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Xu J, Wang D, Ma H, Zhai X, Huo Y, Ren Y, Li W, Chang L, Lu D, Guo Y, Si Y, Gao Y, Wang X, Ma Y, Wang F, Yu J. KHSRP combines transcriptional and posttranscriptional mechanisms to regulate monocytic differentiation. BLOOD SCIENCE 2022; 4:103-115. [DOI: 10.1097/bs9.0000000000000122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/11/2022] [Indexed: 11/25/2022] Open
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Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lécuyer E, Burge CB, Graveley BR, Yeo GW. A large-scale binding and functional map of human RNA-binding proteins. Nature 2020; 583:711-719. [PMID: 32728246 PMCID: PMC7410833 DOI: 10.1038/s41586-020-2077-3] [Citation(s) in RCA: 577] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 07/10/2019] [Indexed: 11/09/2022]
Abstract
Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs.
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Affiliation(s)
- Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Peter Freese
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Xiaofeng Wang
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Rui Xiao
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Neal A L Cody
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Balaji Sundararaman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Cassandra Bazile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Michael O Duff
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Keri E Garcia
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chelsea Gelboin-Burkhart
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Myles Hochman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole J Lambert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael P McGurk
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thai B Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tsultrim Palden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Stanton
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amanda Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ruth Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ashley L Louie
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
| | - Christopher B Burge
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
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3
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Genuth NR, Barna M. Heterogeneity and specialized functions of translation machinery: from genes to organisms. Nat Rev Genet 2019; 19:431-452. [PMID: 29725087 DOI: 10.1038/s41576-018-0008-z] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Regulation of mRNA translation offers the opportunity to diversify the expression and abundance of proteins made from individual gene products in cells, tissues and organisms. Emerging evidence has highlighted variation in the composition and activity of several large, highly conserved translation complexes as a means to differentially control gene expression. Heterogeneity and specialized functions of individual components of the ribosome and of the translation initiation factor complexes eIF3 and eIF4F, which are required for recruitment of the ribosome to the mRNA 5' untranslated region, have been identified. In this Review, we summarize the evidence for selective mRNA translation by components of these macromolecular complexes as a means to dynamically control the translation of the proteome in time and space. We further discuss the implications of this form of gene expression regulation for a growing number of human genetic disorders associated with mutations in the translation machinery.
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Affiliation(s)
- Naomi R Genuth
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Maria Barna
- Departments of Genetics and Developmental Biology, Stanford University, Stanford, CA, USA.
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4
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Cate JHD. Human eIF3: from 'blobology' to biological insight. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0176. [PMID: 28138064 PMCID: PMC5311922 DOI: 10.1098/rstb.2016.0176] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 02/06/2023] Open
Abstract
Translation in eukaryotes is highly regulated during initiation, a process impacted by numerous readouts of a cell's state. There are many cases in which cellular messenger RNAs likely do not follow the canonical ‘scanning’ mechanism of translation initiation, but the molecular mechanisms underlying these pathways are still being uncovered. Some RNA viruses such as the hepatitis C virus use highly structured RNA elements termed internal ribosome entry sites (IRESs) that commandeer eukaryotic translation initiation, by using specific interactions with the general eukaryotic translation initiation factor eIF3. Here, I present evidence that, in addition to its general role in translation, eIF3 in humans and likely in all multicellular eukaryotes also acts as a translational activator or repressor by binding RNA structures in the 5′-untranslated regions of specific mRNAs, analogous to the role of the mediator complex in transcription. Furthermore, eIF3 in multicellular eukaryotes also harbours a 5′ 7-methylguanosine cap-binding subunit—eIF3d—which replaces the general cap-binding initiation factor eIF4E in the translation of select mRNAs. Based on results from cell biological, biochemical and structural studies of eIF3, it is likely that human translation initiation proceeds through dozens of different molecular pathways, the vast majority of which remain to be explored. This article is part of the themed issue ‘Perspectives on the ribosome’.
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Affiliation(s)
- Jamie H D Cate
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA .,Lawrence Berkeley National Laboratory, Division of Molecular Biophysics and Integrated Bioimaging, Berkeley, CA 94720, USA
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5
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Kumar P, Hellen CUT, Pestova TV. Toward the mechanism of eIF4F-mediated ribosomal attachment to mammalian capped mRNAs. Genes Dev 2017; 30:1573-88. [PMID: 27401559 PMCID: PMC4949329 DOI: 10.1101/gad.282418.116] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/01/2016] [Indexed: 11/24/2022]
Abstract
Ribosomal attachment to mammalian capped mRNAs is achieved through the cap-eukaryotic initiation factor 4E (eIF4E)-eIF4G-eIF3-40S chain of interactions, but the mechanism by which mRNA enters the mRNA-binding channel of the 40S subunit remains unknown. To investigate this process, we recapitulated initiation on capped mRNAs in vitro using a reconstituted translation system. Formation of initiation complexes at 5'-terminal AUGs was stimulated by the eIF4E-cap interaction and followed "the first AUG" rule, indicating that it did not occur by backward scanning. Initiation complexes formed even at the very 5' end of mRNA, implying that Met-tRNAi (Met) inspects mRNA from the first nucleotide and that initiation does not have a "blind spot." In assembled initiation complexes, the cap was no longer associated with eIF4E. Omission of eIF4A or disruption of eIF4E-eIF4G-eIF3 interactions converted eIF4E into a specific inhibitor of initiation on capped mRNAs. Taken together, these results are consistent with the model in which eIF4E-eIF4G-eIF3-40S interactions place eIF4E at the leading edge of the 40S subunit, and mRNA is threaded into the mRNA-binding channel such that Met-tRNAi (Met) can inspect it from the first nucleotide. Before entering, eIF4E likely dissociates from the cap to overcome steric hindrance. We also found that the m(7)G cap specifically interacts with eIF3l.
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Affiliation(s)
- Parimal Kumar
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, State University of New York Downstate Medical Center, Brooklyn, New York 11203, USA
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6
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Sundararaman B, Zhan L, Blue SM, Stanton R, Elkins K, Olson S, Wei X, Van Nostrand EL, Pratt GA, Huelga SC, Smalec BM, Wang X, Hong EL, Davidson JM, Lécuyer E, Graveley BR, Yeo GW. Resources for the Comprehensive Discovery of Functional RNA Elements. Mol Cell 2016; 61:903-13. [PMID: 26990993 DOI: 10.1016/j.molcel.2016.02.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/18/2015] [Accepted: 02/08/2016] [Indexed: 10/22/2022]
Abstract
Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell lines, tissues, and developmental stages is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs. In parallel, 362 short-hairpin RNA (shRNA) constructs against 276 unique RBPs were also used to confirm specificity of these antibodies. These antibodies can characterize subcellular RBP localization. With the burgeoning interest in the roles of RBPs in cancer, neurobiology, and development, these resources are invaluable to the broad scientific community. Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/).
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Affiliation(s)
- Balaji Sundararaman
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rebecca Stanton
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Keri Elkins
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Stephanie C Huelga
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Brendan M Smalec
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA
| | - Xiaofeng Wang
- Département de Biochimie, Université de Montréal; Division of Experimental Medicine, McGill University; Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Eurie L Hong
- ENCODE Data Coordinating Center (DCC), Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jean M Davidson
- ENCODE Data Coordinating Center (DCC), Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric Lécuyer
- Département de Biochimie, Université de Montréal; Division of Experimental Medicine, McGill University; Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT 06030, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
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eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature 2016; 536:96-9. [PMID: 27462815 PMCID: PMC5003174 DOI: 10.1038/nature18954] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 06/21/2016] [Indexed: 12/19/2022]
Abstract
Eukaryotic mRNAs contain a 5' cap structure critical for recruitment of the translation machinery and initiation of protein synthesis. mRNA recognition is thought to require direct interactions between eukaryotic initiation factor 4E (eIF4E) and the mRNA cap. However, translation of numerous capped mRNAs remains robust during cellular stress, early development, and cell cycle progression1 despite eIF4E inactivation. Here we describe a new cellular cap-dependent pathway of translation initiation that relies on a previously unknown cap-binding activity of eIF3d, a subunit of the 800-kilodalton eukaryotic initiation factor 3 (eIF3) complex. A 1.4 Å crystal structure of the eIF3d cap-binding domain reveals unexpected homology to endonucleases involved in RNA turnover, and allows modeling of cap recognition by eIF3d. eIF3d makes specific contacts to the cap, as exemplified by cap analog competition, and these interactions are essential for assembly of translation initiation complexes on eIF3-specialized mRNAs2 such as the cell proliferation regulator c-Jun. The c-Jun mRNA further encodes an inhibitory RNA element that blocks eIF4E recruitment, thus enforcing alternative cap recognition by eIF3d. Our results reveal a new mechanism of cap-dependent translation independent of eIF4E, and illustrate how modular RNA elements work in concert to direct specialized forms of translation initiation.
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Forde N, Carter F, Spencer T, Bazer F, Sandra O, Mansouri-Attia N, Okumu L, McGettigan P, Mehta J, McBride R, O'Gaora P, Roche J, Lonergan P. Conceptus-Induced Changes in the Endometrial Transcriptome: How Soon Does the Cow Know She Is Pregnant?1. Biol Reprod 2011; 85:144-56. [DOI: 10.1095/biolreprod.110.090019] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Kolupaeva VG, Unbehaun A, Lomakin IB, Hellen CUT, Pestova TV. Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association. RNA (NEW YORK, N.Y.) 2005; 11:470-86. [PMID: 15703437 PMCID: PMC1370736 DOI: 10.1261/rna.7215305] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Accepted: 12/22/2004] [Indexed: 05/19/2023]
Abstract
The multisubunit eukaryotic initiation factor (eIF) 3 plays various roles in translation initiation that all involve interaction with 40S ribosomal subunits. eIF3 can be purified in two forms: with or without the loosely associated eIF3j subunit (eIF3j+ and eIF3j-, respectively). Although unlike eIF3j+, eIF3j- does not bind 40S subunits stably enough to withstand sucrose density gradient centrifugation, we found that in addition to the known stabilization of the eIF3/40S subunit interaction by the eIF2*GTP*Met-tRNA(i)Met ternary complex, eIF3j-/40S subunit complexes were also stabilized by single-stranded RNA or DNA cofactors that were at least 25 nt long and could be flanked by stable hairpins. Of all homopolymers, oligo(rU), oligo(dT), and oligo(dC) stimulated the eIF3/40S subunit interaction, whereas oligo(rA), oligo(rG), oligo(rC), oligo(dA), and oligo(dG) did not. Oligo(U) or oligo(dT) sequences interspersed by other bases also promoted this interaction. The ability of oligonucleotides to stimulate eIF3/40S subunit association correlated with their ability to bind to the 40S subunit, most likely to its mRNA-binding cleft. Although eIF3j+ could bind directly to 40S subunits, neither eIF3j- nor eIF3j+ alone was able to dissociate 80S ribosomes or protect 40S and 60S subunits from reassociation. Significantly, the dissociation/anti-association activities of both forms of eIF3 became apparent in the presence of either eIF2-ternary complexes or any oligonucleotide cofactor that promoted eIF3/40S subunit interaction. Ribosomal dissociation and anti-association activities of eIF3 were strongly enhanced by eIF1. The potential biological role of stimulation of eIF3/40S subunit interaction by an RNA cofactor in the absence of eIF2-ternary complex is discussed.
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Affiliation(s)
- Victoria G Kolupaeva
- Department of Microbiology and Immunology, SUNY Downstate Medical Center, 450 Clarkson Ave., Box 44, Brooklyn, NY 11203, USA
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Brown JT, Yang X, Johnson AW. Inhibition of mRNA turnover in yeast by an xrn1 mutation enhances the requirement for eIF4E binding to eIF4G and for proper capping of transcripts by Ceg1p. Genetics 2000; 155:31-42. [PMID: 10790382 PMCID: PMC1461062 DOI: 10.1093/genetics/155.1.31] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Null mutants of XRN1, encoding the major cytoplasmic exoribonuclease in yeast, are viable but accumulate decapped, deadenylated transcripts. A screen for mutations synthetic lethal with xrn1Delta identified a mutation in CDC33, encoding eIF4E. This mutation (glutamate to glycine at position 72) affected a highly conserved residue involved in interaction with eIF4G. Synthetic lethality between xrn1 and cdc33 was not relieved by high-copy expression of eIF4G or by disruption of the yeast eIF4E binding protein Caf20p. High-copy expression of a mutant eIF4G defective for eIF4E binding resulted in a dominant negative phenotype in an xrn1 mutant, indicating the importance of this interaction in an xrn1 mutant. Another allele of CDC33, cdc33-1, along with mutations in CEG1, encoding the nuclear guanylyltransferase, were also synthetic lethal with xrn1Delta, whereas mutations in PRT1, encoding a subunit of eIF3, were not. Mutations in CDC33, CEG1, PRT1, PAB1, and TIF4631, encoding eIF4G1, have been shown to lead to destabilization of mRNAs. Although such destabilization in cdc33, ceg1, and pab1 mutants can be partially suppressed by an xrn1 mutation, we observed synthetic lethality between xrn1 and either cdc33 or ceg1 and no suppression of the inviability of a pab1 null mutation by xrn1Delta. Thus, the inhibition of mRNA turnover by blocking Xrn1p function does not suppress the lethality of defects upstream in the turnover pathway but it does enhance the requirement for (7)mG caps and for proper formation of the eIF4E/eIF4G cap recognition complex.
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Affiliation(s)
- J T Brown
- Section of Molecular Genetics and Microbiology and the Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712-1095, USA
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11
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Yasukochi T, Okada O, Hara T, Sagara Y, Sekimizu K, Horiuchi T. Putative functions of phenylalanine-350 of Pseudomonas putida cytochrome P-450cam. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1204:84-90. [PMID: 8305479 DOI: 10.1016/0167-4838(94)90036-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cytochrome P-450cam hydroxylates d-camphor, using molecular oxygen and reducing equivalents transferred via putidaredoxin. We constructed mutant genes in which Phe-350 of P-450cam was replaced by Leu, Tyr, or His by site-directed mutagenesis, expressed them in Escherichia coli, purified the mutant proteins, and compared their enzymic properties with those of the wild type P-450cam. NADH oxidation rate of the Tyr mutant in the reconstituted system with putidaredoxin and putidaredoxin reductase was similar to that of the wild type enzyme, while the Leu mutant and the His mutant showed 67% and 17% activity of that of the wild type, respectively. The affinities of these mutant proteins for camphor and the oxidized form of putidaredoxin were much the same as those of the wild type protein. Rate constants for the reduction reaction of P-450cam by reduced putidaredoxin, a physiological electron donor for P-450cam, of Tyr and His mutants were much the same as that of the wild type enzyme, whereas the Leu mutant showed approx. half that of the wild type. Thus, the aromatic ring of Phe-350 of P-450cam probably contributes to enhancing efficiency of the electron transfer yet does not seem to be essential for the reaction.
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Affiliation(s)
- T Yasukochi
- Department of Microbiology, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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12
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van Heugten HA, Thomas AA, Voorma HO. Interaction of protein synthesis initiation factors with the mRNA cap structure. Biochimie 1992; 74:463-75. [PMID: 1637872 DOI: 10.1016/0300-9084(92)90087-u] [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: 12/28/2022]
Abstract
The mechanism of mRNA recognition by proteins interacting with the mRNA cap structure was investigated by photochemical cross-linking of proteins with 32P-labelled reoviral RNAs. Using ribosomal washes as a source of eukaryotic protein synthesis initiation factors, we identified the well-known cap binding proteins eIF-4B and -4E, but eIF-2 and eIF-3 as well. The interplay of purified eIF-4A, -4B, and -4F was studied in relation to ATP dependence and cap analogue sensitivity of cap binding. Next to their well-known roles in the initiation process, eIF-2 and eIF-3 also cross-linked to the 5' cap. eIF-2 stimulated eIF-4B and -4E cross-linking, an observation that has been previously described more extensively. The interaction of eIF-2 with the 5' end of mRNA was extremely sensitive to K(+)-ions and was resistant to a high concentration of Mg(2+)-ions; this influence of mono- and divalent ions was in contrast with the cross-linking of eIF-4B and -4E. Optimal interaction of these factors was obtained at moderate K+ concentration and low Mg(2+)-ion concentrations. eIF-2 cross-linking was sensitive to high protein to mRNA ratios indicating a weak affinity as compared to eIF-4E and -4B. The interaction of eIF-3 with the cap of mRNA is also weak as it was counteracted by all other cap binding proteins, leading to an inability to detect the cross-linking of this protein in crude eIF preparations. Time kinetics of formation of complexes suggested eIF-2 to be one of the first factors to interact with mRNA. Preformed RNA-protein complexes were dissociated after cap analogue addition, suggesting reversible interactions between RNA and proteins.
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Affiliation(s)
- H A van Heugten
- Department of Molecular Cell Biology, University of Utrecht, The Netherlands
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Carberry SE, Goss DJ. Characterization of the interaction of wheat germ protein synthesis initiation factor eIF-3 with mRNA oligonucleotide and cap analogues. Biochemistry 1992; 31:296-9. [PMID: 1731879 DOI: 10.1021/bi00116a040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Direct fluorescence titration experiments of wheat germ protein synthesis initiation factor eIF-3 with mRNA cap and oligoribonucleotide analogues were performed in order to determine the equilibrium association constants (Keq) for the eIF-3.mRNA interaction as a function of pH and temperature. These data suggest that (i) the eIF-3.mRNA interaction is not cap-specific (i.e., m7G-specific), (ii) ATP hydrolysis is not involved in the interaction, and (iii) the interaction is primarily ionic in nature. Competition experiments between a rabbit alpha-globin mRNA oligoribonucleotide analogue and either mRNA cap analogues or nucleoside triphosphates (NTPs) are also reported; these experiments indicate that NTPs act as both activators and competitive inhibitors of the mRNA.eIF-3 association. The results are consistent with a partially uncompetitive binding mechanism, whereby at low NTP concentrations (less than or equal to 10 microM) the bound NTP enhances subsequent mRNA binding to eIF-3, perhaps by inducing a conformational change, and at higher NTP concentrations, the NTP acts as a competitive inhibitor for the mRNA binding site on eIF-3.
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Affiliation(s)
- S E Carberry
- Department of Chemistry, Hunter College, City University of New York, New York 10021-5024
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Carberry SE, Goss DJ. Interaction of wheat germ protein synthesis initiation factors eIF-3, eIF-(iso)4F, and eIF-4F with mRNA analogues. Biochemistry 1991; 30:6977-82. [PMID: 2069954 DOI: 10.1021/bi00242a024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The interaction of wheat germ eIF-3 with the wheat germ cap-binding proteins eIF-(iso)4F and eIF-4F as a function of pH and ionic strength is described. Direct fluorescence titration experiments are used to measure the equilibrium association constants (Keq) for the binary protein/protein complexes as well as for the interaction of eIF-3 with methylated cap analogues and rabbit alpha-globin mRNA oligonucleotide analogues. The Keq values for ternary eIF-3/eIF-(iso)4F/analogue and eIF-3/eIF-4F/analogue interactions were also measured. The equilibrium binding constants were used to calculate coupling free energies, which provide an estimate of the cooperativity for the interaction of the mRNA analogues, eIF-3, and either eIF-4F or eIF-(iso)4F. These data suggest a mechanism in which the binding of eIF-(iso)4F or eIF-4F to mRNA enhances the subsequent binding of eIF-3 to the message. This may lead to favorable positioning of the complex on the ribosome and thereby enhance translation.
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Affiliation(s)
- S E Carberry
- Department of Chemistry, Hunter College, City University of New York 10021-5024
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Evidence that eukaryotic initiation factor (eIF) 2 is a cap-binding protein that stimulates cap recognition by eIF-4B and eIF-4F. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(20)89641-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Mulcahy FM, Lacey CJ, Barr K, Lacey RW. Resistance in Escherichia coli after single dose ampicillin to treat gonorrhoea. Genitourin Med 1986; 62:166-9. [PMID: 3525384 PMCID: PMC1011929 DOI: 10.1136/sti.62.3.166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Patients with uncomplicated gonorrhoea were treated with a single dose of either ampicillin 3 g orally or procaine penicillin 2.4 MIU by injection, both with probenecid 1 g orally. The proportion of faecal Escherichia coli resistant to ampicillin before and a week after treatment was assessed. Of 55 patients treated with ampicillin who initially possessed sensitive flora, 25 (45.5%) became colonised subsequently by resistant E coli. Resistance to ampicillin, together with resistance to some other antimicrobials, was transferable in vitro. Penicillin, however, selected resistant E coli in only four (14.3%) out of 28 patients with initially sensitive flora. There was no difference in therapeutic response between the two agents. Intramuscular penicillin appeared to offer appreciably greater microbiological benefits than oral ampicillin in treating gonorrhoea.
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Hiremath LS, Webb NR, Rhoads RE. Immunological detection of the messenger RNA cap-binding protein. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39529-7] [Citation(s) in RCA: 141] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Gaedigk R, Oehler S, Köhler K, Setyono B. In vitro reconstitution of messenger ribonucleoprotein particles from globin messenger RNA and cytosol proteins. FEBS Lett 1985; 179:201-7. [PMID: 2857130 DOI: 10.1016/0014-5793(85)80518-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Deproteinized globin poly(A) + mRNAs reassociate readily in vitro with soluble RNA-binding proteins of the cytosol; reconstituted messenger ribonucleoprotein complexes are obtained which are very similar to native globin polyribosomal-mRNP as far as bouyant density in Cs2SO4 and the composition of proteins which can be crosslinked to the mRNA are concerned. Proteins thus identified bind specifically to mRNA and not to ribosomal RNA or any synthetic oligonucleotides, with one exception: a 78-kDa protein could be cross-linked to poly(A).
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Bielka H. Properties and spatial arrangement of components in preinitiation complexes of eukaryotic protein synthesis. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1985; 32:267-89. [PMID: 3911277 DOI: 10.1016/s0079-6603(08)60351-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Rhoads RE. The Cap Structure of Eukaryotic Messenger RNA and its Interaction with Cap-binding Protein. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 1985. [DOI: 10.1007/978-3-642-70203-7_3] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Darlix JL, Zuker M, Spahr PF. Structure-function relationship of Rous sarcoma virus leader RNA. Nucleic Acids Res 1982; 10:5183-96. [PMID: 6292833 PMCID: PMC320864 DOI: 10.1093/nar/10.17.5183] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cells infected by RSV synthesize viral 35S RNA as well as subgenomic 28S and 22S RNAs coding for the Env and Src genes respectively. In addition, at least the 5' 101 nucleotides of the leader are also conserved and we have shown previously that this sequence contains a strong ribosome binding site (J.-L. Darlix et al., J. Virol. 29, 597). We now report the RNA sequence of Rous Sarcoma virus (RSV) leader RNA and propose a folding of this 5' untranslated region which brings the Cap, the initiation codon for Gag and the strong ribosome binding site close to each other. We also show that ribosomes protect a sequence just upstream from initiator Aug of Gag in vitro, and believed to interact with part of the strong ribosome binding site according to the folding proposed for the leader RNA.
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Zumbé A, Stähli C, Trachsel H. Association of a Mr 50,000 cap-binding protein with the cytoskeleton in baby hamster kidney cells. Proc Natl Acad Sci U S A 1982; 79:2927-31. [PMID: 7045875 PMCID: PMC346321 DOI: 10.1073/pnas.79.9.2927] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A monoclonal antibody directed against eukaryotic mRNA 5'-cap-binding protein (anti-CBP antibody) was used to localize cap-binding protein (CBP) in BHK-21 baby hamster kidney cells by immunofluorescence microscopy. It was found that the antibody reacts with a fibrous network extending through the cytoplasm in a radial arrangement. The network behaves like intermediate filaments in colchicine-treated cells, suggesting a direct or indirect linkage of CBP with intermediate filaments. The association of CBP with a cytoskeletal element was further confirmed by isolation of proteins from Triton X-100-extracted cells and identification of CBP in the cytoskeletal fraction with anti-CBP antibody. The major polypeptide reacting with anti-CBP antibody is a Mr 50,000 component. Tryptic peptide mapping showed that this polypeptide is related to a Mr 24,000 polypeptide identified as CBP in earlier experiments [Sonenberg, N., Morgan, M. A., Testa, D., Colonna, R. J. & Shatkin, A. J. (1978) Proc. Natl. Acad. Sci. USA 75, 4843-4847].
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A polypeptide which reverses cap analogue inhibition of cell-free protein synthesis. Purification and binding to capped oligonucleotides. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34685-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Translation of vesicular stomatitis and Sindbis virus mRNAs in cell-free extracts of Aedes albopictus cells. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(18)43025-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Gedamu L, Chaconas G, van de Sande JH, Dixon GH. Studies on the heterogeneity of the 5' ends of the protamine mRNAs from rainbow trout testis. Biosci Rep 1981; 1:61-70. [PMID: 7284575 DOI: 10.1007/bf01115150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The structures of the 5' termini of the protamine mRNAs (PmRNAs) have been investigated by inhibiting their translation in wheat-germ extracts in the presence of 7-methyl guanosine 5'-phosphate (m7-GMP), an analogue of 'cap' structure in mRNAs. Second, the cap structures on PmRNAs were examined by labelling the RNA at the 5' end with T4 polynucleotide kinase and [gamma-32P]ATP before and after removal of these structures with tobacco acid pyrophosphatase and alkaline phosphatase. The results indicate that cap structures of the PmRNAs are heterogeneous. It appears that the mRNAs coding for protamine components CI and CIII have at least a cap 1 structure while the mRNAs coding for CII do not appear to be capped or methylated.
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Goldenberg S, Vincent A, Scherrer K. Ribonucleotide sequences non-adjacent to poly(A) participate in the poly(A)-protein complex in 15S duck globin mRNP particles. Nucleic Acids Res 1980; 8:5057-70. [PMID: 7443531 PMCID: PMC324279 DOI: 10.1093/nar/8.21.5057] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The study of the interaction between mRNA and proteins in the polyribosomal 15 S duck globin messenger ribonucleoprotein complex showed that proteins protect specific mRNA sequences against digestion by the nonspecific micrococcal nuclease (Nucleic Acids Research 6 (8) 2787, 1979). Here we report the isolation of the poly(A)-protein RNP complex from nuclease digested 15 S mRNP by two different methods: sucrose gradient sedimentation and oligo(dT)-cellulose chromatography. We show by fingerprint analysis, that aprt from the periodically fragmented poly(A) segment, mRNA sequences adjacent and non-adjacent to the poly(A) segment are protected by the poly(A) binding proteins against nuclease digestion. The duck globin poly(A)-protein RNP complex, with a sedimentation coefficient between 7 S and 10 S, shows a characteristic protein composition, with a major 73,000 MW polypeptide and some minor components. The results are discussed in view of a dynamic ribonucleoprotein structure.
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Stewart ML, Crouch RJ, Maizel JV. A high-resolution oligonucleotide map generated by restriction of poliovirus type I genomic RNA by ribonuclease III. Virology 1980; 104:375-97. [PMID: 6249034 DOI: 10.1016/0042-6822(80)90341-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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