scholarly journals ELL facilitates RNA polymerase II pause site entry and release

2012 ◽  
Vol 3 (1) ◽  
Author(s):  
Jung S. Byun ◽  
Temesgen D. Fufa ◽  
Clay Wakano ◽  
Alfonso Fernandez ◽  
Cynthia M. Haggerty ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Pause Site

scholarly journals An RNA Polymerase Pause Site Is Associated with the Immunoglobulin μs Poly(A) Site

2002 ◽  
Vol 22 (15) ◽  
pp. 5606-5615 ◽  
Author(s):  
Martha L. Peterson ◽  
Shannon Bertolino ◽  
Frankie Davis
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Processing ◽  
Immunoglobulin A ◽  
Expression Ratio ◽  
B Cell Maturation ◽  
Mrna Ratio ◽  
Site Use ◽  
A Site ◽  
Pause Site

ABSTRACT Immunoglobulin μ alternative RNA processing is regulated during B-cell maturation and requires balanced efficiencies of the competing splice (μm) and cleavage-polyadenylation (μs) reactions. When we deleted sequences 50 to 200 nucleotides beyond the μs poly(A) site, the μs/μm mRNA ratio decreased three- to eightfold in B, plasma, and nonlymphoid cells. The activity could not be localized to a smaller fragment but did function in heterologous contexts. Our data suggest that this region contains an RNA polymerase II pause site that enhances the use of the μs poly(A) site. First, known pause sites replaced the activity of the deleted fragment. Second, the μ fragment, when placed between tandem poly(A) sites, enhanced the use of the upstream poly(A) site. Finally, nuclear run-ons detected an increase in RNA polymerase loading just downstream from the μs poly(A) site, even when the poly(A) site was inactivated. When this μ fragment and another pause site were inserted 1 kb downstream from the μs poly(A) site, they no longer affected the mRNA expression ratio, suggesting that pause sites affect poly(A) site use over a limited distance. Fragments from the immunoglobulin A gene were also found to have RNA polymerase pause site activity.

scholarly journals A pause site for RNA polymerase II is associated with termination of transcription.

1991 ◽  
Vol 10 (7) ◽  
pp. 1833-1842 ◽  
Author(s):  
P. Enriquez-Harris ◽  
N. Levitt ◽  
D. Briggs ◽  
N.J. Proudfoot
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Pause Site

scholarly journals Pause Sites Promote Transcriptional Termination of Mammalian RNA Polymerase II

2006 ◽  
Vol 26 (10) ◽  
pp. 3986-3996 ◽  
Author(s):  
Natalia Gromak ◽  
Steven West ◽  
Nick J. Proudfoot
Keyword(s):  
Steady State ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Cleavage ◽  
Actin Gene ◽  
General Role ◽  
Pol Ii ◽  
Transcriptional Termination ◽  
A Site ◽  
Pause Site

ABSTRACT Polymerase II (Pol II) transcriptional termination depends on two independent genetic elements: poly(A) signals and downstream terminator sequences. The latter may either promote cotranscriptional RNA cleavage or pause elongating Pol II. We demonstrate that the previously characterized MAZ4 pause element promotes Pol II termination downstream of a poly(A) signal, dependent on both the proximity of the pause site and poly(A) signal and the strength of the poly(A) signal. The 5′→3′ exonuclease Xrn2 facilitates this pause-dependent termination by degrading the 3′ product of poly(A) site cleavage. The human β-actin gene also possesses poly(A) site proximal pause sequences, which like MAZ4 are G rich and promote transcriptional termination. Xrn2 depletion causes an increase in both steady-state RNA and Pol II levels downstream of the β-actin poly(A) site. Taken together, we provide new insights into the mechanism of pause site-mediated termination and establish a general role for the 5′→3′ exonuclease Xrn2 in Pol II termination.

Termination and pausing of RNA polymerase II downstream of yeast polyadenylation sites

1993 ◽  
Vol 13 (9) ◽  
pp. 5159-5167
Author(s):  
L E Hyman ◽  
C L Moore
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Termination ◽  
In Vitro Synthesis ◽  
Polyadenylation Sites ◽  
Polymerase Pausing ◽  
A Site ◽  
Pause Site

Little is known about the transcriptional events which occur downstream of polyadenylation sites. Although the polyadenylation site of a gene can be easily identified, it has been difficult to determine the site of transcription termination in vivo because of the rapid processing of pre-mRNAs. Using an in vitro approach, we have shown that sequences from the 3' ends of two different Saccharomyces cerevisiae genes, ADH2 and GAL7, direct transcription termination and/or polymerase pausing in yeast nuclear extracts. In the case of the ADH2 sequence, the RNA synthesized in vitro ends approximately 50 to 150 nucleotides downstream of the poly(A) site. This RNA is not polyadenylated and may represent the primary transcript. A similarly sized nonpolyadenylated [poly(A)-] transcript can be detected in vivo from the same transcriptional template. A GAL7 template also directs the in vitro synthesis of an RNA which extends a short distance past the poly(A) site. However, a significant amount of the GAL7 RNA is polyadenylated at or close to the in vivo poly(A) site. Mutations of GAL7 or ADH2 poly(A) signals prevent polyadenylation but do not affect the in vitro synthesis of the extended poly(A)- transcript. Since transcription of the mutant template continues through this region in vivo, it is likely that a strong RNA polymerase II pause site lies within the 3'-end sequences. Our data support the hypothesis that the coupling of this pause site to a functional polyadenylation signal results in transcription termination.

scholarly journals Termination and pausing of RNA polymerase II downstream of yeast polyadenylation sites.

1993 ◽  
Vol 13 (9) ◽  
pp. 5159-5167 ◽  
Author(s):  
L E Hyman ◽  
C L Moore
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Termination ◽  
In Vitro Synthesis ◽  
Polyadenylation Sites ◽  
Polymerase Pausing ◽  
A Site ◽  
Pause Site

Little is known about the transcriptional events which occur downstream of polyadenylation sites. Although the polyadenylation site of a gene can be easily identified, it has been difficult to determine the site of transcription termination in vivo because of the rapid processing of pre-mRNAs. Using an in vitro approach, we have shown that sequences from the 3' ends of two different Saccharomyces cerevisiae genes, ADH2 and GAL7, direct transcription termination and/or polymerase pausing in yeast nuclear extracts. In the case of the ADH2 sequence, the RNA synthesized in vitro ends approximately 50 to 150 nucleotides downstream of the poly(A) site. This RNA is not polyadenylated and may represent the primary transcript. A similarly sized nonpolyadenylated [poly(A)-] transcript can be detected in vivo from the same transcriptional template. A GAL7 template also directs the in vitro synthesis of an RNA which extends a short distance past the poly(A) site. However, a significant amount of the GAL7 RNA is polyadenylated at or close to the in vivo poly(A) site. Mutations of GAL7 or ADH2 poly(A) signals prevent polyadenylation but do not affect the in vitro synthesis of the extended poly(A)- transcript. Since transcription of the mutant template continues through this region in vivo, it is likely that a strong RNA polymerase II pause site lies within the 3'-end sequences. Our data support the hypothesis that the coupling of this pause site to a functional polyadenylation signal results in transcription termination.

Nutrient-regulated gene expression in eukaryotes

2006 ◽  
Vol 73 ◽  
pp. 85-96 ◽  
Author(s):  
Richard J. Reece ◽  
Laila Beynon ◽  
Stacey Holden ◽  
Amanda D. Hughes ◽  
Karine Rébora ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Control ◽  
Direct Interaction ◽  
Signalling Pathways ◽  
A Cell ◽  
One Step ◽  
Higher Eukaryotes ◽  
Regulated Gene Expression

The recognition of changes in environmental conditions, and the ability to adapt to these changes, is essential for the viability of cells. There are numerous well characterized systems by which the presence or absence of an individual metabolite may be recognized by a cell. However, the recognition of a metabolite is just one step in a process that often results in changes in the expression of whole sets of genes required to respond to that metabolite. In higher eukaryotes, the signalling pathway between metabolite recognition and transcriptional control can be complex. Recent evidence from the relatively simple eukaryote yeast suggests that complex signalling pathways may be circumvented through the direct interaction between individual metabolites and regulators of RNA polymerase II-mediated transcription. Biochemical and structural analyses are beginning to unravel these elegant genetic control elements.

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