scholarly journals Nuclear Phosphoinositides—Versatile Regulators of Genome Functions

Cells ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 649 ◽  
Author(s):  
Enrique Castano ◽  
Sukriye Yildirim ◽  
Veronika Fáberová ◽  
Alžběta Krausová ◽  
Lívia Uličná ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Rna Processing ◽  
Molecular Mechanisms ◽  
Protein Complexes ◽  
The Many ◽  
Polymerase I ◽  
Nuclear Processes ◽  
Rna Polymerase Ii Transcription

The many functions of phosphoinositides in cytosolic signaling were extensively studied; however, their activities in the cell nucleus are much less clear. In this review, we summarize data about their nuclear localization and metabolism, and review the available literature on their involvements in chromatin remodeling, gene transcription, and RNA processing. We discuss the molecular mechanisms via which nuclear phosphoinositides, in particular phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2), modulate nuclear processes. We focus on PI(4,5)P2’s role in the modulation of RNA polymerase I activity, and functions of the nuclear lipid islets—recently described nucleoplasmic PI(4,5)P2-rich compartment involved in RNA polymerase II transcription. In conclusion, the high impact of the phosphoinositide–protein complexes on nuclear organization and genome functions is only now emerging and deserves further thorough studies.

scholarly journals Emerging Views on the CTD Code

2012 ◽  
Vol 2012 ◽  
pp. 1-19 ◽  
Author(s):  
David W. Zhang ◽  
Juan B. Rodríguez-Molina ◽  
Joshua R. Tietjen ◽  
Corey M. Nemec ◽  
Aseem Z. Ansari
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Regulation ◽  
Chromatin Remodeling ◽  
Posttranslational Modifications ◽  
Rna Processing ◽  
Transcription Initiation ◽  
Protein Complexes ◽  
Pol Ii

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.

Molecular mechanisms of RNA polymerase II transcription elongation elucidated by kinetic network models

2018 ◽  
Vol 49 ◽  
pp. 54-62 ◽  
Author(s):  
Ilona Christy Unarta ◽  
Lizhe Zhu ◽  
Carmen Ka Man Tse ◽  
Peter Pak-Hang Cheung ◽  
Jin Yu ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Transcription Elongation ◽  
Network Models ◽  
Rna Polymerase Ii Transcription

scholarly journals P54nrb Forms a Heterodimer with PSP1 That Localizes to Paraspeckles in an RNA-dependent Manner

2005 ◽  
Vol 16 (11) ◽  
pp. 5304-5315 ◽  
Author(s):  
Archa H. Fox ◽  
Charles S. Bond ◽  
Angus I. Lamond
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Sequence Similarity ◽  
Dependent Manner ◽  
Rna Pol Ii ◽  
Nuclear Processes ◽  
Rna Polymerase Ii Transcription

P54nrb is a protein implicated in multiple nuclear processes whose specific functions may correlate with its presence at different nuclear locations. Here we characterize paraspeckles, a subnuclear domain containing p54nrb and other RNA-binding proteins including PSP1, a protein with sequence similarity to p54nrb that acts as a marker for paraspeckles. We show that PSP1 interacts in vivo with a subset of the total cellular pool of p54nrb. We map the domain within PSP1 that is mediating this interaction and show it is required for the correct localization of PSP1 to paraspeckles. This interaction is necessary but not sufficient for paraspeckle targeting by PSP1, which also requires an RRM capable of RNA binding. Blocking the reinitiation of RNA Pol II transcription at the end of mitosis with DRB prevents paraspeckle formation, which recommences after removal of DRB, indicating that paraspeckle formation is dependent on RNA Polymerase II transcription. Thus paraspeckles are the sites where a subset of the total cellular pool of p54nrb is targeted in a RNA Polymerase II-dependent manner.

scholarly journals Loss of Human Ribosomal Gene CpG Methylation Enhances Cryptic RNA Polymerase II Transcription and Disrupts Ribosomal RNA Processing

2009 ◽  
Vol 35 (4) ◽  
pp. 414-425 ◽  
Author(s):  
Thérèse Gagnon-Kugler ◽  
Frédéric Langlois ◽  
Victor Stefanovsky ◽  
Frédéric Lessard ◽  
Tom Moss
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Ribosomal Rna ◽  
Rna Processing ◽  
Ribosomal Gene ◽  
Cpg Methylation ◽  
Ribosomal Rna Processing ◽  
Rna Polymerase Ii Transcription

The yeast alpha 2 protein can repress transcription by RNA polymerases I and II but not III

1993 ◽  
Vol 13 (7) ◽  
pp. 4029-4038
Author(s):  
B M Herschbach ◽  
A D Johnson
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Rna Polymerases ◽  
Rna Polymerase I ◽  
Cell Type ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cell Type Specific ◽  
Polymerase I ◽  
Rna Polymerase Ii Transcription

The alpha 2 protein of the yeast Saccharomyces cerevisiae normally represses a set of cell-type-specific genes (the a-specific genes) that are transcribed by RNA polymerase II. In this study, we determined whether alpha 2 can affect transcription by other RNA polymerases. We find that alpha 2 can repress transcription by RNA polymerase I but not by RNA polymerase III. Additional experiments indicate that alpha 2 represses RNA polymerase I transcription through the same pathway that it uses to repress RNA polymerase II transcription. These results implicate conserved components of the transcription machinery as mediators of alpha 2 repression and exclude several alternate models.

scholarly journals A NETWORK OF PROTEIN COMPLEXES SIGNALING TO THE RNA POLYMERASE II TRANSCRIPTION APPARATUS IN HUMAN CELLS

2006 ◽  
Vol 20 (5) ◽  
Author(s):  
Benoit Coulombe ◽  
Célia Jeronimo ◽  
Annie Bouchard ◽  
Cynthia Thérien ◽  
Gordon Chua ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Protein Complexes ◽  
Human Cells ◽  
Rna Polymerase Ii Transcription

scholarly journals The yeast alpha 2 protein can repress transcription by RNA polymerases I and II but not III.

1993 ◽  
Vol 13 (7) ◽  
pp. 4029-4038 ◽  
Author(s):  
B M Herschbach ◽  
A D Johnson
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Rna Polymerases ◽  
Rna Polymerase I ◽  
Cell Type ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cell Type Specific ◽  
Polymerase I ◽  
Rna Polymerase Ii Transcription

The alpha 2 protein of the yeast Saccharomyces cerevisiae normally represses a set of cell-type-specific genes (the a-specific genes) that are transcribed by RNA polymerase II. In this study, we determined whether alpha 2 can affect transcription by other RNA polymerases. We find that alpha 2 can repress transcription by RNA polymerase I but not by RNA polymerase III. Additional experiments indicate that alpha 2 represses RNA polymerase I transcription through the same pathway that it uses to repress RNA polymerase II transcription. These results implicate conserved components of the transcription machinery as mediators of alpha 2 repression and exclude several alternate models.

scholarly journals Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II

2015 ◽  
Vol 35 (11) ◽  
pp. 1915-1925 ◽  
Author(s):  
Arnob Dutta ◽  
Vinod Babbarwal ◽  
Jianhua Fu ◽  
Deborah Brunke-Reese ◽  
Diane M. Libert ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Protein Complexes ◽  
Elongation Factors ◽  
Genetic Studies ◽  
Content Type ◽  
Mrna Metabolism ◽  
N Terminus ◽  
Biochemical Analyses

Expression of the genome requires RNA polymerase II (RNAPII) to transcribe across many natural and unnatural barriers, and this transcription across barriers is facilitated by protein complexes called elongation factors (EFs). Genetic studies inSaccharomyces cerevisiaeyeast suggest that multiple EFs collaborate to assist RNAPII in completing the transcription of genes, but the molecular mechanisms of how they cooperate to promote elongation are not well understood. The Ccr4-Not complex participates in multiple steps of mRNA metabolism and has recently been shown to be an EF. Here we describe how Ccr4-Not and TFIIS cooperate to stimulate elongation. We find that Ccr4-Not and TFIIS mutations show synthetically enhanced phenotypes, and biochemical analyses indicate that Ccr4-Not and TFIIS work synergistically to reactivate arrested RNAPII. Ccr4-Not increases the recruitment of TFIIS into elongation complexes and enhances the cleavage of the displaced transcript in backtracked RNAPII. This is mediated by an interaction between Ccr4-Not and the N terminus of TFIIS. In addition to revealing insights into how these two elongation factors cooperate to promote RNAPII elongation, our study extends the growing body of evidence suggesting that the N terminus of TFIIS acts as a docking/interacting site that allows it to synergize with other EFs to promote RNAPII transcription.

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