Overexpression of m6A-factors METTL3, ALKBH5, and YTHDC1 alters HPV16 mRNA splicing.

We report that overexpression of the m6A-demethylase alkB homolog 5 RNA demethylase (ALKBH5) promoted production of intron retention on the human papillomavirus type 16 (HPV16) E6 mRNAs thereby promoting E6 mRNA production. ALKBH5 also altered alternative splicing of the late L1 mRNA by an exon skipping mechanism. Knock-down of ALKBH5 had the opposite effect on splicing of these HPV16 mRNAs. Overexpression of the m6A-methylase methyltransferase-like protein 3 (METLL3) induced production of intron-containing HPV16 E1 mRNAs over spliced E2 mRNAs and altered HPV16 L1 mRNA splicing in a manner opposite to ALKBH5. Overexpression of the nuclear m6A-"reader" YTH domain-containing protein 1 (YTHDC1), enhanced retention of the E6-encoding intron and promoted E6 mRNA production. We also show that HPV16 mRNAs are bound to YTHDC1 in human cells and that YTHDC1 affected splicing of HPV16 E6/E7 mRNAs produced from the episomal form of the HPV16 genome. Finally, we show that HPV16 mRNAs are m6A-methylated in tonsillar cancer cells. In summary, HPV16 mRNAs are methylated in HPV16-infected tonsillar cancer cells and overexpression of m6A-"writer" METTL3, m6A-"eraser" ALKBH5 and the m6A-"reader" YTHDC1 affected HPV16 mRNA splicing, suggesting that m6A plays an important role in the HPV16 gene expression program, at least in cancer cells.

The DNA damage response activates HPV16 late gene expression at the level of RNA processing.

We show that the alkylating cancer drug melphalan activated the DNA damage response and induced human papillomavirus type 16 (HPV16) late gene expression in an ATM- and Chk1/2-dependent manner. Activation of HPV16 late gene expression included inhibition of the HPV16 early polyadenylation signal that resulted in read-through into the late region of HPV16. This was followed by activation of the exclusively late, HPV16 splice sites SD3632 and SA5639 and production of spliced late L1 mRNAs. Altered HPV16 mRNA processing was paralleled by increased association of phosphorylated BRCA1, BARD1, BCLAF1 and TRAP150 with HPV16 DNA, and increased association of RNA processing factors U2AF65 and hnRNP C with HPV16 mRNAs. These RNA processing factors inhibited HPV16 early polyadenylation and enhanced HPV16 late mRNA splicing, thereby activating HPV16 late gene expression.

Short half-life of HPV16 E6 and E7 mRNAs sensitizes HPV16-positive tonsillar cancer cell line HN26 to DNA-damaging drugs.

Here we show that treatment of the HPV16-positive tonsillar cancer cell line HN26 with DNA alkylating cancer drug melphalan-induced p53 and activated apoptosis. Melphalan reduced the levels of RNA polymerase II and cellular transcription factor Sp1 that were associated with HPV16 DNA. The resulting inhibition of transcription caused a rapid loss of the HPV16 early mRNAs encoding E6 and E7 as a result of their inherent instability. As a consequence of HPV16 E6 and E7 down-regulation, the DNA damage inflicted on the cells by melphalan caused induction of p53 and activation of apoptosis in the HN26 cells. The BARD1-negative phenotype of the HN26 cells may have contributed to the failure to repair DNA damage caused by melphalan, as well as to the efficient apoptosis induction. Finally, nude mice carrying the HPV16 positive tonsillar cancer cells responded better to melphalan than to cisplatin, the chemotherapeutic drug of choice for tonsillar cancer. We concluded that the short half-life of the HPV16 E6 and E7 mRNAs renders HPV16-driven tonsillar cancer cells particularly sensitive to DNA damaging agents such as melphalan since melphalan both inhibits transcription and causes DNA damage.

hnRNP L controls HPV16 RNA polyadenylation and splicing in an Akt kinase-dependent manner.

Inhibition of the Akt kinase activates HPV16 late gene expression by reducing HPV16 early polyadenylation and by activating HPV16 late L1 mRNA splicing. We identified 'hot spots' for RNA binding proteins at the early polyA signal and at splice sites on HPV16 late mRNAs. We observed that hnRNP L was associated with sequences at all HPV16 late splice sites and at the early polyA signal. Akt kinase inhibition resulted in hnRNP L dephosphorylation and reduced association of hnRNP L with HPV16 mRNAs. This was accompanied by an increased binding of U2AF65 and Sam68 to HPV16 mRNAs. Furthermore, siRNA knock-down of hnRNP L or Akt induced HPV16 gene expression. Treatment of HPV16 immortalized keratinocytes with Akt kinase inhibitor reduced hnRNP L binding to HPV16 mRNAs and induced HPV16 L1 mRNA production. Finally, deletion of the hnRNP L binding sites in HPV16 subgenomic expression plasmids resulted in activation of HPV16 late gene expression. In conclusion, the Akt kinase inhibits HPV16 late gene expression at the level of RNA processing by controlling the RNA-binding protein hnRNP L. We speculate that Akt kinase activity upholds an intracellular milieu that favours HPV16 early gene expression and suppresses HPV16 late gene expression.

hnRNP G prevents inclusion on the HPV16 L1 mRNAs of the central exon between splice sites SA3358 and SD3632.

HPV16 late L1 mRNAs encode a short central exon that is located between HPV16 3'-splice site SA3358 and HPV16 5'-splice site SD3632. While SA3358 is used to produce both HPV16 early mRNAs encoding the E6 and E7 oncogenes, and late mRNAs encoding E4, L1 and L2, SD3632 is used exclusively to produce late L1 mRNA. We have previously identified an 8-nucleotide regulatory RNA element that is required for inclusion of the exon between SA3358 and SD3632 to produce L1 mRNAs at the expense of mRNAs polyadenylated at the HPV16 early polyadenylation signal pAE. Here we show that this HPV16 8-nucleotide splicing enhancer interacts with hnRNP G. Binding of hnRNP G to this element prevents inclusion of the exon between SA3358 and SD3632 on the HPV16 late L1 mRNAs. We concluded that hnRNP G has a splicing inhibitory role and that hnRNP G can control HPV16 mRNA splicing.

Role of the DNA Damage Response in Human Papillomavirus RNA Splicing and Polyadenylation.

Human papillomaviruses (HPVs) have evolved to use the DNA repair machinery to replicate its DNA genome in differentiated cells. HPV activates the DNA damage response (DDR) in infected cells. Cellular DDR factors are recruited to the HPV DNA genome and position the cellular DNA polymerase on the HPV DNA and progeny genomes are synthesized. Following HPV DNA replication, HPV late gene expression is activated. Recent research has shown that the DDR factors also interact with RNA binding proteins and affects RNA processing. DDR factors activated by DNA damage and that associate with HPV DNA can recruit splicing factors and RNA binding proteins to the HPV DNA and induce HPV late gene expression. This induction is the result of altered alternative polyadenylation and splicing of HPV messenger RNA (mRNA). HPV uses the DDR machinery to replicate its DNA genome and to activate HPV late gene expression at the level of RNA processing.

Influenza virus natural sequence heterogeneity in segment 8 affects interactions with cellular RNA-binding proteins and splicing efficiency.

Segment 8 mRNAs of influenza virus A/Brevig Misson/1918/1 (H1N1) are poorly spliced compared to segment 8 mRNAs of influenza virus A/Netherlands/178/95 (H3N2). Using oligonucleotide-mediated protein pull down with oligos spanning the entire length of segment 8 of either influenza virus H1N1 or influenza virus H3N2 we identified cellular RNA binding proteins that interacted with oligonucleotides derived from either H1N1 or H3N2 sequences. When the identified hot spots for RNA binding proteins in H1N1 segment 8 mRNAs were replaced by H3N2 sequences, splicing efficiency increased significantly. Replacing as few as three nucleotides of the H1N1 mRNA with sequences from H3N2 mRNA, enhanced splicing of the H1N1 mRNAs. Cellular proteins U2AF65 and HuR interacted preferentially with the 3'-splice site of H3N2 and overexpression of HuR reduced the levels of unspliced H1N1 mRNAs, suggesting that U2AF65 and HuR contribute to control of influenza virus mRNA splicing.

Efficient production of HPV16 E2 protein from HPV16 late mRNAs spliced from SD880 to SA2709.

Human papillomaviruses (HPVs) produce a large number of alternatively spliced mRNAs, including a number of differently spliced mRNAs with the potential to produce E2 protein. To identify the alternatively spliced HPV16 mRNA with the highest ability to produce E2 protein, we have generated E2 cDNA expression plasmids representing the most common, alternatively spliced E2 mRNAs, and assessed their translational potential. Our results revealed that an mRNA initiated at the HPV16 late promoter p670 and spliced from the HPV16 5'-splice site SD880 to the HPV16 3'-splice site SA2709, located immediately upstream of the E2 ATG, produced higher levels of E2 than any of the other alternatively spliced, E2-encoding mRNAs. Utilization of a known, alternative 3'-splice site located upstream of the E2 ATG named SA2582, generated mRNAs with lower ability to produce E2 than mRNAs spliced to SA2709. Finally, analysis of HPV16 mRNA splicing demonstrated that SA2709 was more efficiently spliced to the upstream 5'-splice site SD880 than to the upstream 5'-splice site SD226. In conclusion, the HPV16 mRNA with the greatest ability to produce E2 protein is generated from the HPV16 late promoter and is spliced between HPV16 5'-splice site SD880 and HPV16 3'-splice site SA2709.

HPV16 E5 is produced from an HPV16 early mRNA spliced from SD226 to SA3358.

The HPV16 E5 open reading frame (ORF) is present on the majority of all alternatively spliced HPV16 mRNAs, but it is currently unknown how well it is translated into E5 protein. To identify HPV16 mRNAs that are efficiently translated into E5, we have generated cDNA plasmids expressing individual, alternatively spliced HPV16 mRNAs with the potential to produce E5. By replacing the E5 ORF with sLuc, we could quantitate sLuc and determine how well each cDNA was translated. Our results showed that the upstream E1 and E7 AUGs inhibited translation of the E5 ORF and revealed that only one HPV16 mRNA produced high levels of E5. This was an HPV16 early mRNA spliced from SD226 to SA3358. These results were confirmed in the context of the entire HPV16 genome. Taken together, our results indicate that E5 is expressed early in the HPV16 replication cycle since it is translated efficiently only by one early mRNA.

Adenosine causes read-through into the late region of the HPV16 genome in a guanosine-dependent manner.

Adenosine plays an important role in cell death and differentiation as well as in tumorigenesis and the intra- and extra-cellular levels range from nanomolar to millimolar levels under various physiological or pathophysiological conditions. Here we report that adenosine can activate HPV16 late gene expression in a dose- and time-dependent manner, but only in the presence of guanosine. This activation occurred within hours after addition of the nucleosides and was primarily dependent on the ENT1 nucleoside transporter protein. Induction of HPV16 late gene expression was mainly the result of increased read-through at the early HPV16 polyadenylation signal into the late region of the HPV16 genome, thereby producing HPV16 late L2 mRNAs. The effect of guanosine and adenosine on HPV16 late gene expression was mediated by the increased binding to HPV16 mRNAs and nuclear export of the cellular HuR protein. Our results demonstrate that nucleosides can affect HPV16 gene expression.

Structure of solvated mercury(II) halides in liquid ammonia, triethyl phosphite and tri-n-butylphosphine solution.

Liquid ammonia, trialkyl phosphites, and especially trialkylphosphines, are very powerful electron-pair donor solvents with soft bonding character. The solvent molecules act as strongly coordinating ligands towards mercury(ii), interacting strongly enough to displace halide ligands. In liquid ammonia mercury(ii) chloride solutions separate into two liquid phases; the upper contains tetraamminemercury(ii) complexes, [Hg(NH(3))(4)](2+), and chloride ions in low concentration, while the lower is a dense highly concentrated solution of [Hg(NH(3))(4)](2+) entities, ca. 1.4 mol dm(-3), probably ion-paired by hydrogen bonds to the chloride ions. Mercury(ii) bromide also dissociates to ionic complexes in liquid ammonia and forms a homogeneous solution for which (199)Hg NMR indicates weak bromide association with mercury(ii). When dissolving mercury(ii) iodide in liquid ammonia and triethyl phosphite solvated molecular complexes form in the solutions. The Raman nu(I-Hg-I) symmetric stretching frequency is 132 cm(-1) for the pseudo-tetrahedral [HgI(2)(NH(3))(2)] complex formed in liquid ammonia, corresponding to D(S) = 56 on the donor strength scale. For the Hg(ClO(4))(2)/NH(4)I system in liquid ammonia a (199)Hg NMR study showed [HgI(4)](2-) to be the dominating mercury(ii) complex for mole ratios n(I(-)) : n(Hg(2+)) > or = 6. A large angle X-ray scattering (LAXS) study of mercury(ii) iodide in triethyl phosphite solution showed a [HgI(2)(P(OC(4)H(9))(3))(2)] complex with the Hg-I and Hg-P bond distances 2.750(3) and 2.457(4) A, respectively, in near tetrahedral configuration. Trialkylphosphines generally form very strong bonds to mercury(ii), dissociating all mercury(ii) halides. Mercury(ii) chloride and bromide form solid solvated mercury(ii) halide salts when treated with tri-n-butylphosphine, because of the low permittivity of the solvent. A LAXS study of a melt of mercury(ii) iodide in tri-n-butylphosphine at 330 K resulted in the Hg-I and Hg-P distances 2.851(3) and 2.468(4) A, respectively. The absence of a distinct I-I distance indicates flexible coordination geometry with weak and non-directional mercury(ii) iodide association within the tri-n-butylphosphine solvated complex.

Coordination chemistry of mercury(II) in liquid and aqueous ammonia solution and the crystal structure of tetraamminemercury(II) perchlorate.

The ammonia solvated mercury(II) ion has been structurally characterized in solution by means of EXAFS, (199)Hg NMR, and Raman spectroscopy and in solid solvates by combining results from X-ray single crystal and powder diffraction, thermogravimetry, differential scanning calorimetry, EXAFS, and Raman spectroscopy. Crystalline tetraamminemercury(II) perchlorate, [Hg(NH3)4](ClO4)2, precipitates from both liquid ammonia and aqueous ammonia solution, containing tetraamminemercury(II) complexes. The orthorhombic space group ( Pnma) imposes C s symmetry on the tetraamminemercury(II) complexes, which is lost at a phase transition at about 220 K. The Hg-N bond distances are 2.175(14), 2.255(16), and 2 x 2.277(9) A, with a wide N-Hg-N angle between the two shortest Hg-N bonds, 122.1(7) degrees , at ambient temperature. A similar distorted tetrahedral coordination geometry is maintained in liquid ammonia and aqueous ammonia solutions with the mean Hg-N bond distances 2.225(12) and 2.226(6) A, respectively. When heated to 400 K the solid tetraamminemercury(II) perchlorate decomposes to diamminemercury(II) perchlorate, [Hg(NH3)2](ClO4)2, with the mean Hg-N bond distance 2.055(6) A in a linear N-Hg-N unit. The mercury atoms in the latter compound form a tetrahedral network, connected by perchlorate oxygen atoms, with the closest Hg...Hg distance being 3.420(3) A. The preferential solvation and coordination changes of the mercury(II) ion in aqueous ammonia, by varying the total NH 3:Hg(II) mole ratio from 0 to 130, were followed by (199)Hg NMR. Solid [Hg(NH 3)4](ClO4)2 precipitates while [Hg(H2O)6](2+) ions remain in solution at mole ratios below 3-4, while at high mole ratios, [Hg(NH3)4](2+) complexes dominate in solution. The principal bands in the vibrational spectrum of the [Hg(NH3)4](2+) complex have been assigned.

Coordination chemistry of the solvated silver(I) ion in the oxygen donor solvents water, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea.

The hydrated and dimethyl sulfoxide and N,N'-dimethylpropyleneurea solvated silver(I) ions have been characterized structurally in solution by means of extended X-ray absorption fine structure (EXAFS) and large-angle X-ray scattering (LAXS). The coordination chemistry of the hydrated and dimethyl sulfoxide solvated silver(I) ions has been reevaluated because of different results from the EXAFS and LAXS methods reported previously. Consistent results are obtained with a linearly distorted tetrahedral model with two short and approximately two long Ag-O bond distances: mean Ag-O bond lengths of 2.32(1) and 2.54(1) A for the hydrate, 2.31(1) and 2.48(2) A for the dimethyl sulfoxide solvate, and 2.31(1) and 2.54(2) A for the N,N'-dimethylpropyleneurea solvate, in solution.

Coordination chemistry of the solvated AgI and AuI ions in liquid and aqueous ammonia, trialkyl and triphenyl phosphite, and tri-n-butylphosphine solutions.

The coordination chemistry of solvated Ag(I) and Au(I) ions has been studied in some of the most strong electron-pair donor solvents, liquid and aqueous ammonia, and the P donor solvents triethyl, tri-n-butyl, and triphenyl phosphite and tri-n-butylphosphine. The solvated Ag(I) ions have been characterized in solution by means of extended X-ray absorption fine structure (EXAFS), Raman, and (107)Ag NMR spectroscopy and the solid solvates by means of thermogravimetry and EXAFS and Raman spectroscopy. The Ag(I) ion is two- and three-coordinated in aqueous and liquid ammonia solutions with mean Ag-N bond distances of 2.15(1) and 2.26(1) A, respectively. The crystal structure of [Ag(NH3)3]ClO4.0.47 NH3 (1) reveals a regular trigonal-coplanar coordination around the Ag(I) ion with Ag-N bond distances of 2.263(6) A and a Ag...Ag distance of 3.278(2) A separating the complexes. The decomposition products of 1 have been analyzed, and one of them, [Ag(NH3)2]ClO4, has been structurally characterized by means of EXAFS, showing [Ag(NH3)2] units connected into chains by double O bridges from perchlorate ions; the Ag...Ag distance is 3.01(1) A. The linear bisamminegold(I) complex, [Au(NH3)2]+, is predominant in both liquid and aqueous ammonia solutions, as well as in solid [Au(NH3)2]BF4, with Au-N bond distances of 2.022(5), 2.025(5), and 2.026(7) A, respectively. The solvated Ag(I) ions are three-coordinated, most probably in triangular fashion, in the P donor solvents with mean Ag-P bond distances of 2.48-2.53 A. The Au(I) ions are three-coordinated in triethyl phosphite and tri-n-butylphosphine solutions with mean Au-P bond distances of 2.37(1) and 2.40(1) A, respectively.

The coordination chemistry of copper(I) in liquid ammonia, trialkyl and triphenyl phosphite, and tri-n-butylphosphine solution.

The coordination chemistry of the solvate complexes of the relatively soft electron-pair acceptor copper(I) has been studied in solution and solid state in seven solvents with strong electron-pair donor properties, liquid ammonia, trimethyl, triethyl, triisopropyl, tri-n-butyl and triphenyl phosphite, and tri-n-butylphosphine. The solvate complexes have been characterised by means of EXAFS and 63Cu NMR spectroscopy, and in some cases also by 65Cu NMR spectroscopy. The copper(I) ion is three-coordinated, most probably in a coplanar trigonal fashion, in liquid ammonia with a mean Cu-N bond distance of 2.00(1) Angstroms. No 63Cu NMR signal has been detected from the ammonia solvated copper(I) ion in liquid ammonia, which supports a three-coordination. The phosphite and phosphine solvated copper(I) ions are tetrahedral with Cu-P bond distances in the range 2.24-2.28 Angstrom in both solution and solid state as determined by EXAFS spectroscopy. The tetrahedral configuration of these complexes has been confirmed by 63Cu and 65Cu NMR spectroscopy through the J(63Cu-31P) and J(65Cu-31P) couplings. The fact that two of the investigated complexes, [Cu(P(OC6H5)3)4]+ and [Cu(P(C4H9)3)4]+, are 63Cu and 65Cu NMR silent is probably caused by a significantly angular distorted tetrahedral configuration.