Heterogeneous nuclear ribonucleoprotein K is a transcription factor.
Abstract
The CT element is a positively acting homopyrimidine tract upstream of the c-myc gene to which the well-characterized transcription factor Spl and heterogeneous nuclear ribonucleoprotein (hnRNP) K, a less well-characterized protein associated with hnRNP complexes, have previously been shown to bind. The present work demonstrates that both of these molecules contribute to CT element-activated transcription in vitro. The pyrimidine-rich strand of the CT element both bound to hnRNP K and competitively inhibited transcription in vitro, suggesting a role for hnRNP K in activating transcription through this single-stranded sequence. Direct addition of recombinant hnRNP K to reaction mixtures programmed with templates bearing single-stranded CT elements increased specific RNA synthesis. If hnRNP K is a transcription factor, then interactions with the RNA polymerase II transcription apparatus are predicted. Affinity columns charged with recombinant hnRNP K specifically bind a component(s) necessary for transcription activation. The depleted factors were biochemically complemented by a crude TFIID phosphocellulose fraction, indicating that hnRNP K might interact with the TATA-binding protein (TBP)-TBP-associated factor complex. Coimmunoprecipitation of a complex formed in vivo between hnRNP K and epitope-tagged TBP as well as binding in vitro between recombinant proteins demonstrated a protein-protein interaction between TBP and hnRNP K. Furthermore, when the two proteins were overexpressed in vivo, transcription from a CT element-dependent reporter was synergistically activated. These data indicate that hnRNP K binds to a specific cis element, interacts with the RNA polymerase II transcription machinery, and stimulates transcription and thus has all of the properties of a transcription factor.
Full Text
The Full Text of this article is available as a PDF (593K).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Altiok S, Groner B. Interaction of two sequence-specific single-stranded DNA-binding proteins with an essential region of the beta-casein gene promoter is regulated by lactogenic hormones. Mol Cell Biol. 1993 Dec;13(12):7303–7310.[PMC free article] [PubMed] [Google Scholar]
- Avigan MI, Strober B, Levens D. A far upstream element stimulates c-myc expression in undifferentiated leukemia cells. J Biol Chem. 1990 Oct 25;265(30):18538–18545. [PubMed] [Google Scholar]
- Bergemann AD, Johnson EM. The HeLa Pur factor binds single-stranded DNA at a specific element conserved in gene flanking regions and origins of DNA replication. Mol Cell Biol. 1992 Mar;12(3):1257–1265.[PMC free article] [PubMed] [Google Scholar]
- Blanco J, Millstein L, Razik MA, Dilworth S, Cote C, Gottesfeld J. Two TFIIIA activities regulate expression of the Xenopus 5S RNA gene families. Genes Dev. 1989 Oct;3(10):1602–1612. [PubMed] [Google Scholar]
- Briggs MR, Kadonaga JT, Bell SP, Tjian R. Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science. 1986 Oct 3;234(4772):47–52. [PubMed] [Google Scholar]
- Burch JB, Weintraub H. Temporal order of chromatin structural changes associated with activation of the major chicken vitellogenin gene. Cell. 1983 May;33(1):65–76. [PubMed] [Google Scholar]
- Caron C, Rousset R, Béraud C, Moncollin V, Egly JM, Jalinot P. Functional and biochemical interaction of the HTLV-I Tax1 transactivator with TBP. EMBO J. 1993 Nov;12(11):4269–4278.[PMC free article] [PubMed] [Google Scholar]
- Chrysogelos S, Pauli U, Stein G, Stein J. Fine mapping of the chromatin structure of a cell cycle-regulated human H4 histone gene. J Biol Chem. 1989 Jan 15;264(2):1232–1237. [PubMed] [Google Scholar]
- Chrysogelos S, Riley DE, Stein G, Stein J. A human histone H4 gene exhibits cell cycle-dependent changes in chromatin structure that correlate with its expression. Proc Natl Acad Sci U S A. 1985 Nov;82(22):7535–7539.[PMC free article] [PubMed] [Google Scholar]
- Condon C, French S, Squires C, Squires CL. Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies. EMBO J. 1993 Nov;12(11):4305–4315.[PMC free article] [PubMed] [Google Scholar]
- Cooney M, Czernuszewicz G, Postel EH, Flint SJ, Hogan ME. Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science. 1988 Jul 22;241(4864):456–459. [PubMed] [Google Scholar]
- Davis TL, Firulli AB, Kinniburgh AJ. Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9682–9686.[PMC free article] [PubMed] [Google Scholar]
- Dejgaard K, Leffers H, Rasmussen HH, Madsen P, Kruse TA, Gesser B, Nielsen H, Celis JE. Identification, molecular cloning, expression and chromosome mapping of a family of transformation upregulated hnRNP-K proteins derived by alternative splicing. J Mol Biol. 1994 Feb 11;236(1):33–48. [PubMed] [Google Scholar]
- DesJardins E, Hay N. Repeated CT elements bound by zinc finger proteins control the absolute and relative activities of the two principal human c-myc promoters. Mol Cell Biol. 1993 Sep;13(9):5710–5724.[PMC free article] [PubMed] [Google Scholar]
- Dignam JD, Martin PL, Shastry BS, Roeder RG. Eukaryotic gene transcription with purified components. Methods Enzymol. 1983;101:582–598. [PubMed] [Google Scholar]
- Dreyfuss G, Matunis MJ, Piñol-Roma S, Burd CG. hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem. 1993;62:289–321. [PubMed] [Google Scholar]
- Dreyfuss G, Swanson MS, Piñol-Roma S. Heterogeneous nuclear ribonucleoprotein particles and the pathway of mRNA formation. Trends Biochem Sci. 1988 Mar;13(3):86–91. [PubMed] [Google Scholar]
- Duncan R, Bazar L, Michelotti G, Tomonaga T, Krutzsch H, Avigan M, Levens D. A sequence-specific, single-strand binding protein activates the far upstream element of c-myc and defines a new DNA-binding motif. Genes Dev. 1994 Feb 15;8(4):465–480. [PubMed] [Google Scholar]
- Dynlacht BD, Hoey T, Tjian R. Isolation of coactivators associated with the TATA-binding protein that mediate transcriptional activation. Cell. 1991 Aug 9;66(3):563–576. [PubMed] [Google Scholar]
- Engelke DR, Ng SY, Shastry BS, Roeder RG. Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell. 1980 Mar;19(3):717–728. [PubMed] [Google Scholar]
- Farina AR, Davis-Smyth T, Gardner K, Levens D. An early response of an AP1-junD complex during T-cell activation. J Biol Chem. 1993 Dec 15;268(35):26466–26475. [PubMed] [Google Scholar]
- Gaillard C, Cabannes E, Strauss F. Identity of the RNA-binding protein K of hnRNP particles with protein H16, a sequence-specific single strand DNA-binding protein. Nucleic Acids Res. 1994 Oct 11;22(20):4183–4186.[PMC free article] [PubMed] [Google Scholar]
- Giardina C, Pérez-Riba M, Lis JT. Promoter melting and TFIID complexes on Drosophila genes in vivo. Genes Dev. 1992 Nov;6(11):2190–2200. [PubMed] [Google Scholar]
- Wolins NE, Donaldson RP. Specific binding of the peroxisomal protein targeting sequence to glyoxysomal membranes. J Biol Chem. 1994 Jan 14;269(2):1149–1153. [PubMed] [Google Scholar]
- Gill G, Tjian R. Eukaryotic coactivators associated with the TATA box binding protein. Curr Opin Genet Dev. 1992 Apr;2(2):236–242. [PubMed] [Google Scholar]
- Gilman MZ, Wilson RN, Weinberg RA. Multiple protein-binding sites in the 5'-flanking region regulate c-fos expression. Mol Cell Biol. 1986 Dec;6(12):4305–4316.[PMC free article] [PubMed] [Google Scholar]
- Gorman CM, Moffat LF, Howard BH. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol Cell Biol. 1982 Sep;2(9):1044–1051.[PMC free article] [PubMed] [Google Scholar]
- Gourse RL, de Boer HA, Nomura M. DNA determinants of rRNA synthesis in E. coli: growth rate dependent regulation, feedback inhibition, upstream activation, antitermination. Cell. 1986 Jan 17;44(1):197–205. [PubMed] [Google Scholar]
- Gourse RL, Takebe Y, Sharrock RA, Nomura M. Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes. Proc Natl Acad Sci U S A. 1985 Feb;82(4):1069–1073.[PMC free article] [PubMed] [Google Scholar]
- Ham J, Steger G, Yaniv M. Cooperativity in vivo between the E2 transactivator and the TATA box binding protein depends on core promoter structure. EMBO J. 1994 Jan 1;13(1):147–157.[PMC free article] [PubMed] [Google Scholar]
- Hay N, Bishop JM, Levens D. Regulatory elements that modulate expression of human c-myc. Genes Dev. 1987 Sep;1(7):659–671. [PubMed] [Google Scholar]
- Hobert O, Jallal B, Schlessinger J, Ullrich A. Novel signaling pathway suggested by SH3 domain-mediated p95vav/heterogeneous ribonucleoprotein K interaction. J Biol Chem. 1994 Aug 12;269(32):20225–20228. [PubMed] [Google Scholar]
- Hoffman EK, Trusko SP, Murphy M, George DL. An S1 nuclease-sensitive homopurine/homopyrimidine domain in the c-Ki-ras promoter interacts with a nuclear factor. Proc Natl Acad Sci U S A. 1990 Apr;87(7):2705–2709.[PMC free article] [PubMed] [Google Scholar]
- Ito K, Sato K, Endo H. Cloning and characterization of a single-stranded DNA binding protein that specifically recognizes deoxycytidine stretch. Nucleic Acids Res. 1994 Jan 11;22(1):53–58.[PMC free article] [PubMed] [Google Scholar]
- Jones KA, Kadonaga JT, Luciw PA, Tjian R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science. 1986 May 9;232(4751):755–759. [PubMed] [Google Scholar]
- Kahn JD, Yun E, Crothers DM. Detection of localized DNA flexibility. Nature. 1994 Mar 10;368(6467):163–166. [PubMed] [Google Scholar]
- Kashanchi F, Piras G, Radonovich MF, Duvall JF, Fattaey A, Chiang CM, Roeder RG, Brady JN. Direct interaction of human TFIID with the HIV-1 transactivator tat. Nature. 1994 Jan 20;367(6460):295–299. [PubMed] [Google Scholar]
- Kerr LD, Ransone LJ, Wamsley P, Schmitt MJ, Boyer TG, Zhou Q, Berk AJ, Verma IM. Association between proto-oncoprotein Rel and TATA-binding protein mediates transcriptional activation by NF-kappa B. Nature. 1993 Sep 30;365(6445):412–419. [PubMed] [Google Scholar]
- Kolluri R, Kinniburgh AJ. Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein. Nucleic Acids Res. 1991 Sep 11;19(17):4771–4771.[PMC free article] [PubMed] [Google Scholar]
- Krumm A, Meulia T, Brunvand M, Groudine M. The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region. Genes Dev. 1992 Nov;6(11):2201–2213. [PubMed] [Google Scholar]
- Larsen A, Weintraub H. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell. 1982 Jun;29(2):609–622. [PubMed] [Google Scholar]
- Lee WS, Kao CC, Bryant GO, Liu X, Berk AJ. Adenovirus E1A activation domain binds the basic repeat in the TATA box transcription factor. Cell. 1991 Oct 18;67(2):365–376. [PubMed] [Google Scholar]
- Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024–7027.[PMC free article] [PubMed] [Google Scholar]
- Marcu KB, Bossone SA, Patel AJ. myc function and regulation. Annu Rev Biochem. 1992;61:809–860. [PubMed] [Google Scholar]
- Matunis MJ, Michael WM, Dreyfuss G. Characterization and primary structure of the poly(C)-binding heterogeneous nuclear ribonucleoprotein complex K protein. Mol Cell Biol. 1992 Jan;12(1):164–171.[PMC free article] [PubMed] [Google Scholar]
- Meisterernst M, Roy AL, Lieu HM, Roeder RG. Activation of class II gene transcription by regulatory factors is potentiated by a novel activity. Cell. 1991 Sep 6;66(5):981–993. [PubMed] [Google Scholar]
- Meyers RE, Sharp PA. TATA-binding protein and associated factors in polymerase II and polymerase III transcription. Mol Cell Biol. 1993 Dec;13(12):7953–7960.[PMC free article] [PubMed] [Google Scholar]
- Mirkovitch J, Darnell JE., Jr Mapping of RNA polymerase on mammalian genes in cells and nuclei. Mol Biol Cell. 1992 Oct;3(10):1085–1094.[PMC free article] [PubMed] [Google Scholar]
- Negishi Y, Nishita Y, Saëgusa Y, Kakizaki I, Galli I, Kihara F, Tamai K, Miyajima N, Iguchi-Ariga SM, Ariga H. Identification and cDNA cloning of single-stranded DNA binding proteins that interact with the region upstream of the human c-myc gene. Oncogene. 1994 Apr;9(4):1133–1143. [PubMed] [Google Scholar]
- Ostrowski J, Van Seuningen I, Seger R, Rauch CT, Sleath PR, McMullen BA, Bomsztyk K. Purification, cloning, and expression of a murine phosphoprotein that binds the kappa B motif in vitro identifies it as the homolog of the human heterogeneous nuclear ribonucleoprotein K protein. Description of a novel DNA-dependent phosphorylation process. J Biol Chem. 1994 Jul 1;269(26):17626–17634. [PubMed] [Google Scholar]
- Pelham HR, Brown DD. A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. Proc Natl Acad Sci U S A. 1980 Jul;77(7):4170–4174.[PMC free article] [PubMed] [Google Scholar]
- Picard B, Wegnez M. Isolation of a 7S particle from Xenopus laevis oocytes: a 5S RNA-protein complex. Proc Natl Acad Sci U S A. 1979 Jan;76(1):241–245.[PMC free article] [PubMed] [Google Scholar]
- Piñol-Roma S, Choi YD, Matunis MJ, Dreyfuss G. Immunopurification of heterogeneous nuclear ribonucleoprotein particles reveals an assortment of RNA-binding proteins. Genes Dev. 1988 Feb;2(2):215–227. [PubMed] [Google Scholar]
- Postel EH, Berberich SJ, Flint SJ, Ferrone CA. Human c-myc transcription factor PuF identified as nm23-H2 nucleoside diphosphate kinase, a candidate suppressor of tumor metastasis. Science. 1993 Jul 23;261(5120):478–480. [PubMed] [Google Scholar]
- Pugh BF, Tjian R. Mechanism of transcriptional activation by Sp1: evidence for coactivators. Cell. 1990 Jun 29;61(7):1187–1197. [PubMed] [Google Scholar]
- Schneider C, Newman RA, Sutherland DR, Asser U, Greaves MF. A one-step purification of membrane proteins using a high efficiency immunomatrix. J Biol Chem. 1982 Sep 25;257(18):10766–10769. [PubMed] [Google Scholar]
- Shichiri M, Hanson KD, Sedivy JM. Effects of c-myc expression on proliferation, quiescence, and the G0 to G1 transition in nontransformed cells. Cell Growth Differ. 1993 Feb;4(2):93–104. [PubMed] [Google Scholar]
- Siomi H, Choi M, Siomi MC, Nussbaum RL, Dreyfuss G. Essential role for KH domains in RNA binding: impaired RNA binding by a mutation in the KH domain of FMR1 that causes fragile X syndrome. Cell. 1994 Apr 8;77(1):33–39. [PubMed] [Google Scholar]
- Siomi H, Matunis MJ, Michael WM, Dreyfuss G. The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. Nucleic Acids Res. 1993 Mar 11;21(5):1193–1198.[PMC free article] [PubMed] [Google Scholar]
- Smith DB, Johnson KS. Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase. Gene. 1988 Jul 15;67(1):31–40. [PubMed] [Google Scholar]
- Takimoto M, Tomonaga T, Matunis M, Avigan M, Krutzsch H, Dreyfuss G, Levens D. Specific binding of heterogeneous ribonucleoprotein particle protein K to the human c-myc promoter, in vitro. J Biol Chem. 1993 Aug 25;268(24):18249–18258. [PubMed] [Google Scholar]
- Tanese N, Pugh BF, Tjian R. Coactivators for a proline-rich activator purified from the multisubunit human TFIID complex. Genes Dev. 1991 Dec;5(12A):2212–2224. [PubMed] [Google Scholar]
- Taylor SJ, Shalloway D. An RNA-binding protein associated with Src through its SH2 and SH3 domains in mitosis. Nature. 1994 Apr 28;368(6474):867–871. [PubMed] [Google Scholar]
- Timmers HT, Sharp PA. The mammalian TFIID protein is present in two functionally distinct complexes. Genes Dev. 1991 Nov;5(11):1946–1956. [PubMed] [Google Scholar]
- Tomonaga T, Levens D. Heterogeneous nuclear ribonucleoprotein K is a DNA-binding transactivator. J Biol Chem. 1995 Mar 3;270(9):4875–4881. [PubMed] [Google Scholar]
- Weng Z, Thomas SM, Rickles RJ, Taylor JA, Brauer AW, Seidel-Dugan C, Michael WM, Dreyfuss G, Brugge JS. Identification of Src, Fyn, and Lyn SH3-binding proteins: implications for a function of SH3 domains. Mol Cell Biol. 1994 Jul;14(7):4509–4521.[PMC free article] [PubMed] [Google Scholar]
- Xu X, Prorock C, Ishikawa H, Maldonado E, Ito Y, Gélinas C. Functional interaction of the v-Rel and c-Rel oncoproteins with the TATA-binding protein and association with transcription factor IIB. Mol Cell Biol. 1993 Nov;13(11):6733–6741.[PMC free article] [PubMed] [Google Scholar]
- Zhou Q, Lieberman PM, Boyer TG, Berk AJ. Holo-TFIID supports transcriptional stimulation by diverse activators and from a TATA-less promoter. Genes Dev. 1992 Oct;6(10):1964–1974. [PubMed] [Google Scholar]
Abstract
The CT element is a positively acting homopyrimidine tract upstream of the c-myc gene to which the well-characterized transcription factor Spl and heterogeneous nuclear ribonucleoprotein (hnRNP) K, a less well-characterized protein associated with hnRNP complexes, have previously been shown to bind. The present work demonstrates that both of these molecules contribute to CT element-activated transcription in vitro. The pyrimidine-rich strand of the CT element both bound to hnRNP K and competitively inhibited transcription in vitro, suggesting a role for hnRNP K in activating transcription through this single-stranded sequence. Direct addition of recombinant hnRNP K to reaction mixtures programmed with templates bearing single-stranded CT elements increased specific RNA synthesis. If hnRNP K is a transcription factor, then interactions with the RNA polymerase II transcription apparatus are predicted. Affinity columns charged with recombinant hnRNP K specifically bind a component(s) necessary for transcription activation. The depleted factors were biochemically complemented by a crude TFIID phosphocellulose fraction, indicating that hnRNP K might interact with the TATA-binding protein (TBP)-TBP-associated factor complex. Coimmunoprecipitation of a complex formed in vivo between hnRNP K and epitope-tagged TBP as well as binding in vitro between recombinant proteins demonstrated a protein-protein interaction between TBP and hnRNP K. Furthermore, when the two proteins were overexpressed in vivo, transcription from a CT element-dependent reporter was synergistically activated. These data indicate that hnRNP K binds to a specific cis element, interacts with the RNA polymerase II transcription machinery, and stimulates transcription and thus has all of the properties of a transcription factor.