RGD Reference Report - Control of transcriptional elongation. - Rat Genome Database

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Control of transcriptional elongation.

Authors: Kwak, H  Lis, JT 
Citation: Kwak H and Lis JT, Annu Rev Genet. 2013;47:483-508. doi: 10.1146/annurev-genet-110711-155440. Epub 2013 Sep 11.
RGD ID: 9681735
Pubmed: PMID:24050178   (View Abstract at PubMed)
PMCID: PMC3974797   (View Article at PubMed Central)
DOI: DOI:10.1146/annurev-genet-110711-155440   (Journal Full-text)

Elongation is becoming increasingly recognized as a critical step in eukaryotic transcriptional regulation. Although traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here, we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II (Pol II) pausing near promoters and how the participating factors were identified. Among the factors we describe are the pausing factors--NELF (negative elongation factor) and DSIF (DRB sensitivity-inducing factor)--and P-TEFb (positive elongation factor b), which is the key player in pause release. We also describe the high-resolution view of Pol II pausing and propose nonexclusive models for how pausing is achieved. We then discuss Pol II elongation through the bodies of genes and the roles of FACT and SPT6, factors that allow Pol II to move through nucleosomes.

Molecular Pathway Annotations    Click to see Annotation Detail View

RGD Manual Annotations

TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
RNA polymerase II transcription elongation pathway  TAS 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOCCNK (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOCCNT1 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOCCNT2 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOCDK9 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOGTF2F1 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOGTF2F2 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISONELFA (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISONELFB (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISONELFCD (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISONELFE (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOSSRP1 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOSUPT16H (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOSUPT4H1 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOSUPT5H (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOTCEA1 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOTCEA2 (Homo sapiens)9681735; 9681735 RGD 
RNA polymerase II transcription elongation pathway  ISOTCEA3 (Homo sapiens)9681735; 9681735 RGD 
Objects Annotated

Genes (Rattus norvegicus)
Ccnk  (cyclin K)
Ccnt1  (cyclin T1)
Ccnt2  (cyclin T2)
Cdk9  (cyclin-dependent kinase 9)
Gtf2f1  (general transcription factor IIF subunit 1)
Gtf2f2  (general transcription factor IIF subunit 2)
Nelfa  (negative elongation factor complex member A)
Nelfb  (negative elongation factor complex member B)
Nelfcd  (negative elongation factor complex member C/D)
Nelfe  (negative elongation factor complex member E)
Ssrp1  (structure specific recognition protein 1)
Supt16h  (SPT16 homolog, facilitates chromatin remodeling subunit)
Supt4h1  (SPT4 homolog, DSIF elongation factor subunit)
Supt5h  (SPT5 homolog, DSIF elongation factor subunit)
Tcea1  (transcription elongation factor A1)
Tcea2  (transcription elongation factor A2)
Tcea3  (transcription elongation factor A3)

Genes (Mus musculus)
Ccnk  (cyclin K)
Ccnt1  (cyclin T1)
Ccnt2  (cyclin T2)
Cdk9  (cyclin dependent kinase 9)
Gtf2f1  (general transcription factor IIF, polypeptide 1)
Gtf2f2  (general transcription factor IIF, polypeptide 2)
Nelfa  (negative elongation factor complex member A, Whsc2)
Nelfb  (negative elongation factor complex member B)
Nelfcd  (negative elongation factor complex member C/D, Th1l)
Nelfe  (negative elongation factor complex member E, Rdbp)
Ssrp1  (structure specific recognition protein 1)
Supt16  (SPT16, facilitates chromatin remodeling subunit)
Supt4a  (SPT4A, DSIF elongation factor subunit)
Supt5  (suppressor of Ty 5, DSIF elongation factor subunit)
Tcea1  (transcription elongation factor A (SII) 1)
Tcea2  (transcription elongation factor A (SII), 2)
Tcea3  (transcription elongation factor A (SII), 3)

Genes (Homo sapiens)
CCNK  (cyclin K)
CCNT1  (cyclin T1)
CCNT2  (cyclin T2)
CDK9  (cyclin dependent kinase 9)
GTF2F1  (general transcription factor IIF subunit 1)
GTF2F2  (general transcription factor IIF subunit 2)
NELFA  (negative elongation factor complex member A)
NELFB  (negative elongation factor complex member B)
NELFCD  (negative elongation factor complex member C/D)
NELFE  (negative elongation factor complex member E)
SSRP1  (structure specific recognition protein 1)
SUPT16H  (SPT16 homolog, facilitates chromatin remodeling subunit)
SUPT4H1  (SPT4 homolog, DSIF elongation factor subunit)
SUPT5H  (SPT5 homolog, DSIF elongation factor subunit)
TCEA1  (transcription elongation factor A1)
TCEA2  (transcription elongation factor A2)
TCEA3  (transcription elongation factor A3)


Additional Information