scholarly journals Author response: Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

2018 ◽  
Author(s):  
Zhipeng Zhou ◽  
Yunkun Dang ◽  
Mian Zhou ◽  
Haiyan Yuan ◽  
Yi Liu
Keyword(s):  
Codon Usage ◽  
Transcription Termination ◽  
Author Response ◽  
Cleavage And Polyadenylation

scholarly journals Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Zhipeng Zhou ◽  
Yunkun Dang ◽  
Mian Zhou ◽  
Haiyan Yuan ◽  
Yi Liu
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Transcription Termination ◽  
Model Organism ◽  
Open Reading Frames ◽  
Strong Negative Correlation ◽  
Rare Codons ◽  
Cleavage And Polyadenylation ◽  
Mouse Cells

Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here, we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and abolishment of full-length mRNA. PTT is a wide-spread phenomenon in Neurospora, and there is a strong negative correlation between codon usage bias and PTT events. Rare codons lead to the formation of putative poly(A) signals and PTT. A similar role for codon usage bias was also observed in mouse cells. Together, these results suggest that codon usage biases co-evolve with the transcription termination machinery to suppress premature termination of transcription and thus allow for optimal gene expression.

Kinetics of mRNA polyadenylation and its relation to transcription termination in eukaryotes

2000 ◽  
Vol 28 (5) ◽  
pp. A461-A461
Author(s):  
Amer Jamil ◽  
Harold G. Martinson
Keyword(s):  
Transcription Termination ◽  
Rnase Protection Assay ◽  
Nascent Transcript ◽  
Rnase Protection ◽  
Multistep Process ◽  
Eukaryotic Mrnas ◽  
Cleavage And Polyadenylation ◽  
A Site ◽  
Antisense Element

Processing of most eukaryotic mRNAs includes and polyadenylation of the nascent transcript. Until now there has been no method for the reliable measurement of these processes in vivo. Therefore, in the present work a new technique was developed for measuring precisely the rate of cleavage and polyadenylation in vivo. The method uses a cis-antisense element targeted to an upstream poly (A) signal. Duplex formation of the antisense element with the poly (A) signal region prevents polyadenylation. In a series of expression vector constructs the antisense element was moved increasing distances downstream of its target poly (A) site, reasoning that if it takes the polymerase longer to reach the antisense element, polyadenylation would have more time to occur. Using this method the half time for commitment to cleavage and polyadenylation at the SV40 early poly (A) site and SPA (synthetic poly A site) was found to be 5 seconds. It was found that strong sites (SV 40 late poly (A) site) were processed faster. Commitment to cleavage and polyadenylation was found to be a multistep process. The expression results were confirmed with the help of RNase protection assay. Relationship between polyadenylation and transcription termination was also studied by using G-free assay and found to be positively correlated. Present data support looping moded suggesting some communication exists between polyadenylation complex and RNA pol. II for transcription termination.

scholarly journals The Glc7 Phosphatase Subunit of the Cleavage and Polyadenylation Factor Is Essential for Transcription Termination on snoRNA Genes

2008 ◽  
Vol 29 (5) ◽  
pp. 577-587 ◽  
Author(s):  
Eduard Nedea ◽  
Demet Nalbant ◽  
Daniel Xia ◽  
Nathaniel T. Theoharis ◽  
Bernhard Suter ◽  
...  
Keyword(s):  
Transcription Termination ◽  
Cleavage And Polyadenylation ◽  
Polyadenylation Factor

scholarly journals Author response: Transcription termination and antitermination of bacterial CRISPR arrays

2020 ◽  
Author(s):  
Anne M Stringer ◽  
Gabriele Baniulyte ◽  
Erica Lasek-Nesselquist ◽  
Kimberley D Seed ◽  
Joseph T Wade
Keyword(s):  
Transcription Termination ◽  
Author Response

scholarly journals The Essential N Terminus of the Pta1 Scaffold Protein Is Required for snoRNA Transcription Termination and Ssu72 Function but Is Dispensable for Pre-mRNA 3′-End Processing

2009 ◽  
Vol 29 (8) ◽  
pp. 2296-2307 ◽  
Author(s):  
Mohamed A. Ghazy ◽  
Xiaoyuan He ◽  
Badri Nath Singh ◽  
Michael Hampsey ◽  
Claire Moore
Keyword(s):  
Amino Acids ◽  
Rna Polymerase Ii ◽  
Transcription Termination ◽  
Inhibitory Effect ◽  
Mrna Cleavage ◽  
Cleavage And Polyadenylation ◽  
Essential Region ◽  
Polyadenylation Factor

ABSTRACT Saccharomyces cerevisiae Pta1 is a component of the cleavage/polyadenylation factor (CPF) 3′-end processing complex and functions in pre-mRNA cleavage, poly(A) addition, and transcription termination. In this study, we investigated the role of the N-terminal region of Pta1 in transcription and processing. We report that a deletion of the first 75 amino acids (pta1-Δ75) causes thermosensitive growth, while the deletion of an additional 25 amino acids is lethal. The pta1-Δ75 mutant is defective for snoRNA termination, RNA polymerase II C-terminal domain Ser5-P dephosphorylation, and gene looping but is fully functional for mRNA 3′-end processing. Furthermore, different regions of Pta1 interact with the CPF subunits Ssu72, Pti1, and Ysh1, supporting the idea that Pta1 acts as a scaffold to organize CPF. The first 300 amino acids of Pta1 are sufficient for interactions with Ssu72, which is needed for pre-mRNA cleavage. By the degron-mediated depletion of Pta1, we show that the removal of this essential region leads to a loss of Ssu72, yet surprisingly, in vitro cleavage and polyadenylation remain efficient. In addition, a fragment containing amino acids 1 to 300 suppresses 3′-end processing in wild-type extracts. These findings suggest that the amino terminus of Pta1 has an inhibitory effect and that this effect can be neutralized through the interaction with Ssu72.

scholarly journals Author response: The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription

2020 ◽  
Author(s):  
A Elizabeth Hildreth ◽  
Mitchell A Ellison ◽  
Alex M Francette ◽  
Julia M Seraly ◽  
Lauren M Lotka ◽  
...  
Keyword(s):  
Transcription Termination ◽  
Author Response ◽  
Exit Site ◽  
Pervasive Transcription

scholarly journals Role of cleavage and polyadenylation specificity factor 100: anchoring poly(A) sites and modulating transcription termination

2017 ◽  
Vol 91 (5) ◽  
pp. 829-839 ◽  
Author(s):  
Juncheng Lin ◽  
Ruqiang Xu ◽  
Xiaohui Wu ◽  
Yingjia Shen ◽  
Qingshun Q. Li
Keyword(s):  
Transcription Termination ◽  
Cleavage And Polyadenylation ◽  
Specificity Factor

scholarly journals Mpe1 senses the polyadenylation signal in pre-mRNA to control cleavage and polyadenylation

2021 ◽  
Author(s):  
Juan B Rodriguez-Molina ◽  
Francis J O'Reilly ◽  
Eleanor Sheekey ◽  
Sarah Maslen ◽  
J Mark Skehel ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Signal Sequence ◽  
Transcription Termination ◽  
Polyadenylation Signal ◽  
Messenger Rnas ◽  
Endonucleolytic Cleavage ◽  
Cleavage And Polyadenylation ◽  
Polyadenylation Factor ◽  
Transcription Interference

Most eukaryotic messenger RNAs (mRNAs) are processed at their 3'-end by the cleavage and polyadenylation factor (CPF/CPSF). CPF mediates endonucleolytic cleavage of the pre-mRNA and addition of a polyadenosine (poly(A)) tail, which together define the 3'-end of the mature transcript. Activation of CPF is highly regulated to maintain fidelity of RNA processing. Here, using cryoEM of yeast CPF, we show that the Mpe1 subunit directly contacts the polyadenylation signal sequence in nascent pre-mRNA. This RNA-mediated link between the nuclease and polymerase modules promotes activation of the CPF endonuclease and controls polyadenylation. Mpe1 rearrangement is antagonized by another subunit, Cft2. In vivo, depletion of Mpe1 leads to widespread defects in transcription termination by RNA Polymerase II, resulting in transcription interference on neighboring genes. Together, our data suggest that Mpe1 plays a major role in selecting the cleavage site, activating CPF and ensuring timely transcription termination. 

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