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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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CTD isoforms and nucleosome distribution around Pol II upstream of TSSs in class I promoters.(A) 3D plots of Tyr1P, Ser5P, Ser7P and nucleosomes midpoints (MP) maximum signal locations as compared to Pol II ChIP-seq maxima for genes of group 1 of Figure 3A. Only genes with a significant signal of antisense ssRNA and higher than sense ssRNA were taken into account (see ‘Materials and methods–CTD isoforms and nucleosomes midpoint maximal peaks spatial organization analysis’ for details). The positive values of the distance to Pol II axis (in bp) indicate that maximum signals are located after Pol II in opposite direction of TSSs whereas negative values are in the inverse orientation. The number of maximal peaks before, after or colocalized with Pol II for Tyr1P, Ser5P, and Ser7P are 90/265/174, 99/152/278, 125/234/170, respectively. Note that most of the Tyr1P max values are located after Pol II whereas Ser5P is mainly found around Pol II main signal. (B) 2D Boxplots of the maximum values shown in (A) (upper panel) and for an independent analysis using Tyr1P max signal as reference (lower panel). In both cases Tyr1P locates at or after the leading edge of Pol II. (C) Distance to Pol II distribution of Tyr1P, Ser5P, and Ser7P for class I promoters selected as described in (A). Data is represented in bins of 10 (‘Materials and methods–Processing of sequenced tags’). The difference of distribution with the whole set of genes (black line) was assessed by a nonparametric Kolmogorov-Smirnov test. p-values are indicated at the top-right of each panel.DOI:http://dx.doi.org/10.7554/eLife.02105.016
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fig3s2: CTD isoforms and nucleosome distribution around Pol II upstream of TSSs in class I promoters.(A) 3D plots of Tyr1P, Ser5P, Ser7P and nucleosomes midpoints (MP) maximum signal locations as compared to Pol II ChIP-seq maxima for genes of group 1 of Figure 3A. Only genes with a significant signal of antisense ssRNA and higher than sense ssRNA were taken into account (see ‘Materials and methods–CTD isoforms and nucleosomes midpoint maximal peaks spatial organization analysis’ for details). The positive values of the distance to Pol II axis (in bp) indicate that maximum signals are located after Pol II in opposite direction of TSSs whereas negative values are in the inverse orientation. The number of maximal peaks before, after or colocalized with Pol II for Tyr1P, Ser5P, and Ser7P are 90/265/174, 99/152/278, 125/234/170, respectively. Note that most of the Tyr1P max values are located after Pol II whereas Ser5P is mainly found around Pol II main signal. (B) 2D Boxplots of the maximum values shown in (A) (upper panel) and for an independent analysis using Tyr1P max signal as reference (lower panel). In both cases Tyr1P locates at or after the leading edge of Pol II. (C) Distance to Pol II distribution of Tyr1P, Ser5P, and Ser7P for class I promoters selected as described in (A). Data is represented in bins of 10 (‘Materials and methods–Processing of sequenced tags’). The difference of distribution with the whole set of genes (black line) was assessed by a nonparametric Kolmogorov-Smirnov test. p-values are indicated at the top-right of each panel.DOI:http://dx.doi.org/10.7554/eLife.02105.016

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)

CTD isoforms and nucleosome distribution around Pol II upstream of TSSs in class I promoters.(A) 3D plots of Tyr1P, Ser5P, Ser7P and nucleosomes midpoints (MP) maximum signal locations as compared to Pol II ChIP-seq maxima for genes of group 1 of Figure 3A. Only genes with a significant signal of antisense ssRNA and higher than sense ssRNA were taken into account (see ‘Materials and methods–CTD isoforms and nucleosomes midpoint maximal peaks spatial organization analysis’ for details). The positive values of the distance to Pol II axis (in bp) indicate that maximum signals are located after Pol II in opposite direction of TSSs whereas negative values are in the inverse orientation. The number of maximal peaks before, after or colocalized with Pol II for Tyr1P, Ser5P, and Ser7P are 90/265/174, 99/152/278, 125/234/170, respectively. Note that most of the Tyr1P max values are located after Pol II whereas Ser5P is mainly found around Pol II main signal. (B) 2D Boxplots of the maximum values shown in (A) (upper panel) and for an independent analysis using Tyr1P max signal as reference (lower panel). In both cases Tyr1P locates at or after the leading edge of Pol II. (C) Distance to Pol II distribution of Tyr1P, Ser5P, and Ser7P for class I promoters selected as described in (A). Data is represented in bins of 10 (‘Materials and methods–Processing of sequenced tags’). The difference of distribution with the whole set of genes (black line) was assessed by a nonparametric Kolmogorov-Smirnov test. p-values are indicated at the top-right of each panel.DOI:http://dx.doi.org/10.7554/eLife.02105.016
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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fig3s2: CTD isoforms and nucleosome distribution around Pol II upstream of TSSs in class I promoters.(A) 3D plots of Tyr1P, Ser5P, Ser7P and nucleosomes midpoints (MP) maximum signal locations as compared to Pol II ChIP-seq maxima for genes of group 1 of Figure 3A. Only genes with a significant signal of antisense ssRNA and higher than sense ssRNA were taken into account (see ‘Materials and methods–CTD isoforms and nucleosomes midpoint maximal peaks spatial organization analysis’ for details). The positive values of the distance to Pol II axis (in bp) indicate that maximum signals are located after Pol II in opposite direction of TSSs whereas negative values are in the inverse orientation. The number of maximal peaks before, after or colocalized with Pol II for Tyr1P, Ser5P, and Ser7P are 90/265/174, 99/152/278, 125/234/170, respectively. Note that most of the Tyr1P max values are located after Pol II whereas Ser5P is mainly found around Pol II main signal. (B) 2D Boxplots of the maximum values shown in (A) (upper panel) and for an independent analysis using Tyr1P max signal as reference (lower panel). In both cases Tyr1P locates at or after the leading edge of Pol II. (C) Distance to Pol II distribution of Tyr1P, Ser5P, and Ser7P for class I promoters selected as described in (A). Data is represented in bins of 10 (‘Materials and methods–Processing of sequenced tags’). The difference of distribution with the whole set of genes (black line) was assessed by a nonparametric Kolmogorov-Smirnov test. p-values are indicated at the top-right of each panel.DOI:http://dx.doi.org/10.7554/eLife.02105.016
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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Related in: MedlinePlus