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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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Average profiling of Pol II and phospho-isoforms at genic and promoter locations using wide relaxed threshold selections.(A) Composite and TSS focused average profiling of ChIP-seq data as in Figure 2C,D, for a selection threshold of 0 as described in Figure 2—figure supplement 1B, at coding genes locations for Pol II (2714 genes), Tyr1P (3D12, 2987 genes), Ser5P (2697 genes), and Ser7P (3002 genes) in Raji B-cells. (B) Boxplots on 4749 genes as in Figure 2E for the less stringent selection showing mean levels of Pol II, Tyr1P, Ser5P, and Ser7P ChIP-seq signal on regions representing each transcription orientation. The p-values (parametric two sided paired t test) of the difference of AS vs S signal are Pol II = 0.2, Tyr1p=3.5 × 10−16, Ser5p=0.2, Ser7p=0.03. Boxplots do not show outliers for Pol II (3933 genes), Tyr1P (3897 genes), Ser5P (3920 genes), and Ser7P (3878 genes).DOI:http://dx.doi.org/10.7554/eLife.02105.010
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fig2s4: Average profiling of Pol II and phospho-isoforms at genic and promoter locations using wide relaxed threshold selections.(A) Composite and TSS focused average profiling of ChIP-seq data as in Figure 2C,D, for a selection threshold of 0 as described in Figure 2—figure supplement 1B, at coding genes locations for Pol II (2714 genes), Tyr1P (3D12, 2987 genes), Ser5P (2697 genes), and Ser7P (3002 genes) in Raji B-cells. (B) Boxplots on 4749 genes as in Figure 2E for the less stringent selection showing mean levels of Pol II, Tyr1P, Ser5P, and Ser7P ChIP-seq signal on regions representing each transcription orientation. The p-values (parametric two sided paired t test) of the difference of AS vs S signal are Pol II = 0.2, Tyr1p=3.5 × 10−16, Ser5p=0.2, Ser7p=0.03. Boxplots do not show outliers for Pol II (3933 genes), Tyr1P (3897 genes), Ser5P (3920 genes), and Ser7P (3878 genes).DOI:http://dx.doi.org/10.7554/eLife.02105.010

Mentions: (A) Co-immunoprecipitation with specific CTD isoforms in Raji B-cells reveals Tyr1P (3D12) association with Ser5P and Ser7P but not with Ser2P and Thr4P. (B) ChIP-seq example illustrating Tyr1P (3D12) association around the promoter of RPL22L1 gene. (C) Composite average profiling of ChIP-seq data at coding genes locations for Pol II (1433 genes), Tyr1P (3D12, 2462 genes), Ser5P (1464 genes), and Ser7P (2186 genes) in Raji B-cells and based on selections described in Figure 2—figure supplement 1B. Less stringent selections with more genes gave equivalent profiling (Figure 2—figure supplement 4A). (D) Profiling of Pol II, Tyr1P (3D12), Ser5P, Ser7P, nucleosomes midpoint and short strand specific RNAs (ssRNAs) around TSS locations with same selections described in (C). (E) Boxplots on 3201 genes without outliers showing mean levels of Pol II (2986 genes), Tyr1P (2964 genes), Ser5P (2909 genes), and Ser7P (2948 genes) ChIP-seq signal on regions representing each transcription orientation. The p-values (parametric two sided paired t test) of the difference of AS vs S signal are Pol II = 0.5, Tyr1p=3.4 × 10−15, Ser5p=0.6, Ser7p=3.5 × 10−2.


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)

Average profiling of Pol II and phospho-isoforms at genic and promoter locations using wide relaxed threshold selections.(A) Composite and TSS focused average profiling of ChIP-seq data as in Figure 2C,D, for a selection threshold of 0 as described in Figure 2—figure supplement 1B, at coding genes locations for Pol II (2714 genes), Tyr1P (3D12, 2987 genes), Ser5P (2697 genes), and Ser7P (3002 genes) in Raji B-cells. (B) Boxplots on 4749 genes as in Figure 2E for the less stringent selection showing mean levels of Pol II, Tyr1P, Ser5P, and Ser7P ChIP-seq signal on regions representing each transcription orientation. The p-values (parametric two sided paired t test) of the difference of AS vs S signal are Pol II = 0.2, Tyr1p=3.5 × 10−16, Ser5p=0.2, Ser7p=0.03. Boxplots do not show outliers for Pol II (3933 genes), Tyr1P (3897 genes), Ser5P (3920 genes), and Ser7P (3878 genes).DOI:http://dx.doi.org/10.7554/eLife.02105.010
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig2s4: Average profiling of Pol II and phospho-isoforms at genic and promoter locations using wide relaxed threshold selections.(A) Composite and TSS focused average profiling of ChIP-seq data as in Figure 2C,D, for a selection threshold of 0 as described in Figure 2—figure supplement 1B, at coding genes locations for Pol II (2714 genes), Tyr1P (3D12, 2987 genes), Ser5P (2697 genes), and Ser7P (3002 genes) in Raji B-cells. (B) Boxplots on 4749 genes as in Figure 2E for the less stringent selection showing mean levels of Pol II, Tyr1P, Ser5P, and Ser7P ChIP-seq signal on regions representing each transcription orientation. The p-values (parametric two sided paired t test) of the difference of AS vs S signal are Pol II = 0.2, Tyr1p=3.5 × 10−16, Ser5p=0.2, Ser7p=0.03. Boxplots do not show outliers for Pol II (3933 genes), Tyr1P (3897 genes), Ser5P (3920 genes), and Ser7P (3878 genes).DOI:http://dx.doi.org/10.7554/eLife.02105.010
Mentions: (A) Co-immunoprecipitation with specific CTD isoforms in Raji B-cells reveals Tyr1P (3D12) association with Ser5P and Ser7P but not with Ser2P and Thr4P. (B) ChIP-seq example illustrating Tyr1P (3D12) association around the promoter of RPL22L1 gene. (C) Composite average profiling of ChIP-seq data at coding genes locations for Pol II (1433 genes), Tyr1P (3D12, 2462 genes), Ser5P (1464 genes), and Ser7P (2186 genes) in Raji B-cells and based on selections described in Figure 2—figure supplement 1B. Less stringent selections with more genes gave equivalent profiling (Figure 2—figure supplement 4A). (D) Profiling of Pol II, Tyr1P (3D12), Ser5P, Ser7P, nucleosomes midpoint and short strand specific RNAs (ssRNAs) around TSS locations with same selections described in (C). (E) Boxplots on 3201 genes without outliers showing mean levels of Pol II (2986 genes), Tyr1P (2964 genes), Ser5P (2909 genes), and Ser7P (2948 genes) ChIP-seq signal on regions representing each transcription orientation. The p-values (parametric two sided paired t test) of the difference of AS vs S signal are Pol II = 0.5, Tyr1p=3.4 × 10−15, Ser5p=0.6, Ser7p=3.5 × 10−2.

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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