Variable effects of the conserved RNA hairpin element upon 3' end processing of histone pre-mRNA in vitro.

We have studied the requirements for efficient histone-specific RNA 3' processing in nuclear extract from mammalian tissue culture cells. Processing is strongly impaired by mutations in the pre-mRNA spacer element that reduce the base-pairing potential with U7 RNA. Moreover, by exchanging the hairpin and spacer elements of two differently processed H4 genes, we find that this difference is exclusively due to the spacer element. Finally, processing is inhibited by the addition of competitor RNAs, if these contain a wild-type spacer sequence, but not if their spacer element is mutated. Conversely, the importance of the hairpin for histone RNA 3' processing is highly variable: A hairpin mutant of the H4-12 gene is processed with almost wild-type efficiency in extract from K21 mouse mastocytoma cells but is strongly affected in HeLa cell extract, whereas an identical hairpin mutant of the H4-1 gene is affected in both extracts. The hairpin defect of H4-12-specific RNA in HeLa cells can be overcome by a compensatory mutation that increases the base complementarity to U7 snRNA. Very similar results were also obtained in RNA competition experiments: processing of H4-12-specific RNA can be competed by RNA carrying a wild-type hairpin element in extract from HeLa, but not K21 cells, whereas processing of H4-1-specific RNA can be competed in both extracts. With two additional histone genes we obtained results that were in one case intermediate and in the other similar to those obtained with H4-1. These results suggest that hairpin binding factor(s) can cooperatively support the ability of U7 snRNPs to form an active processing complex, but is(are) not directly involved in the processing mechanism.

[1]  D. Soldati,et al.  Biochemical demonstration of complex formation of histone pre‐mRNA with U7 small nuclear ribonucleoprotein and hairpin binding factors. , 1992, The EMBO journal.

[2]  W. Ellmeier,et al.  Mature mRNA 3′ end formation stimulates RNA export from the nucleus. , 1991, The EMBO journal.

[3]  H. Smith,et al.  Two-step affinity purification of U7 small nuclear ribonucleoprotein particles using complementary biotinylated 2'-O-methyl oligoribonucleotides. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[4]  W. Marzluff,et al.  Different complexes are formed on the 3' end of histone mRNA with nuclear and polyribosomal proteins. , 1991, Nucleic acids research.

[5]  D. Schümperli,et al.  Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional steps , 1991, Molecular and cellular biology.

[6]  D. Schümperli,et al.  Structure of a mouse histone-encoding gene cluster. , 1990, Gene.

[7]  D. Soldati,et al.  Histone-specific RNA 3' processing in nuclear extracts from mammalian cells. , 1990, Methods in enzymology.

[8]  W. Bonner,et al.  H2A.X. a histone isoprotein with a conserved C-terminal sequence, is encoded by a novel mRNA with both DNA replication type and polyA 3' processing signals. , 1989, Nucleic acids research.

[9]  A. Skoultchi,et al.  Different 3'-end processing produces two independently regulated mRNAs from a single H1 histone gene. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[10]  A. Skoultchi,et al.  The efficiency of 3'-end formation contributes to the relative levels of different histone mRNAs , 1989, Molecular and cellular biology.

[11]  J. Steitz,et al.  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 , 1989, Molecular and cellular biology.

[12]  M. Birnstiel,et al.  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. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[13]  A. Skoultchi,et al.  Differential expression of individual members of the histone multigene family due to sequences in the 5' and 3' regions of the genes , 1988, Molecular and cellular biology.

[14]  D. Soldati,et al.  Structural and functional characterization of mouse U7 small nuclear RNA active in 3' processing of histone pre-mRNA. , 1988, Molecular and cellular biology.

[15]  M. Birnstiel,et al.  Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles , 1988, Springer Berlin Heidelberg.

[16]  G. Schaffner,et al.  Specific contacts between mammalian U7 snRNA and histone precursor RNA are indispensable for the in vitro 3′ RNA processing reaction. , 1988, The EMBO journal.

[17]  A. Krämer,et al.  Heat-labile regulatory factor is required for 3' processing of histone precursor mRNAs. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[18]  D. Schümperli,et al.  RNA 3′ processing regulates histone mRNA levels in a mammalian cell cycle mutant. A processing factor becomes limiting in G1‐arrested cells. , 1987, The EMBO journal.

[19]  J. Steitz,et al.  Both conserved signals on mammalian histone pre-mRNAs associate with small nuclear ribonucleoproteins during 3' end formation in vitro , 1987, Molecular and cellular biology.

[20]  R. Graves,et al.  Translation is required for regulation of histone mRNA degradation , 1987, Cell.

[21]  A. Krämer,et al.  Generation of histone mRNA 3′ ends by endonucleolytic cleavage of the pre‐mRNA in a snRNP‐dependent in vitro reaction. , 1986, The EMBO journal.

[22]  M. Birnstiel,et al.  Compensatory mutations suggest that base-pairing with a small nuclear RNA is required to form the 3′ end of H3 messenger RNA , 1986, Nature.

[23]  J. D. Engel,et al.  Replacement variant histone genes contain intervening sequences , 1985, Molecular and cellular biology.

[24]  R. Graves,et al.  Differential expression of two clusters of mouse histone genes. , 1985, Journal of molecular biology.

[25]  L. Kedes,et al.  Structure of a human histone cDNA: evidence that basally expressed histone genes have intervening sequences and encode polyadenylylated mRNAs. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[26]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[27]  R. Roeder,et al.  Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. , 1983, Nucleic acids research.

[28]  M. Birnstiel,et al.  Structure and expression in L-cells of a cloned H4 histone gene of the mouse. , 1981, Journal of molecular biology.

[29]  M. Busslinger,et al.  A regulatory sequence near the 3' end of sea urchin histone genes. , 1979, Nucleic acids research.

[30]  D. Peattie,et al.  Direct chemical method for sequencing RNA. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[31]  O. Uhlenbeck,et al.  3′-Terminal labelling of RNA with T4 RNA ligase , 1978, Nature.

[32]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.