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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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Pol II and CTD PTMs correlate positively with expression.Based on microarray expression data, three groups of genes with low (L, 3414 genes), medium (M, 1238 genes), and high (H, 1007 genes) expression were used to profile Pol II isoforms and short ssRNA at promoters. (A) Heatmaps of signal densities for the three defined groups. (B) Average profiles of Pol II phospho-isoforms and ssRNA at the three defined groups. (C) Boxplots of the mean values retrieved at TSS −/+ 500 bp in the three classes for Pol II (3095, 1169, 957 genes), Tyr1P (3159, 1150, 958 genes), Ser5P (3072, 1157, 956 genes), and Ser7P (3184, 1130, 942 genes). (D) Boxplot of regions representing each transcription orientation as in Figure 2E for each class divided by Pol II binding values. p-value (parametric two sided paired t test) are respectively: 2.3 × 10−13; 5 × 10−4; 6 × 10−3 (low), 2.4 × 10−13; 6 × 10−3; 2 × 10−4 (medium), 7 × 10−6; 0.02; 0.8 (high). Represented number of genes are 3175, 3126, 3074, 3051, 3123, 3134 (low); 1154, 1079, 1154, 1125, 1139, 1084 (medium); 955, 930, 941, 941, 935, 913 (high).DOI:http://dx.doi.org/10.7554/eLife.02105.008
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fig2s2: Pol II and CTD PTMs correlate positively with expression.Based on microarray expression data, three groups of genes with low (L, 3414 genes), medium (M, 1238 genes), and high (H, 1007 genes) expression were used to profile Pol II isoforms and short ssRNA at promoters. (A) Heatmaps of signal densities for the three defined groups. (B) Average profiles of Pol II phospho-isoforms and ssRNA at the three defined groups. (C) Boxplots of the mean values retrieved at TSS −/+ 500 bp in the three classes for Pol II (3095, 1169, 957 genes), Tyr1P (3159, 1150, 958 genes), Ser5P (3072, 1157, 956 genes), and Ser7P (3184, 1130, 942 genes). (D) Boxplot of regions representing each transcription orientation as in Figure 2E for each class divided by Pol II binding values. p-value (parametric two sided paired t test) are respectively: 2.3 × 10−13; 5 × 10−4; 6 × 10−3 (low), 2.4 × 10−13; 6 × 10−3; 2 × 10−4 (medium), 7 × 10−6; 0.02; 0.8 (high). Represented number of genes are 3175, 3126, 3074, 3051, 3123, 3134 (low); 1154, 1079, 1154, 1125, 1139, 1084 (medium); 955, 930, 941, 941, 935, 913 (high).DOI:http://dx.doi.org/10.7554/eLife.02105.008

Mentions: To assess its relation to transcription genome-wide, we next performed Tyr1P ChIP-seq, using 3D12 mAb, and compared it to Pol II and the other phospho-isoforms. We isolated significantly associated regions based on the signal distribution of the background-subtracted data (Figure 2—figure supplement 1B) and found that Pol II and all isoforms, including Tyr1P, correlated with transcription levels of genes (Figure 2—figure supplement 2). At many gene locations, a predominant signal of Tyr1P at promoters was observed (Figure 2B, Figure 2—figure supplement 3). We further confirmed this by genome-wide profiling of Pol II isoforms at coding-gene locations (Figure 2C, Figure 2—figure supplement 4, Figure 2—figure supplement 5A for Ser2P profile). Our profiling analysis shows that Tyr1P signal is predominantly found at promoters similarly to Ser5P, weak or essentially absent at gene bodies and weak at 3′ends in contrast to Ser2P elongating mark and Ser7P (associated to both promoters and gene bodies). These observations are further supported by quantification of signals at various genic sections (Figure 2—figure supplement 6) and reinforce our conclusion that human Tyr1P is mainly associated to promoters in an early, post-initiation step of transcription. Although we did not further investigate this possibility, in the accompanying manuscript, Hsin et al show that Chicken Tyr1 is found phosphorylated in the nucleoplasm, raising the possibility that Tyr1P is also associated with recruitment of the enzyme and transcription initiation.


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)

Pol II and CTD PTMs correlate positively with expression.Based on microarray expression data, three groups of genes with low (L, 3414 genes), medium (M, 1238 genes), and high (H, 1007 genes) expression were used to profile Pol II isoforms and short ssRNA at promoters. (A) Heatmaps of signal densities for the three defined groups. (B) Average profiles of Pol II phospho-isoforms and ssRNA at the three defined groups. (C) Boxplots of the mean values retrieved at TSS −/+ 500 bp in the three classes for Pol II (3095, 1169, 957 genes), Tyr1P (3159, 1150, 958 genes), Ser5P (3072, 1157, 956 genes), and Ser7P (3184, 1130, 942 genes). (D) Boxplot of regions representing each transcription orientation as in Figure 2E for each class divided by Pol II binding values. p-value (parametric two sided paired t test) are respectively: 2.3 × 10−13; 5 × 10−4; 6 × 10−3 (low), 2.4 × 10−13; 6 × 10−3; 2 × 10−4 (medium), 7 × 10−6; 0.02; 0.8 (high). Represented number of genes are 3175, 3126, 3074, 3051, 3123, 3134 (low); 1154, 1079, 1154, 1125, 1139, 1084 (medium); 955, 930, 941, 941, 935, 913 (high).DOI:http://dx.doi.org/10.7554/eLife.02105.008
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4042876&req=5

fig2s2: Pol II and CTD PTMs correlate positively with expression.Based on microarray expression data, three groups of genes with low (L, 3414 genes), medium (M, 1238 genes), and high (H, 1007 genes) expression were used to profile Pol II isoforms and short ssRNA at promoters. (A) Heatmaps of signal densities for the three defined groups. (B) Average profiles of Pol II phospho-isoforms and ssRNA at the three defined groups. (C) Boxplots of the mean values retrieved at TSS −/+ 500 bp in the three classes for Pol II (3095, 1169, 957 genes), Tyr1P (3159, 1150, 958 genes), Ser5P (3072, 1157, 956 genes), and Ser7P (3184, 1130, 942 genes). (D) Boxplot of regions representing each transcription orientation as in Figure 2E for each class divided by Pol II binding values. p-value (parametric two sided paired t test) are respectively: 2.3 × 10−13; 5 × 10−4; 6 × 10−3 (low), 2.4 × 10−13; 6 × 10−3; 2 × 10−4 (medium), 7 × 10−6; 0.02; 0.8 (high). Represented number of genes are 3175, 3126, 3074, 3051, 3123, 3134 (low); 1154, 1079, 1154, 1125, 1139, 1084 (medium); 955, 930, 941, 941, 935, 913 (high).DOI:http://dx.doi.org/10.7554/eLife.02105.008
Mentions: To assess its relation to transcription genome-wide, we next performed Tyr1P ChIP-seq, using 3D12 mAb, and compared it to Pol II and the other phospho-isoforms. We isolated significantly associated regions based on the signal distribution of the background-subtracted data (Figure 2—figure supplement 1B) and found that Pol II and all isoforms, including Tyr1P, correlated with transcription levels of genes (Figure 2—figure supplement 2). At many gene locations, a predominant signal of Tyr1P at promoters was observed (Figure 2B, Figure 2—figure supplement 3). We further confirmed this by genome-wide profiling of Pol II isoforms at coding-gene locations (Figure 2C, Figure 2—figure supplement 4, Figure 2—figure supplement 5A for Ser2P profile). Our profiling analysis shows that Tyr1P signal is predominantly found at promoters similarly to Ser5P, weak or essentially absent at gene bodies and weak at 3′ends in contrast to Ser2P elongating mark and Ser7P (associated to both promoters and gene bodies). These observations are further supported by quantification of signals at various genic sections (Figure 2—figure supplement 6) and reinforce our conclusion that human Tyr1P is mainly associated to promoters in an early, post-initiation step of transcription. Although we did not further investigate this possibility, in the accompanying manuscript, Hsin et al show that Chicken Tyr1 is found phosphorylated in the nucleoplasm, raising the possibility that Tyr1P is also associated with recruitment of the enzyme and transcription initiation.

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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