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Kristofich J, Nicchitta CV. Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics. Nat Commun 2023; 14:5868. [PMID: 37735163 PMCID: PMC10514315 DOI: 10.1038/s41467-023-41284-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Recent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven analytically challenging and prone to error. Here we report a method termed LEAP-RBP (Liquid-Emulsion-Assisted-Purification of RNA-Bound Protein) for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. In this work, the utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
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2
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Kühn-Hölsken E, Lenz C, Sander B, Lührmann R, Urlaub H. Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles. RNA (NEW YORK, N.Y.) 2005; 11:1915-30. [PMID: 16314460 PMCID: PMC1370879 DOI: 10.1261/rna.2176605] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 09/12/2005] [Indexed: 05/05/2023]
Abstract
Protein-RNA cross-linking combined with mass spectrometry is a powerful tool to elucidate hitherto non-characterized protein-RNA contacts in ribonucleoprotein particles, as, for example, within spliceosomes. Here, we describe an improved methodology for the sequence analysis of purified peptide-RNA oligonucleotide cross-links that is based solely on MALDI-ToF mass spectrometry. The utility of this methodology is demonstrated on cross-links isolated from UV-irradiated spliceosomal particles; these were (1) [15.5K-61 K-U4 atac] small nuclear ribonucleoprotein (snRNP) particles prepared by reconstitution in vitro, and (2) U1 snRNP particles purified from HeLa cells. We show that the use of 2',4',6'-trihydroxyacetophenone (THAP) as MALDI matrix allows analysis of cross-linked peptide-RNA oligonucleotides in the reflectron mode at high resolution, enabling sufficient accuracy to assign unambiguously cross-linked RNA sequences. Most important, post-source decay (PSD) analysis under these conditions was successfully applied to obtain sequence information about the cross-linked peptide and RNA moieties within a single spectrum, including the identification of the actual cross-linking site. Thus, in U4 atac snRNA we identified His 270 in the spliceosomal U4/U6 snRNP-specific protein 61 K (hPrp31p) cross-linked to U 44; in the U1 snRNP we show that Leu175 of the U1 snRNP-specific 70K protein is cross-linked to U 30 of U1 snRNA. This type of analysis is applicable to any type of RNP complex and may be expected to pave the way for the further analysis of protein-RNA complexes in much lower abundance and/or of cross-links that are obtained in low yield.
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MESH Headings
- Amino Acid Sequence
- Cross-Linking Reagents/pharmacology
- Crystallography, X-Ray
- HeLa Cells
- Humans
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Oligonucleotides/analysis
- Peptides
- RNA/chemistry
- Ribonucleoprotein, U1 Small Nuclear/chemistry
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Sequence Homology, Amino Acid
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Ultraviolet Rays
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Affiliation(s)
- Eva Kühn-Hölsken
- Bioanalytical Mass Spectrometry Group, Max Planck institute for Biophysical Chemistry, 37077 Göttingen, Germany
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El-Kemary MA, El-Gezawy HS, El-Baradie HY, Issa RM. Spectral and photophysical studies of inclusion complexes of 2-amino-4,6-dimethyl pyrimidine with beta-cyclodextrin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2002; 58:493-500. [PMID: 11905534 DOI: 10.1016/s1386-1425(01)00550-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The interaction of 2-amino-4,6-dimethyl pyrimidine (ADMP) with beta-cyclodextrin (beta-CD) has been studied by means of UV absorption, steady state and time resolved fluorescence techniques. Spectral characteristics, bandwidths and photophysical parameters indicating that ADMP experience two different environments in aqueous solutions: bulk water and 1:1 (ADMP:beta-CD) inclusion complexation. The size restriction of the upper rim of beta-CD partially include ADMP and prevent the possibility of formation of 1:2 complex. The effective polarity of the cyclodextrin cavity experienced by the induced ADMP is equivalent with the polarity of an 80:20 methanol-water mixture.
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Affiliation(s)
- M A El-Kemary
- Chemnistry Department, Faculty of Education, Tanta University, Kafr El-Sheikh, Egypt.
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Kim NJ, Jeong G, Kim YS, Sung J, Keun Kim S, Park YD. Resonant two-photon ionization and laser induced fluorescence spectroscopy of jet-cooled adenine. J Chem Phys 2000. [DOI: 10.1063/1.1322072] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Meisenheimer KM, Koch TH. Photocross-linking of nucleic acids to associated proteins. Crit Rev Biochem Mol Biol 1997; 32:101-40. [PMID: 9145285 DOI: 10.3109/10409239709108550] [Citation(s) in RCA: 213] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes. It can be accomplished by one or two photon excitations of wild-type nucleoprotein complexes or by one photon excitation of nucleoprotein complexes bearing one or more substitutions with photoreactive chromophores. Chromophores that have been incorporated into nucleic acids for this purpose include aryl azides, 5-azidouracil, 8-azidoadenine, 8-azidoguanine, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-iodocytosine. The various techniques and chromophores are described and compared, with attention to the photochemical mechanism.
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Affiliation(s)
- K M Meisenheimer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
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Wamhoff H, Dzenis J, Hirota K. Uracils: Versatile Starting Materials in Heterocyclic Synthesis. ADVANCES IN HETEROCYCLIC CHEMISTRY 1992. [DOI: 10.1016/s0065-2725(08)60222-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Hettich RL, Buchanan MV, Ho CH. Characterization of photo-induced pyrimidine cyclobutane dimers by laser desorption Fourier transform mass spectrometry. BIOMEDICAL & ENVIRONMENTAL MASS SPECTROMETRY 1990; 19:55-62. [PMID: 2306549 DOI: 10.1002/bms.1200190202] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Laser desorption Fourier transform mass spectrometry was used to characterize the cis-syn cyclobutane photodimers of uracil-uracil, uracil-thymine and thymine-thymine. This soft ionization technique generated [M-H]- ions as well as some fragment ions. Investigation of the laser desorption process indicated that gas-phase dimerization reactions do not occur for pyrimidine monomers and dimers under these experimental conditions. Collisional dissociation of the [M-H]- ions provided structural information for the pyrimidine rings of the dimers. The fragment ions observed in the collisional dissociation spectra of these cyclobutane dimers suggested rearrangement of the [M-H]- parent ions to a macrocycle prior to dissociation.
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Affiliation(s)
- R L Hettich
- Analytical Chemistry Division, Oak Ridge National Laboratory, Tennessee 37831-6120
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Moan J, Peak MJ. Effects of UV radiation of cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1989; 4:21-34. [PMID: 2509659 DOI: 10.1016/1011-1344(89)80099-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
UV radiation interacts with mammalian cells in a very complex manner, although DNA appears to be the main chromophore. Recent literature within this field is reviewed. The review is concentrated on the following main topics: Chromophores for UV action, photoproducts in DNA, repair of UV-induced DNA damage, wavelength interactions, inactivation, mutagenesis, transformation and protection mechanisms against UV damage.
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Affiliation(s)
- J Moan
- Institute for Cancer Research, Montebello, Oslo, Norway
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Budowsky EI, Abdurashidova GG. Polynucleotide-protein cross-links induced by ultraviolet light and their use for structural investigation of nucleoproteins. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1989; 37:1-65. [PMID: 2475887 DOI: 10.1016/s0079-6603(08)60694-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Shetlar MD, Hom K, Distefano S, Ekpenyong K, Yang J. Photochemical reactions of cytosine and 5-methylcytosine with methylamine and n-butylamine. Photochem Photobiol 1988; 47:779-86. [PMID: 3217431 DOI: 10.1111/j.1751-1097.1988.tb01659.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Shetlar MD, Hom K. Mixed products of thymine and cysteine produced by direct and acetone-sensitized photoreactions. Photochem Photobiol 1987; 45:703-12. [PMID: 3628495 DOI: 10.1111/j.1751-1097.1987.tb07871.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Araki K, Shiraishi S. OXIDATION OF RIBOSE MOIETY OF ADENOSINE INDUCED BY IRRADIATION OF NEAR-UV LIGHT IN THE PRESENCE OF IRON(III) CHLORIDE. Photochem Photobiol 1987. [DOI: 10.1111/j.1751-1097.1987.tb08418.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Franklin WA, Haseltine WA. The role of the (6-4) photoproduct in ultraviolet light-induced transition mutations in E. coli. Mutat Res 1986; 165:1-7. [PMID: 3001515 DOI: 10.1016/0167-8817(86)90002-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Available evidence rules out the possibility that cyclobutane dimers are the major premutagenic lesions responsible for point mutations at sites of adjacent pyrimidine residues in the experiment systems examined to date in sufficient detail, that is, UV-induced mutations in chromosome loci in E. coli and UV-induced mutations in the cI gene of phage lambda. However, it is likely that the major cytotoxic effects of UV irradiation can be attributed to the cyclobutane pyrimidine dimer, as these lesions occur at 10 times the frequency of other UV-induced photoproducts in the dose range of 0.1-100 J/m2. The evidence also suggests that cyclobutane pyrimidine dimers are the major lesions responsible for induction of the SOS response and that as such they play an important, though indirect role, in the formation of mutations in irradiated DNA. Cyclobutane dimers may also be the major lesions responsible for other types of UV-light-induced mutations such as deletions. None of the available evidence rules out (6-4) photoproducts as a major premutagenic lesion induced by UV irradiation using these experimental systems. On the contrary, the mutation spectrum induced both in the lacI gene and the cI gene of phage lambda is that predicted for mutations induced by (6-4) photoproducts. The observation that neither the premutagenic lesions nor the (6-4) photoproduct is subject to enzymatic photoreactivation also implies that the (6-4) photoproducts are premutagenic. As reviewed above, neither the photosensitization experiments nor the action spectrum of the (6-4) photoproducts rules out such a role. Might a lesion other than the (6-4) photoproduct be the major premutagenic lesion responsible for point mutations in these experimental systems? It cannot be ruled out that another as yet undefined minor photoproduct that occurs with the same sequence distribution specificity as that of the (6-4) photoproduct and that is also not subject to the reactivating treatments is more mutagenic than the (6-4) photoproduct itself. Candidates for such a lesion might include a photohydrate of the (6-4) photoproduct itself or as yet undefined photoproducts. However, we believe these alternative possibilities to be remote.(ABSTRACT TRUNCATED AT 400 WORDS)
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Cadet J, Voituriez L, Grand A, Hruska FE, Vigny P, Kan LS. Recent aspects of the photochemistry of nucleic acids and related model compounds. Biochimie 1985; 67:277-92. [PMID: 3929843 DOI: 10.1016/s0300-9084(85)80070-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This survey focuses on recent developments in the far ultraviolet photochemistry of nucleic acids and related model compounds. The photoproducts discussed are the cyclobutidipyrimidines, the pyrimidine-pyrimidone adducts, the purine-pyrimidine adducts and the addition products of amino acids to pyrimidine bases. The specific aspects of the high-intensity laser photochemistry of nucleic acid components are also briefly reviewed.
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Ikehira H, Matsuura T, Saito I. Photochemistry of 6-halo- and 5,6-dihalouracils. A simple synthesis of fluorescent uracil derivatives. Tetrahedron Lett 1985. [DOI: 10.1016/s0040-4039(00)98327-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Saito I, Sugiyama H, Matsuura T, Fukuyama K, Katsube Y. Photochemical reaction between tryptophan and thymine. Tetrahedron Lett 1984. [DOI: 10.1016/s0040-4039(01)91021-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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