Emerging Views on the CTD Code

Table 1

Proteins known to bind RNA polymerase II C-terminal domain in S. cerevisiae.

Protein/complex	Role in RNA biogenesis	Phospho-CTD bound	References
TFIIE	Preinitiation complex	Hypophosphorylated CTD	[63, 77]
TFIIF	Preinitiation complex	Hypophosphorylated CTD	[77]
TBP	Preinitiation complex (TFIID)	Hypophosphorylated CTD	[78]
Mediator Complex	Transcription activation/repression	Hypophosphorylated CTD	[48, 79]
Ceg1	Capping	Ser5-P	[80–85]
Abd1	Capping	PCTD	[83]
Set1	Histone methylation	Ser5-P	[86]
Rpd3C(Rco1)	Histone deacetylation	Ser2-P + Ser5-P	[87, 88]
Spt6	Histone chaperone	Ser2-P	[89]
Nrd1	Transcription termination/processing	Ser5-P	[90]
Sen1	Transcription termination/processing	Unknown	[91]
Asr1	Pol II ubiquitylation (Rpb4/7 Ejection)	Ser5-P	[92]
Ess1	Proline isomerase	Ser2-P	[93, 94]
Set2	Histone methylation	Ser2-P + Ser5-P	[95, 96]
Prp40	Splicing	PCTD	[97]
Npl3	Promotes elongation/prevents polyadenylation	Ser2-P	[98]
Pcf11	Cleavage/polyadenylation (CF1A)	Ser2-P	[99, 100]
Rna14	Cleavage/polyadenylation (CF1A)	PCTD	[101]
Rna15	Cleavage/polyadenylation (CF1A)	PCTD	[101]
Ydh1	Cleavage/polyadenylation (CPF)	PCTD	[102]
Yhh1	Cleavage/polyadenylation (CPF)	PCTD	[103]
Pta1	Cleavage/polyadenylation (CPF)	Ser5-P	[104]
Rtt103	5′-3′ Exonuclease (Rat1)	Ser2-P	[105]
Sus1	mRNA export	Ser5-P	[106]
Yra1	mRNA export	Hyperphosphorylated CTD	[107]
Rsp5	Pol II ubiquitylation (DNA damage response)	Ser2-P	[108, 109]
Hrr25	DNA damage repair	PCTD	[24, 110]

CTD-interacting proteins, the processes they are involved in, the phosphorylation state of the CTD with which they associate, and where in the literature the interaction is documented. Ser2-P refers to phosphorylated serine 2, Ser5-P refers to phosphorylated serine 5, and PCTD refers to a mixed phosphorylation state generated by in vitro phosphorylation of a CTD peptide with cell extracts. Additional protein-CTD interactions are described [110] but have not been directly tested.