RGD Reference Report - Updating the RNA polymerase CTD code: adding gene-specific layers. - Rat Genome Database

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Updating the RNA polymerase CTD code: adding gene-specific layers.

Authors: Egloff, S  Dienstbier, M  Murphy, S 
Citation: Egloff S, etal., Trends Genet. 2012 Jul;28(7):333-41. doi: 10.1016/j.tig.2012.03.007. Epub 2012 May 21.
RGD ID: 9681737
Pubmed: PMID:22622228   (View Abstract at PubMed)
DOI: DOI:10.1016/j.tig.2012.03.007   (Journal Full-text)

The carboxyl-terminal domain (CTD) of RNA polymerase (pol) II comprises multiple tandem repeats with the consensus sequence Tyr(1)-Ser(2)-Pro(3)-Thr(4)-Ser(5)-Pro(6)-Ser(7) that can be extensively and reversibly modified in vivo. CTD modifications orchestrate the interplay between transcription and processing of mRNA. Although phosphorylation of Ser2 (Ser2P) and Ser5 (Ser5P) residues has been described as being essential for the expression of most pol II-transcribed genes, recent findings highlight gene-specific effects of newly discovered CTD modifications. Here, we incorporate these latest findings in an updated review of the currently known elements that contribute to the CTD code and how it is recognized by proteins involved in transcription and RNA maturation. As modification of the CTD has a major impact on gene expression, a better understanding of the CTD code is integral to the understanding of how gene expression is regulated.

Molecular Pathway Annotations    Click to see Annotation Detail View

RGD Manual Annotations

TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
RNA polymerase II transcription pathway   TAS 9681737; 9681737; 9681737; 9681737; 9681737; 9681737; 9681737; 9681737; 9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCDC14A (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCDC14B (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCDK12 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCDK7 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCDK8 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCDK9 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCTDP1 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOCTDSP1 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISORPAP2 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
RNA polymerase II transcription pathway   ISOSSU72 (Homo sapiens)9681737; 9681737pol II carboxyl-terminal domain (CTD)RGD 
Objects Annotated

Genes (Rattus norvegicus)
Cdc14a  (cell division cycle 14A)
Cdc14b  (cell division cycle 14B)
Cdk12  (cyclin-dependent kinase 12)
Cdk7  (cyclin-dependent kinase 7)
Cdk8  (cyclin-dependent kinase 8)
Cdk9  (cyclin-dependent kinase 9)
Ctdp1  (CTD phosphatase subunit 1)
Ctdsp1  (CTD small phosphatase 1)
Rpap2  (RNA polymerase II associated protein 2)
Ssu72  (SSU72 homolog, RNA polymerase II CTD phosphatase)

Genes (Mus musculus)
Cdc14a  (CDC14 cell division cycle 14A)
Cdc14b  (CDC14 cell division cycle 14B)
Cdk12  (cyclin dependent kinase 12)
Cdk7  (cyclin dependent kinase 7)
Cdk8  (cyclin dependent kinase 8)
Cdk9  (cyclin dependent kinase 9)
Ctdp1  (CTD phosphatase subunit 1)
Ctdsp1  (CTD small phosphatase 1)
Rpap2  (RNA polymerase II associated protein 2)
Ssu72  (Ssu72 RNA polymerase II CTD phosphatase homolog (yeast))

Genes (Homo sapiens)
CDC14A  (cell division cycle 14A)
CDC14B  (cell division cycle 14B)
CDK12  (cyclin dependent kinase 12)
CDK7  (cyclin dependent kinase 7)
CDK8  (cyclin dependent kinase 8)
CDK9  (cyclin dependent kinase 9)
CTDP1  (CTD phosphatase subunit 1)
CTDSP1  (CTD small phosphatase 1)
RPAP2  (RNA polymerase II associated protein 2)
SSU72  (SSU72 homolog, RNA polymerase II CTD phosphatase)


Additional Information