Home LiteratureArticle Details
PMID: 7899087 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

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 research ·Vol. 23 ·No. 4 ·1995-02-25 ·Pages 654-62

Williams AS, Marzluff WF

Abstract

Complexes of different electrophoretic mobility containing the stem-loop binding protein, a 45 kDa protein, bound to the stem-loop at the 3' end of histone mRNA, are present in both nuclear and cytoplasmic extracts from mammalian cells. We have determined the effect of changes in the loop, in the stem and in the flanking sequences on the affinity of the SLBP for the 3' end of histone mRNA. The sequence of the stem is particularly critical for SLBP binding. Specific sequences both 5' and 3' of the stem-loop are also required for high-affinity binding. Expanding the four base loop by one or two uridines reduced but did not abolish SLBP binding. RNA footprinting experiments show that the flanking sequences on both sides of the stem-loop are critical for efficient binding, but that cleavages in the loop do not abolish binding. Thus all three regions of the RNA sequence contribute to SLBP binding, suggesting that the 26 nt at the 3' end of histone mRNA forms a defined tertiary structure recognized by the SLBP.

MeSH Terms
Animals Base Sequence Consensus Sequence Histones/genetics Mice Molecular Sequence Data Mutagenesis, Site-Directed Nuclear Proteins Nucleic Acid Conformation Protein Binding RNA Processing, Post-Transcriptional RNA, Messenger/chemistry,metabolism RNA-Binding Proteins/metabolism mRNA Cleavage and Polyadenylation Factors
Chemicals
Histones Nuclear Proteins RNA, Messenger RNA-Binding Proteins Slbp protein, mouse mRNA Cleavage and Polyadenylation Factors
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Williams A S
Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill 27599.
Marzluff W F
References (39)
39 references, click to expand
  1. Conformation of the TAR RNA-arginine complex by NMR spectroscopy.
    Science. 1992 Jul 3;257(5066):76-80 PMID: 1621097
  2. Biochemical demonstration of complex formation of histone pre-mRNA with U7 small nuclear ribonucleoprotein and hairpin binding factors.
    EMBO J. 1992 Feb;11(2):691-7 PMID: 1531633
  3. Translation initiation requires the PAB-dependent poly(A) ribonuclease in yeast.
    Cell. 1992 Sep 18;70(6):961-73 PMID: 1339314
  4. The histone mRNA 3' end is required for localization of histone mRNA to polyribosomes.
    Nucleic Acids Res. 1992 Nov 25;20(22):6057-66 PMID: 1461736
  5. Hydrogen-bonding contacts in the major groove are required for human immunodeficiency virus type-1 tat protein recognition of TAR RNA.
    J Mol Biol. 1993 Mar 5;230(1):111-23 PMID: 8450529
  6. High affinity binding of TAR RNA by the human immunodeficiency virus type-1 tat protein requires base-pairs in the RNA stem and amino acid residues flanking the basic region.
    J Mol Biol. 1993 Mar 5;230(1):90-110 PMID: 8450553
  7. 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):1569-75 PMID: 8479907
  8. Individual purified core and linker histones induce histone H4 mRNA destabilization in vitro.
    J Biol Chem. 1993 Jul 15;268(20):14637-44 PMID: 8325840
  9. RNA recognition by the human immunodeficiency virus Tat and Rev proteins.
    Trends Biochem Sci. 1993 Jul;18(7):255-9 PMID: 8212135
  10. The interaction between the iron-responsive element binding protein and its cognate RNA is highly dependent upon both RNA sequence and structure.
    Nucleic Acids Res. 1993 Sep 25;21(19):4627-31 PMID: 8233801
  11. 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):1709-20 PMID: 8114706
  12. The site of 3' end formation of histone messenger RNA is a fixed distance from the downstream element recognized by the U7 snRNP.
    EMBO J. 1994 May 15;13(10):2432-40 PMID: 8194533
  13. Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain.
    Biochemistry. 1994 Aug 23;33(33):10076-88 PMID: 7520277
  14. Changes in the stem-loop at the 3' terminus of histone mRNA affects its nucleocytoplasmic transport and cytoplasmic regulation.
    Nucleic Acids Res. 1994 Nov 11;22(22):4660-6 PMID: 7984415
  15. Transcription termination and 3' processing: the end is in site!
    Cell. 1985 Jun;41(2):349-59 PMID: 2580642
  16. Faithful cell-cycle regulation of a recombinant mouse histone H4 gene is controlled by sequences in the 3'-terminal part of the gene.
    Proc Natl Acad Sci U S A. 1985 Jul;82(13):4389-93 PMID: 3925455
  17. Generation of histone mRNA 3' ends by endonucleolytic cleavage of the pre-mRNA in a snRNP-dependent in vitro reaction.
    EMBO J. 1986 Jun;5(6):1319-26 PMID: 3015597
  18. H4 histone messenger RNA decay in cell-free extracts initiates at or near the 3' terminus and proceeds 3' to 5'.
    J Mol Biol. 1986 Apr 20;188(4):579-93 PMID: 3525849
  19. Heat-labile regulatory factor is required for 3' processing of histone precursor mRNAs.
    Proc Natl Acad Sci U S A. 1987 Dec;84(24):8937-40 PMID: 2962194
  20. Histone mRNA degradation in vivo: the first detectable step occurs at or near the 3' terminus.
    Mol Cell Biol. 1986 Dec;6(12):4362-71 PMID: 3467177
  21. A signal regulating mouse histone H4 mRNA levels in a mammalian cell cycle mutant and sequences controlling RNA 3' processing are both contained within the same 80-bp fragment.
    EMBO J. 1986 Dec 1;5(12):3297-303 PMID: 3816761
  22. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.
    Nucleic Acids Res. 1987 Nov 11;15(21):8783-98 PMID: 3684574
  23. Identification of the human U7 snRNP as one of several factors involved in the 3' end maturation of histone premessenger RNA's.
    Science. 1987 Dec 18;238(4834):1682-7 PMID: 2825355
  24. 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):4557-9 PMID: 3437896
  25. Specific contacts between mammalian U7 snRNA and histone precursor RNA are indispensable for the in vitro 3' RNA processing reaction.
    EMBO J. 1988 Mar;7(3):801-8 PMID: 3396543
  26. 3' processing of pre-mRNA plays a major role in proliferation-dependent regulation of histone gene expression.
    Nucleic Acids Res. 1988 Oct 25;16(20):9399-414 PMID: 3141900
  27. Multiple regulatory steps control histone mRNA concentrations.
    Trends Biochem Sci. 1988 Feb;13(2):49-52 PMID: 3070846
  28. RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA.
    Science. 1989 May 19;244(4906):783-90 PMID: 2658053
  29. 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):4345-9 PMID: 2734288
  30. Nucleotide sequences of Caenorhabditis elegans core histone genes. Genes for different histone classes share common flanking sequence elements.
    J Mol Biol. 1989 Apr 20;206(4):567-77 PMID: 2544730
  31. 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):3105-8 PMID: 2779556
  32. Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional steps.
    Mol Cell Biol. 1991 May;11(5):2416-24 PMID: 2017161
  33. 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):1709-22 PMID: 1885007
  34. Identification of molecular contacts between the U1 A small nuclear ribonucleoprotein and U1 RNA.
    EMBO J. 1991 Nov;10(11):3447-56 PMID: 1833186
  35. Mature mRNA 3' end formation stimulates RNA export from the nucleus.
    EMBO J. 1991 Nov;10(11):3513-22 PMID: 1833188
  36. U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts.
    Nucleic Acids Res. 1991 Sep 25;19(18):4931-6 PMID: 1717938
  37. Different complexes are formed on the 3' end of histone mRNA with nuclear and polyribosomal proteins.
    Nucleic Acids Res. 1991 Oct 25;19(20):5653-9 PMID: 1834994
  38. RNA-protein interactions.
    Cell. 1991 Dec 20;67(6):1041-6 PMID: 1722140
  39. Histone 3' ends: essential and regulatory functions.
    Gene Expr. 1992;2(2):93-7 PMID: 1633440
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/23.4.654
Published
1995-02-25
Pages
654-62
Language
English
Region
England
NLM ID
0411011
PMCID
PMC306734
Subset
IM
Grants
NIGMS NIH HHS · GM29832 · United States
External Links
PubMed source DOI: 10.1093/nar/23.4.654 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2