Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.

João D Dias,Ana Pombo,Elena Torlai Triglia,Alexander Kukalev,Mita Chotalia,Hiroshi Kimura,Tiago Rito,Emily Brookes,Carmelo Ferrai

doi:10.7554/elife.11215

Abstract

Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and processing of nascent RNA. Extensive phosphorylation of serine residues at the largest RNAPII subunit occurs at its structurally-disordered C-terminal domain (CTD), which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. In contrast, K7ac is associated with RNAPII elongation, Serine-2 phosphorylation and mRNA expression. We identify an unexpected balance between RNAPII K7 methylation and acetylation at gene promoters, which fine-tunes gene expression levels.

Highlights

Transcription of protein-coding genes is a complex process involving a sequence of ribonucleic acid (RNA) processing events that occur at different stages of the transcription cycle
We avoided the more traditional lysine to arginine substitution, as a non-canonical arginine residue is present at the C-terminal domain (CTD) in position 7 of repeat 31 and Figure 2 continued on page
Consistent with the specificity of K7me1 and K7me2 to expressed genes, we found that K7me1 and K7me2 do not mark poised RNA polymerase II (RNAPII) at PRCr genes marked by H3K27me3 and H2Aub1 (Figure 5—figure supplement 2a and 2b) and that they are associated with promoters marked by H3K4me3 (Figure 5—figure supplement 2c)

Summary

Introduction

Transcription of protein-coding genes is a complex process involving a sequence of RNA processing events that occur at different stages of the transcription cycle. Co-transcriptional recruitment of chromatin modifiers and RNA processing machinery is modulated through a complex array of posttranslational modifications at the C-terminal domain (CTD) of RPB1, the largest subunit of RNAPII. This unique domain constitutes a docking platform for protein complexes that cap, splice and polyadenylate newly-made RNAs (Bentley, 2014; Buratowski, 2009; Egloff et al, 2012; Eick and Geyer, 2013; Hsin and Manley, 2012).

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Conclusion