, participates in polyadenylation, along with CF I. These factors are directed to the appropriate site on the mRNA by two sequences: one A-rich and one UA-rich. CF I contains five proteins, two of which, Rna15 and Hrp1, interact with the mRNA through RNA recognition motif-type RNA binding motifs. Previous work demonstrated that the UV cross-linking of purified Hrp1 to RNA required the UA-rich element, but the contact point of Rna15 was not known. We show here that Rna15 does not recognize a particular sequence in the absence of other proteins. However, in complex with Hrp1 and Rna14, Rna15 specifically interacts with the A-rich element. The Pcf11 and Clp1 subunits of CF I are not needed to position Rna15 at this site. This interaction is essential to the function of CF I. A mutant Rna15 with decreased affinity for RNA is defective for in vitro RNA processing and lethal in vivo, while an RNA with a mutation in the A-rich element is not processed in vitro and can no longer be UV cross-linked to the Rna15 subunit assembled into CF I. Thus, the recognition of the A-rich element depends on the tethering of Rna15 through an Rna14 bridge to Hrp1 bound to the UA-rich motif. These results illustrate that the yeast 3' end is defined and processed by a mechanism surprisingly different from that used by the mammalian system.
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Affiliation(s)
- S Gross
- Department of Molecular Biology and Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, USA
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