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Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells.

Descostes N, Heidemann M, Spinelli L, Schüller R, Maqbool MA, Fenouil R, Koch F, Innocenti C, Gut M, Gut I, Eick D, Andrau JC - Elife (2014)

Bottom Line: Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation.Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of promoter (5' associated) Pol II in mammalian cells, in contrast to what was described in yeast.Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the truncated Pol IIB form, and results in a lethal phenotype.

View Article: PubMed Central - PubMed

Affiliation: Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Marseille, France Centre National de la Recherche Scientifique (CNRS) UMR6102, Marseille, France Inserm U631, Marseille, France Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS-UMR5535, Montpellier, France.

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Three classes of Pol II-bound promoters ordered by Tyr1P location in human Raji cells.(A) Heatmaps of a selection of Pol II-bound promoters for ssRNAs, nucleosome and AT, GC contents ordered by Tyr1P (3D12) maximum signal from the most upstream to the most downstream of the annotated TSSs (as previously described in mouse lymphocytes, Fenouil et al., 2012). Note that Pol II main accumulation areas occur at proximity of the main nucleosome position for each promoter class. As described before (Fenouil et al., 2012), GC content and CpG islands correlate with nucleosome depletion. (B) Profiles of ssRNAs (sense and antisense) and nucleosome in the three groups. (C) Profiles of Pol II and CTD isoforms in the three classes of promoters as indicated.DOI:http://dx.doi.org/10.7554/eLife.02105.015
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fig3s1: Three classes of Pol II-bound promoters ordered by Tyr1P location in human Raji cells.(A) Heatmaps of a selection of Pol II-bound promoters for ssRNAs, nucleosome and AT, GC contents ordered by Tyr1P (3D12) maximum signal from the most upstream to the most downstream of the annotated TSSs (as previously described in mouse lymphocytes, Fenouil et al., 2012). Note that Pol II main accumulation areas occur at proximity of the main nucleosome position for each promoter class. As described before (Fenouil et al., 2012), GC content and CpG islands correlate with nucleosome depletion. (B) Profiles of ssRNAs (sense and antisense) and nucleosome in the three groups. (C) Profiles of Pol II and CTD isoforms in the three classes of promoters as indicated.DOI:http://dx.doi.org/10.7554/eLife.02105.015

Mentions: (A) Correlation plots of biological replicates (for all but H3K36me3 i.e., a technical replicate) of ChIP-seq experiments used in this study at gene locations (‘Materials and methods–Correlation of biological replicates and cross-correlation’). Spearman correlation coefficient is indicated on the top left of the plots. (B) Distribution and threshold of background-subtracted signal used for profiling of significantly bound gene (Total, i.e., whole genic regions) in Figure 2, Figure 2—figure supplement 5A, and Figure 2—figure supplement 7C. The mean values used for distribution were computed on [TSS-1000 bp:TES+2000 bp] (TSS: transcription start site; TES: transcription end site). Note that the thresholds were set to the mean of the second Gaussian of the distribution (‘Materials and methods–Gene selection and average binding profiles’). Numbers of genes selected for Pol II, Ser2P, Ser5P, Ser7P, Tyr1P 3D12, and Tyr1P 8G5 are 1521, 1536, 1543, 2382, 2652, and 2608, respectively. (C) Distribution and threshold of Pol II significantly bound promoters (TSS) as in (B). The selection is used in Figure 3, Figure 3—figure supplement 1, and Figure 3—figure supplement 2. 2044 genes were selected based on their mean values on TSS −/+ 500 bp.


Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells.

Descostes N, Heidemann M, Spinelli L, Schüller R, Maqbool MA, Fenouil R, Koch F, Innocenti C, Gut M, Gut I, Eick D, Andrau JC - Elife (2014)

Three classes of Pol II-bound promoters ordered by Tyr1P location in human Raji cells.(A) Heatmaps of a selection of Pol II-bound promoters for ssRNAs, nucleosome and AT, GC contents ordered by Tyr1P (3D12) maximum signal from the most upstream to the most downstream of the annotated TSSs (as previously described in mouse lymphocytes, Fenouil et al., 2012). Note that Pol II main accumulation areas occur at proximity of the main nucleosome position for each promoter class. As described before (Fenouil et al., 2012), GC content and CpG islands correlate with nucleosome depletion. (B) Profiles of ssRNAs (sense and antisense) and nucleosome in the three groups. (C) Profiles of Pol II and CTD isoforms in the three classes of promoters as indicated.DOI:http://dx.doi.org/10.7554/eLife.02105.015
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4042876&req=5

fig3s1: Three classes of Pol II-bound promoters ordered by Tyr1P location in human Raji cells.(A) Heatmaps of a selection of Pol II-bound promoters for ssRNAs, nucleosome and AT, GC contents ordered by Tyr1P (3D12) maximum signal from the most upstream to the most downstream of the annotated TSSs (as previously described in mouse lymphocytes, Fenouil et al., 2012). Note that Pol II main accumulation areas occur at proximity of the main nucleosome position for each promoter class. As described before (Fenouil et al., 2012), GC content and CpG islands correlate with nucleosome depletion. (B) Profiles of ssRNAs (sense and antisense) and nucleosome in the three groups. (C) Profiles of Pol II and CTD isoforms in the three classes of promoters as indicated.DOI:http://dx.doi.org/10.7554/eLife.02105.015
Mentions: (A) Correlation plots of biological replicates (for all but H3K36me3 i.e., a technical replicate) of ChIP-seq experiments used in this study at gene locations (‘Materials and methods–Correlation of biological replicates and cross-correlation’). Spearman correlation coefficient is indicated on the top left of the plots. (B) Distribution and threshold of background-subtracted signal used for profiling of significantly bound gene (Total, i.e., whole genic regions) in Figure 2, Figure 2—figure supplement 5A, and Figure 2—figure supplement 7C. The mean values used for distribution were computed on [TSS-1000 bp:TES+2000 bp] (TSS: transcription start site; TES: transcription end site). Note that the thresholds were set to the mean of the second Gaussian of the distribution (‘Materials and methods–Gene selection and average binding profiles’). Numbers of genes selected for Pol II, Ser2P, Ser5P, Ser7P, Tyr1P 3D12, and Tyr1P 8G5 are 1521, 1536, 1543, 2382, 2652, and 2608, respectively. (C) Distribution and threshold of Pol II significantly bound promoters (TSS) as in (B). The selection is used in Figure 3, Figure 3—figure supplement 1, and Figure 3—figure supplement 2. 2044 genes were selected based on their mean values on TSS −/+ 500 bp.

Bottom Line: Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation.Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of promoter (5' associated) Pol II in mammalian cells, in contrast to what was described in yeast.Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the truncated Pol IIB form, and results in a lethal phenotype.

View Article: PubMed Central - PubMed

Affiliation: Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Marseille, France Centre National de la Recherche Scientifique (CNRS) UMR6102, Marseille, France Inserm U631, Marseille, France Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS-UMR5535, Montpellier, France.

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