Abstract
The hairpin structure at the 3' end of animal histone mRNAs controls histone RNA 3' processing, nucleocytoplasmic transport, translation and stability of histone mRNA. Functionally overlapping, if not identical, proteins binding to the histone RNA hairpin have been identified in nuclear and polysomal extracts. Our own results indicated that these hairpin binding proteins (HBPs) bind their target RNA as monomers and that the resulting ribonucleoprotein complexes are extremely stable. These features prompted us to select for HBP-encoding human cDNAs by RNA-mediated three-hybrid selection in Saccharomyces cerevesiae. Whole cell extract from one selected clone contained a Gal4 fusion protein that interacted with histone hairpin RNA in a sequence- and structure-specific manner similar to a fraction enriched for bovine HBP, indicating that the cDNA encoded HBP. DNA sequence analysis revealed that the coding sequence did not contain any known RNA binding motifs. The HBP gene is composed of eight exons covering 19.5 kb on the short arm of chromosome 4. Translation of the HBP open reading frame in vitro produced a 43 kDa protein with RNA binding specificity identical to murine or bovine HBP. In addition, recombinant HBP expressed in S. cerevisiae was functional in histone pre-mRNA processing, confirming that we have indeed identified the human HBP gene.
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- Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- Bond U. M., Yario T. A., Steitz J. A. Multiple processing-defective mutations in a mammalian histone pre-mRNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro. Genes Dev. 1991 Sep;5(9):1709–1722. doi: 10.1101/gad.5.9.1709. [DOI] [PubMed] [Google Scholar]
- Dominski Z., Sumerel J., Hanson R. J., Marzluff W. F. The polyribosomal protein bound to the 3' end of histone mRNA can function in histone pre-mRNA processing. RNA. 1995 Nov;1(9):915–923. [PMC free article] [PubMed] [Google Scholar]
- Durfee T., Becherer K., Chen P. L., Yeh S. H., Yang Y., Kilburn A. E., Lee W. H., Elledge S. J. The retinoblastoma protein associates with the protein phosphatase type 1 catalytic subunit. Genes Dev. 1993 Apr;7(4):555–569. doi: 10.1101/gad.7.4.555. [DOI] [PubMed] [Google Scholar]
- Eckner R., Ellmeier W., Birnstiel M. L. Mature mRNA 3' end formation stimulates RNA export from the nucleus. EMBO J. 1991 Nov;10(11):3513–3522. doi: 10.1002/j.1460-2075.1991.tb04915.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fields S., Song O. A novel genetic system to detect protein-protein interactions. Nature. 1989 Jul 20;340(6230):245–246. doi: 10.1038/340245a0. [DOI] [PubMed] [Google Scholar]
- Galli G., Hofstetter H., Stunnenberg H. G., Birnstiel M. L. Biochemical complementation with RNA in the Xenopus oocyte: a small RNA is required for the generation of 3' histone mRNA termini. Cell. 1983 Oct;34(3):823–828. doi: 10.1016/0092-8674(83)90539-1. [DOI] [PubMed] [Google Scholar]
- Gietz D., St Jean A., Woods R. A., Schiestl R. H. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 1992 Mar 25;20(6):1425–1425. doi: 10.1093/nar/20.6.1425. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Good P. D., Engelke D. R. Yeast expression vectors using RNA polymerase III promoters. Gene. 1994 Dec 30;151(1-2):209–214. doi: 10.1016/0378-1119(94)90658-0. [DOI] [PubMed] [Google Scholar]
- Hanson R. J., Sun J., Willis D. G., Marzluff W. F. Efficient extraction and partial purification of the polyribosome-associated stem-loop binding protein bound to the 3' end of histone mRNA. Biochemistry. 1996 Feb 20;35(7):2146–2156. doi: 10.1021/bi9521856. [DOI] [PubMed] [Google Scholar]
- Hoffman C. S., Winston F. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene. 1987;57(2-3):267–272. doi: 10.1016/0378-1119(87)90131-4. [DOI] [PubMed] [Google Scholar]
- Holler A., Bashkirov V. I., Solinger J. A., Reinhart U., Heyer W. D. Use of monoclonal antibodies in the functional characterization of the Saccharomyces cerevisiae Sep1 protein. Eur J Biochem. 1995 Jul 15;231(2):329–336. doi: 10.1111/j.1432-1033.1995.tb20704.x. [DOI] [PubMed] [Google Scholar]
- Johnson A. W., Kolodner R. D. Strand exchange protein 1 from Saccharomyces cerevisiae. A novel multifunctional protein that contains DNA strand exchange and exonuclease activities. J Biol Chem. 1991 Jul 25;266(21):14046–14054. [PubMed] [Google Scholar]
- Jones E. W. Tackling the protease problem in Saccharomyces cerevisiae. Methods Enzymol. 1991;194:428–453. doi: 10.1016/0076-6879(91)94034-a. [DOI] [PubMed] [Google Scholar]
- Kozak M. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 1986 Jan 31;44(2):283–292. doi: 10.1016/0092-8674(86)90762-2. [DOI] [PubMed] [Google Scholar]
- Marzluff W. F. Histone 3' ends: essential and regulatory functions. Gene Expr. 1992;2(2):93–97. [PMC free article] [PubMed] [Google Scholar]
- Marzluff W. F., Pandey N. B. Multiple regulatory steps control histone mRNA concentrations. Trends Biochem Sci. 1988 Feb;13(2):49–52. doi: 10.1016/0968-0004(88)90027-8. [DOI] [PubMed] [Google Scholar]
- McCombie W. R., Martin-Gallardo A., Gocayne J. D., FitzGerald M., Dubnick M., Kelley J. M., Castilla L., Liu L. I., Wallace S., Trapp S. Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3. Nat Genet. 1992 Aug;1(5):348–353. doi: 10.1038/ng0892-348. [DOI] [PubMed] [Google Scholar]
- Melin L., Soldati D., Mital R., Streit A., Schümperli D. Biochemical demonstration of complex formation of histone pre-mRNA with U7 small nuclear ribonucleoprotein and hairpin binding factors. EMBO J. 1992 Feb;11(2):691–697. doi: 10.1002/j.1460-2075.1992.tb05101.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mowry K. L., Oh R., Steitz J. A. Each of the conserved sequence elements flanking the cleavage site of mammalian histone pre-mRNAs has a distinct role in the 3'-end processing reaction. Mol Cell Biol. 1989 Jul;9(7):3105–3108. doi: 10.1128/mcb.9.7.3105. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mowry K. L., Steitz J. A. Both conserved signals on mammalian histone pre-mRNAs associate with small nuclear ribonucleoproteins during 3' end formation in vitro. Mol Cell Biol. 1987 May;7(5):1663–1672. doi: 10.1128/mcb.7.5.1663. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Osley M. A. The regulation of histone synthesis in the cell cycle. Annu Rev Biochem. 1991;60:827–861. doi: 10.1146/annurev.bi.60.070191.004143. [DOI] [PubMed] [Google Scholar]
- Pandey N. B., Marzluff W. F. The stem-loop structure at the 3' end of histone mRNA is necessary and sufficient for regulation of histone mRNA stability. Mol Cell Biol. 1987 Dec;7(12):4557–4559. doi: 10.1128/mcb.7.12.4557. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pandey N. B., Sun J. H., Marzluff W. F. Different complexes are formed on the 3' end of histone mRNA with nuclear and polyribosomal proteins. Nucleic Acids Res. 1991 Oct 25;19(20):5653–5659. doi: 10.1093/nar/19.20.5653. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pandey N. B., Williams A. S., Sun J. H., Brown V. D., Bond U., Marzluff W. F. Point mutations in the stem-loop at the 3' end of mouse histone mRNA reduce expression by reducing the efficiency of 3' end formation. Mol Cell Biol. 1994 Mar;14(3):1709–1720. doi: 10.1128/mcb.14.3.1709. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schaufele F., Gilmartin G. M., Bannwarth W., Birnstiel M. L. Compensatory mutations suggest that base-pairing with a small nuclear RNA is required to form the 3' end of H3 messenger RNA. 1986 Oct 30-Nov 5Nature. 323(6091):777–781. doi: 10.1038/323777a0. [DOI] [PubMed] [Google Scholar]
- Schümperli D. Multilevel regulation of replication-dependent histone genes. Trends Genet. 1988 Jul;4(7):187–191. doi: 10.1016/0168-9525(88)90074-1. [DOI] [PubMed] [Google Scholar]
- SenGupta D. J., Zhang B., Kraemer B., Pochart P., Fields S., Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo. Proc Natl Acad Sci U S A. 1996 Aug 6;93(16):8496–8501. doi: 10.1073/pnas.93.16.8496. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spycher C., Streit A., Stefanovic B., Albrecht D., Koning T. H., Schümperli D. 3' end processing of mouse histone pre-mRNA: evidence for additional base-pairing between U7 snRNA and pre-mRNA. Nucleic Acids Res. 1994 Oct 11;22(20):4023–4030. doi: 10.1093/nar/22.20.4023. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stauber C., Soldati D., Lüscher B., Schümperli D. Histone-specific RNA 3' processing in nuclear extracts from mammalian cells. Methods Enzymol. 1990;181:74–89. doi: 10.1016/0076-6879(90)81113-9. [DOI] [PubMed] [Google Scholar]
- Streit A., Koning T. W., Soldati D., Melin L., Schümperli D. Variable effects of the conserved RNA hairpin element upon 3' end processing of histone pre-mRNA in vitro. Nucleic Acids Res. 1993 Apr 11;21(7):1569–1575. doi: 10.1093/nar/21.7.1569. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sun J., Pilch D. R., Marzluff W. F. The histone mRNA 3' end is required for localization of histone mRNA to polyribosomes. Nucleic Acids Res. 1992 Nov 25;20(22):6057–6066. doi: 10.1093/nar/20.22.6057. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vasserot A. P., Schaufele F. J., Birnstiel M. L. Conserved terminal hairpin sequences of histone mRNA precursors are not involved in duplex formation with the U7 RNA but act as a target site for a distinct processing factor. Proc Natl Acad Sci U S A. 1989 Jun;86(12):4345–4349. doi: 10.1073/pnas.86.12.4345. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang Z. F., Whitfield M. L., Ingledue T. C., 3rd, Dominski Z., Marzluff W. F. The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. Genes Dev. 1996 Dec 1;10(23):3028–3040. doi: 10.1101/gad.10.23.3028. [DOI] [PubMed] [Google Scholar]
- Williams A. S., Marzluff W. F. The sequence of the stem and flanking sequences at the 3' end of histone mRNA are critical determinants for the binding of the stem-loop binding protein. Nucleic Acids Res. 1995 Feb 25;23(4):654–662. doi: 10.1093/nar/23.4.654. [DOI] [PMC free article] [PubMed] [Google Scholar]