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A novel TBP-TAF complex on RNA Polymerase II-transcribed snRNA genes

By Justyna Zaborowska, Alice Taylor, Robert G. Roeder and Shona Murphy

Abstract

Initiation of transcription of most human genes transcribed by RNA polymerase II (RNAP II) requires the formation of a preinitiation complex comprising TFIIA, B, D, E, F, H and RNAP II. The general transcription factor TFIID is composed of the TATA-binding protein and up to 13 TBP-associated factors. During transcription of snRNA genes, RNAP II does not appear to make the transition to long-range productive elongation, as happens during transcription of protein-coding genes. In addition, recognition of the snRNA gene-type specific 3′ box RNA processing element requires initiation from an snRNA gene promoter. These characteristics may, at least in part, be driven by factors recruited to the promoter. For example, differences in the complement of TAFs might result in differential recruitment of elongation and RNA processing factors. As precedent, it already has been shown that the promoters of some protein-coding genes do not recruit all the TAFs found in TFIID. Although TAF5 has been shown to be associated with RNAP II-transcribed snRNA genes, the full complement of TAFs associated with these genes has remained unclear. Here we show, using a ChIP and siRNA-mediated approach, that the TBP/TAF complex on snRNA genes differs from that found on protein-coding genes. Interestingly, the largest TAF, TAF1, and the core TAFs, TAF10 and TAF4, are not detected on snRNA genes. We propose that this snRNA gene-specific TAF subset plays a key role in gene type-specific control of expression

Topics: Research Paper
Publisher: Landes Bioscience
OAI identifier: oai:pubmedcentral.nih.gov:3337830
Provided by: PubMed Central
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    1. (1994). A glutamine-rich hydrophobic patch in transcription factor
    2. (1998). A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID.
    3. (2005). a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell
    4. (1998). A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell
    5. (1995). A TBP-TAF complex required for transcription of human snRNA genes by RNA polymerase II and III. Nature
    6. (2002). A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved
    7. Activation of the U2 snRNA promoter by the octamer motif defines a new class of RNA polymerase II enhancer elements. Genes Dev 1988; 2:1764-78; PMID:2853685; http://dx.doi.org/10.1101/ gad.2.12b.1764.
    8. (1985). An enhancer-like sequence within the Xenopus U2 gene promoter facilitates the formation of stable transcription complexes. Nature
    9. (1994). Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell
    10. (1995). Basal promoter elements as a selective determinant of transcriptional activator function.
    11. (2009). Chromatin structure is implicated in “late” elongation checkpoints on the U2 snRNA and beta-actin genes. Mol Cell Biol
    12. (1995). Cloning of an intrinsic human TFIID subunit that interacts with multiple transcriptional activators. Science
    13. (1993). Common and unique transcription factor requirements of human U1 and U6 snRNA genes.
    14. (2007). Conserved region I of human coactivator TAF4 binds to a short hydrophobic motif present in transcriptional regulators.
    15. (2011). Control of eukaryotic gene expression: gene loops and transcriptional memory. Adv Enzyme Regul
    16. (2005). Core promoter binding by histonelike TAF complexes. Mol Cell Biol
    17. (2008). Cracking the RNA polymerase II CTD code. Trends Genet
    18. (1994). Direct recognition of initiator elements by a component of the transcription factor IID complex. Genes Dev
    19. (2007). Distinct GCN5/PCAF-containing complexes function as co-activators and are involved in transcription factor and global histone acetylation. Oncogene
    20. (2009). Distinct modes of gene regulation by a cell-specific transcriptional activator.
    21. (2003). Distinct transcriptional pathways regulate basal and activated major histocompatibility complex class I expression. Mol Cell Biol
    22. (1999). DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250-TAF(II)150 complex recognizes the initiator.
    23. (2008). Expression of human snRNA genes from beginning to end. Biochem Soc Trans
    24. (1985). Formation of the 3' end of U1 snRNA is directed by a conserved sequence located downstream of the coding region.
    25. (1986). Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements. Cell
    26. (1998). Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II. Nature
    27. (2005). Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol Cell Biol
    28. (1992). functional interactions of a transcription factor with the proximal sequence element of small nuclear RNA genes. Mol Cell Biol
    29. (2007). Genome-wide mapping of in vivo protein-DNA interactions. Science
    30. (2001). Histone folds mediate selective heterodimerization of yeast
    31. (1998). HIV-1 tat binds TAFII250 and represses TAFII250-dependent transcription of major histocompatibility class I genes.
    32. (2005). HIV-1 Tat stimulates transcription complex assembly through recruitment of TBP in the absence of TAFs. PLoS Biol
    33. (1984). Human genes for U2 small nuclear RNA are tandemly repeated. Mol Cell Biol
    34. (2001). Human STAGA complex is a chromatin-acetylating transcription coactivator that interacts with pre-mRNA splicing and DNA damage-binding factors in vivo. Mol Cell Biol
    35. (1998). Human TAF(II)28 and TAF(II)18 interact through a histone fold encoded by atypical evolutionary conserved motifs also found in the SPT3 family. Cell
    36. (1984). Human U2 and U1 RNA genes use similar transcription signals.
    37. (2004). Identification and distinct regulation of yeast TATA box-containing genes. Cell
    38. (2007). Identification of a small TAF complex and its role in the assembly of TAF-containing complexes. PLoS One
    39. (1999). Identification of TATA-binding protein-free TAFII-containing complex subunits suggests a role in nucleosome acetylation and signal transduction.
    40. (2002). Mapping histone fold TAFs within yeast TFIID.
    41. (2009). Mapping the initiator binding Taf2 subunit in the structure of hydrated yeast TFIID. Structure
    42. (1998). Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol Mol Biol Rev
    43. (2009). Multiple hTAF(II)31-binding motifs in the intrinsically unfolded transcriptional activation domain of VP16. BMB Rep
    44. (2005). P-TEFb is not an essential elongation factor for the intronless human U2 snRNA and histone H2b genes.
    45. (2006). Pause sites promote transcriptional termination of mammalian RNA polymerase II. Mol Cell Biol
    46. (2009). Recent advances in understanding the structure and function of general transcription factor TFIID. Cell Mol Life Sci
    47. (2002). Regulation of RNA polymerase II activity by CTD phosphorylation and cell cycle control.
    48. (2000). Requirement for TAF(II)250 acetyltransferase activity in cell cycle progression. Mol Cell Biol
    49. (2008). RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes. Nat Struct Mol Biol
    50. (2008). Structural changes in TAF4bTFIID correlate with promoter selectivity. Mol Cell
    51. (2004). TAF1 activates transcription by phosphorylation of serine 33 in histone H2B. Science
    52. (2003). TAF10 (TAF(II)30) is necessary for TFIID stability and early embryogenesis in mice. Mol Cell Biol
    53. (2006). TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter.
    54. (2006). TAF7: a possible transcription initiation check-point regulator.
    55. (2001). TAFII55 binding to TAFII250 inhibits its acetyltransferase activity.
    56. (1993). Targeting TBP to a non-TATA box cis-regulatory element: a TBP-containing complex activates transcription from snRNA promoters through the PSE. Genes Dev
    57. TATA binding protein associated factor 3 (TAF3) interacts with p53 and inhibits its function. BMC Mol Biol 2008; 9:57; PMID:18549481; http://
    58. (2000). TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes. Trends Biochem Sci
    59. (1993). TBP, a universal eukaryotic transcription factor? Genes Dev
    60. (1994). TFIID sequence recognition of the initiator and sequences farther downstream
    61. (2009). TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing and termination by RNA polymerase II. Mol Cell Biol
    62. (2003). The 3' ends of human presnRNAs are produced by RNA polymerase II CTDdependent RNA processing.
    63. (2003). The C-terminal domain of pol II and a DRB-sensitive kinase are required for 3' processing of U2 snRNA.
    64. (1999). The general transcription factors IIA IIB, IIF and IIE are required for RNA polymerase II transcription from the human U1 small nuclear RNA promoter. Mol Cell Biol
    65. (2006). The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol
    66. (2001). The histone fold is a key structural motif of transcription factor TFIID. Trends Biochem Sci
    67. (1990). The human U1 snRNA promoter correctly initiates transcription in vitro and is activated by PSE1. Genes Dev
    68. (2003). The RNA polymerase II core promoter. Annu Rev Biochem
    69. (1996). The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci
    70. (2007). Transcription factor TAFII250 promotes Mdm2-dependent turnover of p53. Oncogene
    71. (1997). Transcription factor TFIID recruits factor CPSF for formation of 3' end of mRNA. Nature
    72. (2001). Transcriptional coactivator complexes. Annu Rev Biochem
    73. (1994). Transcriptional elongation by RNA polymerase II is stimulated by transactivators. Cell
    74. (2000). Ubiquitin-activating/conjugating activity of TAFII250, a mediator of activation of gene expression in Drosophila. Science

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