Formation of the 3' end of histone mRNA

Gene

Volumn 239, Issue 1, 1999, Pages 1-14

  Dominski, Zbigniew ^a   Marzluff, William F ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

3' end formation; Histone mRNA; Polyadenylation; RNA processing; U7 snRNA

Indexed keywords

HISTONE; MESSENGER RNA;

CELL CYCLE; GENE EXPRESSION REGULATION; GENE REPLICATION; METAZOON; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS; REVIEW; RNA ANALYSIS; RNA PROCESSING; RNA SYNTHESIS; SEQUENCE ANALYSIS;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; HISTONES; HUMANS; MOLECULAR SEQUENCE DATA; MRNA CLEAVAGE AND POLYADENYLATION FACTORS; NUCLEAR PROTEINS; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; RIBONUCLEOPROTEIN, U7 SMALL NUCLEAR; RNA PRECURSORS; RNA, MESSENGER; RNA-BINDING PROTEINS;

EID: 0032826096     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(99)00367-4     Document Type: Review

References (100)

1. Abbott J., Marzluff W.F., Gall J.G. The stem loop binding protein (SLBP1) is present in coiled bodies of the Xenopus germinal vesicle. Mol. Biol. Cell. 10:1999;487-499.
2. Albig W., Doenecke D. The human histone gene cluster at the D6S105 locus. Hum. Genet. 101:1997;284-294.
3. Albig W., Kioschis P., Poustka A., Meergans K., Doenecke D. Human histone gene organization: Nonregular arrangement within a large cluster. Genomics. 40:1997;314-322.
4. Allen B.S., Stein J.L., Stein G.S., Ostrer H. Single-copy flanking sequences in human histone gene clusters map to chromosomes 1 and 6. Genomics. 10:1991;486-488.
5. Birchmeier C., Grosschedl R., Birnstiel M.L. Generation of authentic 3′ termini of an H2A mRNA in vivo is dependent on a short inverted DNA repeat and on spacer sequences. Cell. 28:1982;739-745.
6. Birnstiel M.L., Busslinger M., Strub K. Transcription termination and 3′ processing: the end is in site! Cell. 41:1985;349-359.
7. Birnstiel M.L., Schaufele F.J. Structure and function of minor snRNPs. Birnstiel M.L. Structure and Function of Major and Minor Small Ribonucleoprotein Particles. 1988;155-182 Springer, Berlin.
8. Bond U., Yario T.A. The steady state levels and structure of the U7 snRNP are constant during the human cell cycle: lack of cell cycle regulation of histone mRNA 3′ end formation. Cell. Mol. Biol. Res. 40:1994;27-34.
9. Bond U.M., Yario T.A., Steitz J.A. Multiple processing-defective mutations in a mammalian histone premessenger RNA are suppressed by compensatory changes in U7 RNA both in vivo and in vitro. Genes Dev. 5:1991;1709-1722.
10. Bonner W.M., Mannironi C., Orr A., Pilch D.R., Hatch C.L. Histone H2A.X gene transcription is regulated differently than transcription of other replication-linked histone genes. Mol. Cell. Biol. 13:1993;984-992.
11. Brush D., Dodgson J.B., Choi O.R., Stevens P.W., Engel J.D. Replacement variant histone genes contain intervening sequences. Mol. Cell. Biol. 5:1985;1307-1317.
12. Callan H.G., Gall J.G., Murphy C. Histone genes are located at the sphere loci of Xenopus lampbrush chromosomes. Chromosoma. 101:1991;245-251.
13. Challoner P.B., Moss S.B., Groudine M. Expression of replication-dependent histone genes in avian spermatids involves an alternate pathway of mRNA 3′-end formation. Mol. Cell. Biol. 9:1989;902-913.
14. Cheng G., Skoultchi A.I. Rapid induction of polyadenylated H1 histone mRNAs in mouse erythroleukemia cells is regulated by c-myc. Mol. Cell. Biol. 9:1989;2332-2340.
15. Cho D.C., Scharl E.C., Steitz J.A. Decreasing the distance between the two conserved sequence elements of histone pre-messenger RNA interferes with 3′ processing in vitro. RNA. 1:1995;905-914.
16. Chodchoy N., Pandey N.B., Marzluff W.F. An intact histone 3′ processing site is required for transcription termination in a mouse histone H2a gene. Mol. Cell. Biol. 11:1991;497-509.
17. Cohn R.H., Lowry J.C., Kedes L.H. Histone genes of the sea urchin (S. purpuratus) cloned in E. coli, order, polarity and strandedness of the five histone coding and spacer regions. Cell. 9:1976;147-161.
18. Colgan D.F., Manley J.L. Mechanism and regulation of mRNA polyadenylation. Genes Dev. 11:1997;2755-2766.
19. Collart D., Romain P.L., Huebner K., Pockwinse S., Pilapil S., Cannizzaro L.A., Lian J.B., Croce C.M., Stein J.L., Stein G.S. A human histone H2B.1 variant gene, located on chromosome 1, utilizes alternative 3′ end processing. J. Cell. Biochem. 50:1992;374-385.
20. Cotten M., Gick O., Vasserot A., Schaffner G., Birnstiel M.L. Specific contacts between mammalian U7 snRNA and histone precursor RNA are indispensable for the in vitro RNA processing reaction. EMBO J. 7:1988;801-808.
21. Cotten M., Oberhauser B., Brunar H., Holzner A., Issakides G., Noe C.R., Schaffner G., Wagner E., Birnstiel M.L. 2′-O-methyl, 2′-O-ethyl oligoribonucleotides and phosphorothioate oligodeoxyribonucleotides as inhibitors of the in vitro U7 snRNP-dependent mRNA processing event. Nucleic Acids Res. 19:1991;2629-2635.
22. DeLorenzi M., Rohrer U., Birnstiel M.L. Analysis of a sea urchin gene cluster coding for the small nuclear U7 RNA, a rare RNA species implicated in the 3′ editing of histone precursor mRNAs. Proc. Natl. Acad. Sci. USA. 83:1986;3243-3247.
23. 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. 1:1995;915-923.
24. Dominski Z., Zheng L.-X., Sanchez R., Marzluff W.F. The stem-loop binding protein facilitates 3′ end formation by stabilizing U7 snRNP binding to the histone pre-mRNA. Mol. Cell. Biol. 19:1999;3561-3570.
25. Fabry S., Müller K., Lindauer A., Park P.B., Cornelius T., Schmitt R. The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes. Curr. Genet. 28:1995;333-345.
26. Frey M.R., Matera A.G. Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequences in interphase human cells. Proc. Natl. Acad. Sci. USA. 92:1995;5915-5919.
27. Frey M.R., Bailey A.D., Weiner A.M., Matera A.G. Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts. Curr. Biol. 9:1999;126-135.
28. Furger A., Schaller A., Schümperli D. Functional importance of conserved nucleotides at the histone RNA 3′ processing site. RNA. 4:1998;246-256.
29. 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. 34:1983;823-828.
30. Gallie D.R., Lewis N.J., Marzluff W.F. The histone 3′-terminal stem-loop is necessary for translation in Chinese hamster ovary cells. Nucleic Acids Res. 24:1996;1954-1962.
31. Gao L., Frey M.R., Matera A.G. Human genes encoding U3 snRNA associate with coiled bodies in interphase cells and are clustered on chromosome 17p11.2 in a complex inverted repeat structure. Nucleic Acids Res. 25:1997;4740-4747.
32. Georgiev O., Birnstiel M.L. The conserved CAAGAAAGA spacer sequence is an essential element for the formation of 3′ termini of the sea urchin H3 histone mRNA by RNA processing. EMBO J. 4:1985;481-489.
33. Gick O., Krämer A., Keller W., Birnstiel M.L. Generation of histone mRNA 3′ ends by endonucleolytic cleavage of the pre-mRNA in a snRNP-dependent in vitro reaction. EMBO J. 5:1986;1319-1326.
34. Gick O., Krämer A., Vasserot A., Birnstiel M.L. Heat-labile regulatory factor is required for 3′ processing of histone precursor mRNAs. Proc. Natl. Acad. Sci. USA. 84:1987;8937-8940.
35. Gilmartin G.M., Schaufele F., Schaffner G., Birnstiel M.L. Functional analysis of the sea urchin U7 small nuclear RNA. Mol. Cell. Biol. 8:1988;1076-1084.
36. Graves R.A., Marzluff W.F. Rapid, reversible alterations in histone gene transcription and histone mRNA levels in mouse myeloma cells. Mol. Cell. Biol. 4:1984;351-357.
37. Graves R.A., Wellman S.E., Chiu I.M., Marzluff W.F. Differential expression of two clusters of mouse histone genes. J. Mol. Biol. 183:1985;179-194.
38. Grimm C., Stefanovic B., Schümperli D. The low abundance of U7 snRNA is partly determined by its Sm binding site. EMBO J. 12:1993;1229-1238.
39. Gruber A., Soldati D., Burri M., Schümperli D. Isolation of an active gene and of two pseudogenes for mouse U7 small nuclear RNA. Biochim. Biophys. Acta Gene Struct. Expression. 1088:1991;151-154.
40. Hanson R.J., Sun J.H., Willis D.G., Marzluff W.F. Efficient extraction and partial purification of the polyribosomal-associated stem-loop binding protein bound to the 3′ end of histone mRNA. Biochemistry. 35:1996;2146-2156.
41. Harris M.E., Böhni R., Schneiderman M.H., Ramamurthy L., Schümperli D., Marzluff W.F. Regulation of histone mRNA in the unperturbed cell cycle: Evidence suggesting control at two posttranscriptional steps. Mol. Cell. Biol. 11:1991;2416-2424.
42. Hoffmann I., Birnstiel M.L. Cell cycle-dependent regulation of histone precursor mRNA processing by modulation of U7 snRNA accessibility. Nature. 346:1990;665-668.
43. Ivanova V.S., Zimonjic D., Popescu N., Bonner W.M. Chromosomal localization of the human histone H2A.X gene to 11q23.2-q23.3 by fluorescence in situ hybridization. Hum. Genet. 94:1994;303-306.
44. Jacobs E.Y., Frey M.R., Gebuhr T.C., Wu W., Ingledue T.C., Gao L., Marzluff W.F., Matera A.G. Coiled bodies preferentially associate with U4, U11 and U12 snRNA genes in interphase HeLa cells, but not with U6 and U7 genes. Mol. Biol. Cell. 10:1999;1653-1663.
45. Kremer H., Hennig W. Isolation and characterization of a Drosophila hydei histone DNA repeat unit. Nucleic Acids Res. 18:1990;1573-1580.
46. Krieg P.A., Melton D.A. Formation of the 3′ end of histone mRNA by post-transcriptional processing. Nature. 308:1984;203-206.
47. Lindauer A., Müller K., Schmitt R. Two histone H1-encoding genes of the green alga Volvox carteri with features intermediate between plant and animal genes. Gene. 129:1993;59-68.
48. Lou H., Gagel R.F., Berget S.M. An intron enhancer recognized by splicing factors activates polyadenylation. Genes Dev. 10:1996;208-219.
49. Lüscher B., Schümperli D. RNA 3′ processing regulates histone mRNA levels in a mammalian cell mutant. A processing factor becomes limiting in G1-arrested cells. EMBO J. 6:1987;1721-1726.
50. Martin F., Schaller A., Eglite S., Schümperli D., Müller B. The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein. EMBO J. 16:1997;769-778.
51. Marzluff W.F., Pandey N.B. Multiple levels of regulation of histone mRNA concentrations. Trends Biochem. Sci. 13:1988;49-52.
52. Marzluff W.F. Histone 3′ ends: essential and regulatory functions. Gene Expression. 2:1992;93-97.
53. 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. 11:1992;691-697.
54. Moss S.B., Ferry R.A., Groudine M. An alternative pathway of histone mRNA 3′ end formation in mouse round spermatids. Nucleic Acids Res. 22:1994;3160-3166.
55. Mowry K.L., Steitz J.A. Identification of the human U7 snRNP as one of several factors involved in the 3′ end maturation of histone premessenger RNA′s. Science. 238:1987;1682-1687.
56. 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. 7:1987;1663-1672.
57. 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. 9:1989;3105-3108.
58. Müller K., Lindauer A., Brüderlein M., Schmitt R. Organization and transcription of Volvox histone-encoding genes: Similarities between algal and animal genes. Gene. 93:1990;167-175.
59. Nagata T., Kato T., Morita T., Nozaki M., Kubota H., Yagi H., Matsushiro A. Polyadenylated and 3′ processed mRNAs are transcribed from the mouse histone H2A.X gene. Nucleic Acids Res. 19:1991;2441-2447.
60. Nakayama T., Takechi S., Takami Y. The chicken histone gene family. Comp. Biochem. Physiol. 104B:1993;635-639.
61. Osley M.A. The regulation of histone synthesis in the cell cycle. Annu. Rev. Biochem. 60:1991;827-861.
62. Pandey N.B., Chodchoy N., Liu T.J., Marzluff W.F. Introns in histone genes alter the distribution of 3′ ends. Nucleic Acids Res. 18:1990;3161-3170.
63. Pandey N.B., Sun J.H., Marzluff W.F. Different complexes are formed on the 3′ end of histone mRNA in nuclear and polysomal extracts. Nucleic Acids Res. 19:1991;5653-5659.
64. 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. 14:1994;1709-1720.
65. Phillips S.C., Turner P.C. The mouse U7 small nuclear RNA gene promoter functions efficiently in Xenopus oocytes. Biochem. Soc. Trans. 19:1991;339S-339S.
66. Phillips S.C., Birnstiel M.L. Analysis of a gene cluster coding for the Xenopus laevis U7 snRNA. Biochim. Biophys. Acta Gene Struct. Expression. 1131:1992;95-98.
67. Roberts S.B., Sanicola M., Emmons S.W., Childs G. Molecular characterization of the histone gene family of Caenorhabditis elegans. J. Mol. Biol. 196:1987;27-38.
68. Roberts S.B., Emmons S.W., Childs G. Nucleotide sequences of Caenorhabditis elegans core histone genes. Genes for different histone classes share common flanking sequence elements. J. Mol. Biol. 206:1989;567-577.
69. Scharl E.C., Steitz J.A. 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. 13:1994;2432-2440.
70. Scharl E.C., Steitz J.A. Length suppression in histone messenger RNA 3′-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA. Proc. Natl. Acad. Sci. USA. 93:1996;14659-14664.
71. 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. Nature. 323:1986;777-781.
72. SenGupta D.J., Zhang B.L., Kraemer B., Prochart P., Fields S., Wickens M. A three-hybrid system to detect RNA-protein interactions in vivo. Proc. Natl. Acad. Sci. USA. 93:1996;8496-8501.
73. Smith H.O., Tabiti K., Schaffner G., Soldati D., Albrecht U., Birnstiel M.L. Two-step affinity purification of U7 small nuclear ribonucleoprotein particles using complementary biotinylated 2′-O-methyl oligoribonucleotides. Proc. Natl. Acad. Sci. USA. 88:1991;9784-9788.
74. Soldati D., Schümperli D. Structural and functional characterization of mouse U7 small nuclear RNA active in 3′ processing of histone pre-mRNA. Mol. Cell. Biol. 8:1988;1518-1524.
75. Southgate C., Busslinger M. In vivo and in vitro expression of U7 snRNA genes: cis- and trans-acting elements required for RNA polymerase II-directed transcription. EMBO J. 8:1989;539-549.
76. Spycher C., Streit A., Stefanovic B., Albrecht D., Koning T.H.W., Schümperli D. 3′ end processing of mouse histone pre-mRNA: Evidence for additional base-pairing between U7 snRNA and pre-mRNA. Nucleic Acids Res. 22:1994;4023-4030.
77. Stauber C., Schümperli D. 3′ processing of pre-mRNA plays a major role in proliferation-dependent regulation of histone gene expression. Nucleic Acids Res. 16:1988;9399-9413.
78. Stauber C., Soldati D., Lüscher B., Schümperli D. Histone-specific RNA 3′ processing in nuclear extracts from mammalian cells. Meth. Enzymol. 181:1990;74-88.
79. Stefanovic B., Hackl W., Lührmann R., Schümperli D. Assembly, nuclear import and function of U7 snRNPs studied by microinjection of synthetic U7 RNA into Xenopus oocytes. Nucleic Acids Res. 23:1995;3141-3151.
80. 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. 21:1993;1569-1575.
81. Strub K., Galli G., Busslinger M., Birnstiel M.L. The cDNA sequences of the sea urchin U7 small nuclear RNA suggest specific contacts between histone mRNA precursor and U7 RNA during RNA processing. EMBO J. 3:1984;2801-2807.
82. Strub K., Birnstiel M.L. Genetic complementation in the Xenopus oocyte: co-expression of sea urchin histone and U7 RNAs restores 3′ processing of H3 pre-mRNA in the oocyte. EMBO J. 5:1986;1675-1682.
83. Sures I., Lowry J., Kedes L.H. The DNA sequence of sea urchin (S. purpuratus) H2a, H2b, and H3 histone coding and spacer regions. Cell. 15:1978;1033-1044.
84. Tuma R.S., Stolk J.A., Roth M.B. Identification and characterization of a sphere organelle protein. J. Cell Biol. 122:1993;767-773.
85. 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. USA. 86:1989;4345-4349.
86. Wahle E. A novel poly(A)-binding protein acts as a specificity factor in the second phase of messenger RNA polyadenylation. Cell. 66:1991;759-768.
87. Wahle E., Keller W. The biochemistry of polyadenylation. Trends Biochem. Sci. 21:1996;247-250.
88. Walther T.N., Wittop K.T., Schümperli D., Müller B. A 5′-3′ exonuclease activity involved in forming the 3′ products of histone pre-mRNA processing in vitro. RNA. 4:1998;1034-1046.
89. Wang Z.F., Tisovec R., Debry R.W., Frey M.R., Matera A.G., Marzluff W.F. Characterization of the 55 kilobase mouse histone gene cluster on chromosome 3. Genome Res. 6:1996;702-714.
90. Wang Z.F., Krasikov T., Frey M.R., Wang J., Matera A.G., Marzluff W.F. Characterization of the mouse histone gene cluster on chromosome 13: 45 histone genes in three patches spread over one megabase. Genome Res. 6:1996;688-701.
91. Wang Z.F., Whitfield M.L., Ingledue T.I., Dominski Z., Marzluff W.F. The protein which binds the 3′ end of histone mRNA: a novel RNA- binding protein required for histone pre-mRNA processing. Genes Dev. 10:1996;3028-3040.
92. Wang Z.F., Ingledue T.C., Dominski Z., Sanchez R., Marzluff W.F. Two Xenopus proteins that bind the 3′ end of histone mRNA: Implications for translational control of histone synthesis during oogenesis. Mol. Cell. Biol. 19:1999;835-845.
93. Wells D., Kedes L. Structure of a human histone cDNA: Evidence that basally expressed histone genes have intervening sequences and encode polyadenylated mRNAs. Proc. Natl. Acad. Sci. USA. 82:1985;2834-2838.
94. Williams A.S., Ingledue T.C., Kay B.K., Marzluff W.F. Changes in the stem-loop at the 3′ terminus of histone mRNA affects its nucleocytoplasmic transport and cytoplasmic regulation. Nucleic Acids Res. 22:1994;4660-4666.
95. 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. 23:1995;654-662.
96. Woudt L.P., Patink A., Kempers-Veenstra A.E., Jansen A.E.M., Mager W.H., Planta R.J. The genes encoding histone H3 and H4 in Neurospora crassa are unique and contain intervening sequences. Nucleic Acids Res. 11:1983;5347-5347.
97. Wu C.-H.H., Gall J.G. U7 small nuclear RNA in C snurposomes of the Xenopus germinal vesicle. Proc. Natl. Acad. Sci. USA. 90:1993;6257-6259.
98. Wu C.H., Murphy C., Gall J.G. The Sm binding site targets U7 snRNA to coiled bodies (spheres) of amphibian oocytes. RNA. 2:1996;811-823.
99. Wu R.S., Bonner W.M. Separation of basal histone synthesis from S phase histone synthesis in dividing cells. Cell. 27:1981;321-330.
100. Zweidler A. Core histone variants of the mouse: Primary structure and expression. Stein G., Stein W., Marzluff W.F. Histone Genes: Structure, Organization and Regulation. 1984;373-395 Wiley, New York.