scholarly journals The INO80 remodeler couples premature termination of mRNA synthesis with transcription elongation

2020 ◽  
Author(s):  
Sara Luzzi ◽  
Ugo Szachnowski ◽  
Sarah Greener ◽  
Camille Gautier ◽  
Kang Hoo Han ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Polymerase Ii ◽  
Premature Termination ◽  
Transcription Termination ◽  
Transcriptional Elongation ◽  
Rna Quality ◽  
Mrna Transcripts ◽  
Rna Quality Control ◽  
Transcriptional Pausing ◽  
Elongation Process

SUMMARYRNA quality control and timely termination of aberrant transcription are critical for functional gene expression. Here, we report that in Saccharomyces cerevisiae premature transcription termination of mRNAs is coordinated with the transcriptional elongation process and regulated by the evolutionarily conserved ATP-dependent chromatin remodeling complex INO80. Loss of INO80 sensitizes cells to the transcriptional elongation stress drug 6-azauracil and leads to enhanced pausing of elongating RNA Polymerase II across the genome. Transcriptional pausing positively correlates with premature termination of mRNA transcription and is pronounced proximally to promoters at sites of enhanced histone H3 binding to DNA. Cells with deficient INO80 complex accumulate short, unproductive mRNA transcripts on chromatin and are defective in transcription termination mediated by the Nrd1-Nab3-Sen1 (NNS) complex. We find that loss of INO80 compromises the interaction of the RNA surveillance factor Nab2 with short promoter-proximal mRNA transcripts. INO80 promotes co-transcriptional recruitment of Nab2 to chromatin by enabling its interaction with the histone variant H2A.Z. Finally, inactivation of the histone deacetylase complex Rpd3S/Rco1 reduces promoter-proximal pausing and enhances productive transcription through an NNS-dependent termination site when INO80 is compromised. Our work suggests that, by regulation of H2A.Z-containing nucleosomes, INO80 orchestrates a mechanism for premature transcription termination, linking RNA quality control to the transcriptional process.

scholarly journals In Vivo Evidence that Defects in the Transcriptional Elongation Factors RPB2, TFIIS, and SPT5 Enhance Upstream Poly(A) Site Utilization

2003 ◽  
Vol 23 (21) ◽  
pp. 7887-7901 ◽  
Author(s):  
Yajun Cui ◽  
Clyde L. Denis
Keyword(s):  
Rna Polymerase Ii ◽  
Genetic Study ◽  
Elongation Factor ◽  
Model Systems ◽  
In Vivo Model ◽  
Transcriptional Elongation ◽  
Transcriptional Pausing ◽  
Elongation Process ◽  
A Site

ABSTRACT While a number of proteins are involved in elongation processes, the mechanism for action of most of these factors remains unclear primarily because of the lack of suitable in vivo model systems. We identified in yeast several genes that contain internal poly(A) sites whose full-length mRNA formation is reduced by mutations in RNA polymerase II subunit RPB2, elongation factor SPT5, or TFIIS. RPB2 and SPT5 defects also promoted the utilization of upstream poly(A) sites for genes that contain multiple 3′ poly(A) signaling sequences, supporting a role for elongation in differential poly(A) site choice. Our data suggest that elongation defects cause increased transcriptional pausing or arrest that results in increased utilization of internal or upstream poly(A) sites. Transcriptional pausing or arrest can therefore be visualized in vivo if a gene contains internal poly(A) sites, allowing biochemical and genetic study of the elongation process.

microRNA in erythrocytes

2010 ◽  
Vol 38 (1) ◽  
pp. 229-231 ◽  
Author(s):  
Andrew J. Hamilton
Keyword(s):  
Quality Control ◽  
Recent Work ◽  
Total Content ◽  
Human Erythrocytes ◽  
Rna Quality ◽  
Rna Quality Control ◽  
Non Coding Rnas ◽  
Low Levels ◽  
External Signals

Mammalian erythrocytes are generally thought to lack RNA and therefore to be unable to translate new proteins in response to internal or external signals. Support for this long-standing view has accumulated from diverse studies, most of which have focused on the total content of RNA or the overall level of translation. However, more recent work on specific types of RNA has shown the presence in human erythrocytes of both Y RNA and microRNA. The latter seem particularly incongruous given that their normal role is to attenuate the translation of mRNA. Y RNA binds the Ro autoantigen which may have a role in cellular RNA quality control. Therefore the presence of both of these non-coding RNAs indicates the possible existence of other cryptic RNAs in erythrocytes. It also suggests either the existence of low levels of translation or new uncharacterized processes involving microRNA in these cells.

scholarly journals Integrity of SRP RNA is ensured by La and the nuclear RNA quality control machinery

2014 ◽  
Vol 42 (16) ◽  
pp. 10698-10710 ◽  
Author(s):  
Eileen Leung ◽  
Claudia Schneider ◽  
Fu Yan ◽  
Hatem Mohi-El-Din ◽  
Grzegorz Kudla ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Quality ◽  
Nuclear Rna ◽  
Rna Quality Control ◽  
Srp Rna

scholarly journals Ribosome states signal RNA quality control

2021 ◽  
Vol 81 (7) ◽  
pp. 1372-1383 ◽  
Author(s):  
Karole N. D’Orazio ◽  
Rachel Green
Keyword(s):  
Quality Control ◽  
Rna Quality ◽  
Rna Quality Control

scholarly journals A machine learning-based framework for modeling transcription elongation

2021 ◽  
Vol 118 (6) ◽  
pp. e2007450118
Author(s):  
Peiyuan Feng ◽  
An Xiao ◽  
Meng Fang ◽  
Fangping Wan ◽  
Shuya Li ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
High Throughput Sequencing ◽  
Gene Expression Regulation ◽  
Transcription Elongation ◽  
Transcriptional Elongation ◽  
Sequencing Data ◽  
Pol Ii ◽  
High Throughput Sequencing Data ◽  
Pol Ii Pausing ◽  
Elongation Process

RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gene expression regulation. Characterizing the transcriptional elongation dynamics can thus help us understand many essential biological processes in eukaryotic cells. However, experimentally measuring Pol II elongation rates is generally time and resource consuming. We developed PEPMAN (polymerase II elongation pausing modeling through attention-based deep neural network), a deep learning-based model that accurately predicts Pol II pausing sites based on the native elongating transcript sequencing (NET-seq) data. Through fully taking advantage of the attention mechanism, PEPMAN is able to decipher important sequence features underlying Pol II pausing. More importantly, we demonstrated that the analyses of the PEPMAN-predicted results around various types of alternative splicing sites can provide useful clues into understanding the cotranscriptional splicing events. In addition, associating the PEPMAN prediction results with different epigenetic features can help reveal important factors related to the transcription elongation process. All these results demonstrated that PEPMAN can provide a useful and effective tool for modeling transcription elongation and understanding the related biological factors from available high-throughput sequencing data.

scholarly journals The RNA quality control pathway nonsense-mediated mRNA decay targets cellular and viral RNAs to restrict KSHV

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yang Zhao ◽  
Xiang Ye ◽  
Myriam Shehata ◽  
William Dunker ◽  
Zhihang Xie ◽  
...  
Keyword(s):  
Quality Control ◽  
Mrna Decay ◽  
Viral Rnas ◽  
Rna Quality ◽  
Rna Quality Control ◽  
Nonsense Mediated Mrna Decay

NMD-Based Gene Regulation—A Strategy for Fitness Enhancement in Plants?

2019 ◽  
Vol 60 (9) ◽  
pp. 1953-1960 ◽  
Author(s):  
Misato Ohtani ◽  
Andreas Wachter
Keyword(s):  
Quality Control ◽  
Gene Regulation ◽  
Current Knowledge ◽  
Qualitative And Quantitative ◽  
Rna Quality ◽  
Quantitative Level ◽  
Splicing Variants ◽  
Rna Quality Control ◽  
Nonsense Mediated Mrna Decay ◽  
Environmental Responses

Abstract Post-transcriptional RNA quality control is a vital issue for all eukaryotes to secure accurate gene expression, both on a qualitative and quantitative level. Among the different mechanisms, nonsense-mediated mRNA decay (NMD) is an essential surveillance system that triggers degradation of both aberrant and physiological transcripts. By targeting a substantial fraction of all transcripts for degradation, including many alternative splicing variants, NMD has a major impact on shaping transcriptomes. Recent progress on the transcriptome-wide profiling and physiological analyses of NMD-deficient plant mutants revealed crucial roles for NMD in gene regulation and environmental responses. In this review, we will briefly summarize our current knowledge of the recognition and degradation of NMD targets, followed by an account of NMD’s regulation and physiological functions. We will specifically discuss plant-specific aspects of RNA quality control and its functional contribution to the fitness and environmental responses of plants.

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