The RNA exosome shapes the expression of key protein-coding genes

Abstract The ribonucleolytic exosome complex is central for nuclear RNA degradation, primarily targeting non-coding RNAs. Still, the nuclear exosome could have protein-coding (pc) gene-specific regulatory activities. By depleting an exosome core component, or components of exosome adaptor complexes, we identify ∼2900 transcription start sites (TSSs) from within pc genes that produce exosome-sensitive transcripts. At least 1000 of these overlap with annotated mRNA TSSs and a considerable portion of their transcripts share the annotated mRNA 3′ end. We identify two types of pc-genes, both employing a single, annotated TSS across cells, but the first type primarily produces full-length, exosome-sensitive transcripts, whereas the second primarily produces prematurely terminated transcripts. Genes within the former type often belong to immediate early response transcription factors, while genes within the latter are likely transcribed as a consequence of their proximity to upstream TSSs on the opposite strand. Conversely, when genes have multiple active TSSs, alternative TSSs that produce exosome-sensitive transcripts typically do not contribute substantially to overall gene expression, and most such transcripts are prematurely terminated. Our results display a complex landscape of sense transcription within pc-genes and imply a direct role for nuclear RNA turnover in the regulation of a subset of pc-genes.

Download Full-text

Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica

Scientific Reports ◽

10.1038/s41598-020-77010-4 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Damien Mornico ◽

Chung-Chau Hon ◽

Mikael Koutero ◽

Christian Weber ◽

Jean-Yves Coppee ◽

...

Keyword(s):

Gene Expression ◽

Entamoeba Histolytica ◽

Regulatory System ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Protein Coding ◽

Transcription Start Sites ◽

Spurious Transcription ◽

Intergenic Regions ◽

Opposite Strand

AbstractNatural antisense transcripts (NAT) have been reported in prokaryotes and eukaryotes. While the functions of most reported NATs remain unknown, their potentials in regulating the transcription of their counterparts have been speculated. Entamoeba histolytica, which is a unicellular eukaryotic parasite, has a compact protein-coding genome with very short intronic and intergenic regions. The regulatory mechanisms of gene expression in this compact genome are under-described. In this study, by genome-wide mapping of RNA-Seq data in the genome of E. histolytica, we show that a substantial fraction of its protein-coding genes (28%) has significant transcription on their opposite strand (i.e. NAT). Intriguingly, we found the location of transcription start sites or polyadenylation sites of NAT are determined by the specific motifs encoded on the opposite strand of the gene coding sequences, thereby providing a compact regulatory system for gene transcription. Moreover, we demonstrated that NATs are globally up-regulated under various environmental conditions including temperature stress and pathogenicity. While NATs do not appear to be consequences of spurious transcription, they may play a role in regulating gene expression in E. histolytica, a hypothesis which needs to be tested.

Download Full-text

Comparative poly(A)+ RNA interactome capture of fission yeast RNA exosome mutants reveals insights into RNA biogenesis

10.1101/2020.07.01.181719 ◽

2020 ◽

Author(s):

Adrien Birot ◽

Cornelia Kilchert ◽

Krzysztof Kus ◽

Emily Priest ◽

Ahmad Al Alwash ◽

...

Keyword(s):

Quality Control ◽

Rna Polymerase Ii ◽

Rna Binding ◽

Zinc Finger Protein ◽

Rna Binding Proteins ◽

Protein Coding ◽

Multiple Protein ◽

Nuclear Rna ◽

Control Step ◽

Rna Exosome

ABSTRACTThe nuclear RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given it has multiple roles in RNA regulation. Here we have analysed changes in the poly(A)+ RNA transcriptome and interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. We have identified multiple proteins whose occupancy on RNA is altered in the exosome mutants. We demonstrate that the Zinc-finger protein Mub1 regulates exosome dependent transcripts that encode stress-responsive proteins. Furthermore, we assess impact of the exosome inactivation upon RNA binding of the components of the mRNA processing machineries such as spliceosome and mRNA cleavage polyadenylation complex. We show that mutations in the exosome lead to accumulation of the components of U1 and U2 snRNPs on poly(A)+ RNA and depletion of the components of the activated spliceosome from RNA suggesting that the early stages of spliceosome assembly might provide a critical quality control step. Collectively, our data provide a global view of how RNA metabolism is affected in the exosome-deficient cells and reveal RNA-binding proteins that may act as novel exosome cofactors.

Download Full-text

RNA-binding protein Mub1 and the nuclear RNA exosome act to fine-tune environmental stress response

Life Science Alliance ◽

10.26508/lsa.202101111 ◽

2021 ◽

Vol 5 (2) ◽

pp. e202101111

Author(s):

Adrien Birot ◽

Krzysztof Kus ◽

Emily Priest ◽

Ahmad Al Alwash ◽

Alfredo Castello ◽

...

Keyword(s):

Zinc Finger ◽

Rna Binding ◽

Zinc Finger Protein ◽

Rna Binding Proteins ◽

Dependent Manner ◽

Environmental Stress Response ◽

Protein Coding ◽

Altered Expression ◽

Nuclear Rna ◽

Rna Exosome

The nuclear RNA exosome plays a key role in controlling the levels of multiple protein-coding and non-coding RNAs. Recruitment of the exosome to specific RNA substrates is mediated by RNA-binding co-factors. The transient interaction between co-factors and the exosome as well as the rapid decay of RNA substrates make identification of exosome co-factors challenging. Here, we use comparative poly(A)+ RNA interactome capture in fission yeast expressing three different mutants of the exosome to identify proteins that interact with poly(A)+ RNA in an exosome-dependent manner. Our analyses identify multiple RNA-binding proteins whose association with RNA is altered in exosome mutants, including the zinc-finger protein Mub1. Mub1 is required to maintain the levels of a subset of exosome RNA substrates including mRNAs encoding for stress-responsive proteins. Removal of the zinc-finger domain leads to loss of RNA suppression under non-stressed conditions, altered expression of heat shock genes in response to stress, and reduced growth at elevated temperature. These findings highlight the importance of exosome-dependent mRNA degradation in buffering gene expression networks to mediate cellular adaptation to stress.

Download Full-text

Distinct and evolutionary conserved structural features of the human nuclear exosome complex

eLife ◽

10.7554/elife.38686 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 18

Author(s):

Piotr Gerlach ◽

Jan M Schuller ◽

Fabien Bonneau ◽

Jérôme Basquin ◽

Peter Reichelt ◽

...

Keyword(s):

Structural Features ◽

Core Complex ◽

The Core ◽

Biochemical Assays ◽

Nuclear Rna ◽

Nuclear Exosome ◽

Non Coding Rnas ◽

Rna Exosome ◽

Distinct Features ◽

Exosome Complex

The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.

Download Full-text

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

Science ◽

10.1126/science.1164096 ◽

2008 ◽

Vol 322 (5909) ◽

pp. 1851-1854 ◽

Cited By ~ 492

Author(s):

Pascal Preker ◽

Jesper Nielsen ◽

Susanne Kammler ◽

Søren Lykke-Andersen ◽

Marianne S. Christensen ◽

...

Keyword(s):

Rna Polymerase Ii ◽

Gene Promoter ◽

Rna Degradation ◽

Transcription Start ◽

Transcription Start Sites ◽

Tiling Microarray ◽

Active Transcription ◽

Regulatory Potential ◽

Rna Exosome ◽

Eukaryotic Genomes

Studies have shown that the bulk of eukaryotic genomes is transcribed. Transcriptome maps are frequently updated, but low-abundant transcripts have probably gone unnoticed. To eliminate RNA degradation, we depleted the exonucleolytic RNA exosome from human cells and then subjected the RNA to tiling microarray analysis. This revealed a class of short, polyadenylated and highly unstable RNAs. These promoter upstream transcripts (PROMPTs) are produced ∼0.5 to 2.5 kilobases upstream of active transcription start sites. PROMPT transcription occurs in both sense and antisense directions with respect to the downstream gene. In addition, it requires the presence of the gene promoter and is positively correlated with gene activity. We propose that PROMPT transcription is a common characteristic of RNA polymerase II (RNAPII) transcribed genes with a possible regulatory potential.

Download Full-text

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

Scientific Reports ◽

10.1038/s41598-021-83541-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ammar Zaghlool ◽

Adnan Niazi ◽

Åsa K. Björklund ◽

Jakub Orzechowski Westholm ◽

Adam Ameur ◽

...

Keyword(s):

Human Brain ◽

Expression Analysis ◽

Differential Expression Analysis ◽

Adult Brain ◽

Sequencing Data ◽

Human Brain Tissue ◽

Protein Coding ◽

Rna Transcripts ◽

Nuclear Rna ◽

The Impact

AbstractTranscriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.

Download Full-text

RNA polyadenylation and its consequences in prokaryotes

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2018.0166 ◽

2018 ◽

Vol 373 (1762) ◽

pp. 20180166 ◽

Cited By ~ 7

Author(s):

Eliane Hajnsdorf ◽

Vladimir R. Kaberdin

Keyword(s):

Gene Expression ◽

State Level ◽

Rna Degradation ◽

Plasmid Copy Number ◽

Plasmid Copy ◽

Protein Coding ◽

Mrna Metabolism ◽

Isolation And Characterization ◽

Polymerase I ◽

The Impact

Post-transcriptional addition of poly(A) tails to the 3′ end of RNA is one of the fundamental events controlling the functionality and fate of RNA in all kingdoms of life. Although an enzyme with poly(A)-adding activity was discovered in Escherichia coli more than 50 years ago, its existence and role in prokaryotic RNA metabolism were neglected for many years. As a result, it was not until 1992 that E. coli poly(A) polymerase I was purified to homogeneity and its gene was finally identified. Further work revealed that, similar to its role in surveillance of aberrant nuclear RNAs of eukaryotes, the addition of poly(A) tails often destabilizes prokaryotic RNAs and their decay intermediates, thus facilitating RNA turnover. Moreover, numerous studies carried out over the last three decades have shown that polyadenylation greatly contributes to the control of prokaryotic gene expression by affecting the steady-state level of diverse protein-coding and non-coding transcripts including antisense RNAs involved in plasmid copy number control, expression of toxin–antitoxin systems and bacteriophage development. Here, we review the main findings related to the discovery of polyadenylation in prokaryotes, isolation, and characterization and regulation of bacterial poly(A)-adding activities, and discuss the impact of polyadenylation on prokaryotic mRNA metabolism and gene expression. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.

Download Full-text