Analysis of the signals for transcription termination by purified RNA polymerase II.

Eukaryotic RNA polymerase II recognizes certain DNA sequences as effective signals for transcription termination in vitro. Previously, we have shown that such termination occurs within T-rich sequences; however, not all T runs stop the enzyme nor is the efficiency of termination correlated with the length of the T run. Here we have investigated the sequence elements that signal transcription termination by purified RNA polymerase II. We have examined terminators located within introns of the human histone H3.3 gene and the human c-myc gene. Deletion analysis of the H3.3 termination region indicates that the sequences between -6 and +24 relative to the strongest termination site are sufficient to cause transcription termination. The minimal termination signal at this site has been localized to the sequence TTTTTTTC-CCTTTTTT in the nontranscribed strand. A similar but nonidentical sequence has been defined for the c-myc termination site. Since RNA polymerase II terminates transcription only within the first run of T residues in these sequences, at least part of the termination signal lies in downstream nontranscribed DNA sequences. Restriction fragment mobility analysis indicates that the H3.3 termination region contains a bend in the DNA helix. Oligonucleotides containing the minimal termination signals also cause restriction fragments to migrate with anomalous mobility. A region of the SV40 genome containing a previously characterized bend also causes RNA polymerase II to terminate transcription. We suggest that a structural element causing a bend in the DNA helix may be part of the signal for transcription termination by purified RNA polymerase II.

[1]  M. Chamberlin,et al.  Transcription elongation factor SII (TFIIS) enables RNA polymerase II to elongate through a block to transcription in a human gene in vitro. , 1989, The Journal of biological chemistry.

[2]  M. Chamberlin,et al.  Terminator-distal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7. , 1989, Biochemistry.

[3]  J. Steitz,et al.  Function of the mammalian La protein: evidence for its action in transcription termination by RNA polymerase III. , 1989, The EMBO journal.

[4]  J. Hutton,et al.  Cell type-specific transcriptional regulation of the human adenosine deaminase gene. , 1989, Nucleic acids research.

[5]  O. Resnekov,et al.  RNA polymerase II is capable of pausing and prematurely terminating transcription at a precise location in vivo and in vitro. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[6]  J. Bishop,et al.  DNA sequences that mediate attenuation of transcription from the mouse protooncogene myc. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[7]  T. Kerppola,et al.  Intrinsic sites of transcription termination and pausing in the c-myc gene , 1988, Molecular and cellular biology.

[8]  D. Tessier,et al.  RNA polymerases stall and/or prematurely terminate nearby both early and late promoters on polyomavirus DNA. , 1988, Journal of molecular biology.

[9]  A. Saltzman,et al.  Transcription elongation factor SII interacts with a domain of the large subunit of human RNA polymerase II , 1988, Molecular and cellular biology.

[10]  M. Groudine,et al.  Sequence requirements for premature termination of transcription in the human c-myc gene , 1988, Cell.

[11]  J. Manley,et al.  A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. , 1988, Genes & development.

[12]  G. Padmanaban,et al.  Heme regulates cytochrome P-450 gene transcription elongation. , 1988, Biochemical and biophysical research communications.

[13]  Jack D. Griffith,et al.  The terminus of SV40 DNA replication and transcription contains a sharp sequence-directed curve , 1988, Cell.

[14]  E. Geiduschek,et al.  Transcription by RNA polymerase III. , 1988, Annual review of biochemistry.

[15]  P. Luciw,et al.  Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product , 1987, Nature.

[16]  J E Darnell,et al.  A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[17]  M. Groudine,et al.  Mutations in the first exon are associated with altered transcription of c-myc in Burkitt lymphoma. , 1987, Science.

[18]  W. Kuehl,et al.  Differential expression of c-myb mRNA in murine B lymphomas by a block to transcription elongation. , 1987, Science.

[19]  P. Fort,et al.  Regulation of c-fos gene expression in hamster fibroblasts: initiation and elongation of transcription and mRNA degradation. , 1987, Nucleic acids research.

[20]  M. Chamberlin,et al.  Identification of intrinsic termination sites in vitro for RNA polymerase II within eukaryotic gene sequences. , 1987, Journal of molecular biology.

[21]  M. Chamberlin,et al.  Purified RNA polymerase II recognizes specific termination sites during transcription in vitro. , 1987, The Journal of biological chemistry.

[22]  M. Chamberlin,et al.  Mapping and characterization of transcriptional pause sites in the early genetic region of bacteriophage T7. , 1987, Journal of molecular biology.

[23]  C. Richardson,et al.  DNA sequence analysis with a modified bacteriophage T7 DNA polymerase. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[24]  D. Scherly,et al.  Structure and transcription termination of a lysine tRNA gene from Xenopus laevis. , 1987, Journal of molecular biology.

[25]  R. Jove,et al.  RNA polymerase II terminates transcription in vitro in the SV40 origin region. , 1987, Nucleic acids research.

[26]  Edward N. Trifonov,et al.  Estimation of wedge components in curved DNA , 1987, Nature.

[27]  D. Reinberg,et al.  Factors involved in specific transcription by mammalian RNA polymerase II. Transcription factor IIS stimulates elongation of RNA chains. , 1987, The Journal of biological chemistry.

[28]  K. Struhl,et al.  Mutagenesis with degenerate oligonucleotides: an efficient method for saturating a defined DNA region with base pair substitutions. , 1987, Methods in enzymology.

[29]  D. Eick,et al.  Transcriptional arrest within the first exon is a fast control mechanism in c-myc gene expression. , 1986, Nucleic acids research.

[30]  H. E. N. D. Vegvar,et al.  3′ end formation of U1 snRNA precursors is coupled to transcription from snRNA promoters , 1986, Cell.

[31]  A. Weiner,et al.  Formation of the 3′ end of U1 snRNA requires compatible snRNA promoter elements , 1986, Cell.

[32]  J. Nordstrom,et al.  Requirement of A-A-U-A-A-A and adjacent downstream sequences for SV40 early polyadenylation. , 1986, Nucleic acids research.

[33]  Mark Groudine,et al.  A block to elongation is largely responsible for decreased transcription of c-myc in differentiated HL60 cells , 1986, Nature.

[34]  Hen-Ming Wu,et al.  DNA bending at adenine · thymine tracts , 1986, Nature.

[35]  J. Tower,et al.  Transcription of cloned eukaryotic ribosomal RNA genes. , 1986, Annual review of biochemistry.

[36]  T Platt,et al.  Transcription termination and the regulation of gene expression. , 1986, Annual review of biochemistry.

[37]  J. Greenblatt,et al.  Isolation of three proteins that bind to mammalian RNA polymerase II. , 1985, The Journal of biological chemistry.

[38]  M. Chamberlin,et al.  Studies on transcription of 3'-extended templates by mammalian RNA polymerase II. Parameters that affect the initiation and elongation reactions. , 1985, Biochemistry.

[39]  C. Yanisch-Perron,et al.  Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. , 1985, Gene.

[40]  L. Bossi,et al.  Conformational change in the DNA associated with an unusual promoter mutation in a tRNA operon of Salmonella , 1984, Cell.

[41]  S. Chen‐Kiang,et al.  Premature termination by human RNA polymerase II occurs temporally in the adenovirus major late transcriptional unit , 1984, Molecular and cellular biology.

[42]  S. Chen‐Kiang,et al.  Pausing and premature termination of human RNA polymerase II during transcription of adenovirus in vivo and in vitro. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[43]  Hen-Ming Wu,et al.  The locus of sequence-directed and protein-induced DNA bending , 1984, Nature.

[44]  J. Brosius.  Toxicity of an overproduced foreign gene product in Escherichia coli and its use in plasmid vectors for the selection of transcription terminators. , 1984, Gene.

[45]  M. Horikoshi,et al.  Analysis of the stimulatory factor of RNA polymerase II in the initiation and elongation complex. , 1984, The Journal of biological chemistry.

[46]  N. Cozzarelli,et al.  Purified RNA polymerase III accurately and efficiently terminates transcription of 5s RNA genes , 1983, Cell.

[47]  H. Okayama,et al.  A cDNA cloning vector that permits expression of cDNA inserts in mammalian cells. , 1983, Molecular and cellular biology.

[48]  N. Salzman,et al.  Interaction between calf thymus RNA polymerase II and singly nicked Simian virus 40 DNA. , 1982, The Journal of biological chemistry.

[49]  B. Howard,et al.  Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells , 1982, Molecular and cellular biology.

[50]  M. Chamberlin,et al.  Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template. , 1982, The Journal of biological chemistry.

[51]  N. Hay,et al.  Attenuation in the control of SV40 gene expression , 1982, Cell.

[52]  D. Bogenhagen,et al.  Nucleotide sequences in Xenopus 5S DNA required for transcription termination , 1981, Cell.

[53]  J. Nevins,et al.  Regulation of adenovirus-2 gene expression at the level of transcriptional termination and RNA processing , 1981, Nature.

[54]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[55]  R. Duggleby,et al.  A computer program for determining the size of DNA restriction fragments. , 1981, Analytical biochemistry.

[56]  S. Weissman,et al.  Simian virus 40 early mRNA's. I. Genomic localization of 3' and 5' termini and two major splices in mRNA from transformed and lytically infected cells , 1979, Journal of virology.

[57]  J. Darnell,et al.  Premature termination during adenovirus transcription , 1979, Nature.

[58]  W. Salser.  Globin mRNA sequences: analysis of base pairing and evolutionary implications. , 1978, Cold Spring Harbor symposia on quantitative biology.

[59]  M. Chamberlin,et al.  A simple procedure for resolution of Escherichia coli RNA polymerase holoenzyme from core polymerase. , 1977, Archives of biochemistry and biophysics.