C-terminal Domain Code Research Articles

Emerging Views on the CTD Code.

The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that function as a binding platform for different protein complexes involved in transcription, RNA processing, export, and chromatin remodeling. The CTD repeats are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the “CTD code” hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. Here, we highlight the role of CTD modifications in directing transcription initiation, elongation, and termination. We examine the major readers, writers, and erasers of the CTD code and examine the relevance of describing patterns of posttranslational modifications as a “code.” Finally, we discuss major questions regarding the function of the newly discovered CTD modifications and the fundamental insights into transcription regulation that will necessarily emerge upon addressing those challenges.

Gene-specific RNA polymerase II phosphorylation and the CTD code

Dynamic phosphorylation of the RNA polymerase II CTD repeats (YS2PTS5PS7) is coupled to transcription and may act as a “code” that controls mRNA synthesis and processing. To examine the "code" in budding yeast, we mapped genome-wide CTD S2, 5 and 7 phosphorylations (PO4) and compared them with the CTD-associated termination factors, Nrd1 and Pcf11. CTD-PO4 dynamics are not scaled to the size of the gene. At 5’ ends, the onset of S2-PO4 is delayed by about 450 bases relative to S5-PO4, regardless of gene length. Phospho-CTD dynamics are gene-specific, with high S5/7-PO4 at the 5' end being characteristic of well-expressed genes with nucleosome-occupied promoters. Furthermore, the CTD kinases Kin28 and Ctk1 profoundly affect pol II distribution along genes in a highly gene-specific way. The "code" is therefore written differently on different genes, probably under the control of promoters. S7-PO4 is enriched on introns and at sites of Nrd1 accumulation suggesting that this modification may function in splicing and Nrd1 recruitment. Nrd1 and Pcf11 frequently co-localized, suggesting functional overlap between these terminators. Surprisingly, Pcf11 is also recruited to centromeres and pol III transcribed genes.

Chemical-genomic dissection of the CTD code

SummarySequential modifications of the RNA polymerase II (Pol II) carboxyl-terminal domain (CTD) coordinate the stage-specific association and release of cellular machines during transcription. Here we examine the genome-wide distributions of the “early” (phospho-serine 5), “mid” (phospho-serine 7) and “late” (phospho-serine 2) CTD marks. We identify gene-class specific patterns and find widespread co-occurrence of the CTD marks. Contrary to its role in 3’ processing of non-coding RNA, the Ser7-P marks are placed early and retained until transcription termination at all Pol II-dependent genes. Chemical-genomic analysis reveals that the promoter-distal Ser7-P marks are not remnants of early phosphorylation, but are placed anew by the CTD kinase Bur1. Consistent with the ability of Bur1 to facilitate transcription elongation and suppress cryptic transcription, high levels of Ser7-P are observed at highly transcribed genes. We propose that Ser7-P could facilitate elongation and suppress cryptic transcription.

Expression of human snRNA genes from beginning to end

In addition to protein-coding genes, mammalian pol II (RNA polymerase II) transcribes independent genes for some non-coding RNAs, including the spliceosomal U1 and U2 snRNAs (small nuclear RNAs). snRNA genes differ from protein-coding genes in several key respects and some of the mechanisms involved in expression are gene-type-specific. For example, snRNA gene promoters contain an essential PSE (proximal sequence element) unique to these genes, the RNA-encoding regions contain no introns, elongation of transcription is P-TEFb (positive transcription elongation factor b)-independent and RNA 3'-end formation is directed by a 3'-box rather than a cleavage and polyadenylation signal. However, the CTD (C-terminal domain) of pol II closely couples transcription with RNA 5' and 3' processing in expression of both gene types. Recently, it was shown that snRNA promoter-specific recognition of the 3'-box RNA processing signal requires a novel phosphorylation mark on the pol II CTD. This new mark plays a critical role in the recruitment of the snRNA gene-specific RNA-processing complex, Integrator. These new findings provide the first example of a phosphorylation mark on the CTD heptapeptide that can be read in a gene-type-specific manner, reinforcing the notion of a CTD code. Here, we review the control of expression of snRNA genes from initiation to termination of transcription.