scholarly journals The Nuclear Exosome Contributes to Autogenous Control of NAB2 mRNA Levels

2005 ◽  
Vol 25 (5) ◽  
pp. 1577-1585 ◽  
Author(s):  
Kelly M. Roth ◽  
Maria K. Wolf ◽  
Marie Rossi ◽  
J. Scott Butler
Keyword(s):  
Rna Processing ◽  
Untranslated Region ◽  
Rna Binding ◽  
Noncoding Rnas ◽  
Mrna Levels ◽  
Dependent Manner ◽  
Autogenous Control ◽  
Regulatory Circuit ◽  
Mrna Surveillance ◽  
Nuclear Exosome

ABSTRACT The RNA-processing exosome is a complex of riboexonucleases required for 3′-end formation of some noncoding RNAs and for the degradation of mRNAs in eukaryotes. The nuclear form of the exosome functions in an mRNA surveillance pathway that retains and degrades improperly processed precursor mRNAs within the nucleus. We report here that the nuclear exosome controls the level of NAB2 mRNA, encoding the nuclear poly(A)+-RNA-binding protein Nab2p. Mutations affecting the activity of the nuclear, but not the cytoplasmic, exosome cause an increase in the amount of NAB2 mRNA. Cis- and trans-acting mutations that inhibit degradation by the nuclear-exosome subunit Rrp6p result in elevated levels of NAB2 mRNA. Control of NAB2 mRNA levels occurs posttranscriptionally and requires a sequence of 26 consecutive adenosines (A26) in the NAB2 3′ untranslated region, which represses NAB2 3′-end formation and sensitizes the transcript to degradation by Rrp6p. Analysis of NAB2 mRNA levels in a nab2-1 mutant and in the presence of excess Nab2p indicates that Nab2p activity negatively controls NAB2 mRNA levels in an A26- and Rrp6p-dependent manner. These findings suggest a novel regulatory circuit in which the nuclear exosome controls the level of NAB2 mRNA in response to changes in the activity of Nab2 protein.

scholarly journals The RNA-binding protein Puf5 contributes to buffering of mRNA upon chromatin-mediated changes in nascent transcription

2021 ◽  
Author(s):  
David Z. Kochan ◽  
Julia S. P. Mawer ◽  
Jennifer Massen ◽  
Kiril Tishinov ◽  
Swati Parekh ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Rna Binding ◽  
Mrna Levels ◽  
Dependent Manner ◽  
Feedback Mechanisms ◽  
Mrna Targets ◽  
Genome Wide ◽  
A Genome ◽  
Mrna Surveillance ◽  
Global Increase

Gene expression involves regulation of chromatin structure and transcription, as well as processing of the transcribed mRNA. While there are feedback mechanisms, it is not clear whether these include crosstalk between chromatin architecture and mRNA decay. To address this, we performed a genome-wide genetic screen using a yeast strain harbouring the H3K56A mutation known to perturb chromatin structure and nascent transcription. We identified Puf5 as essential in an H3K56A background. Depletion of Puf5 in this background leads to downregulation of Puf5 targets. We suggest that Puf5 plays a role in post-transcriptional buffering of mRNAs and support this by transcriptional shutoff experiments in which Puf5 mRNA targets are degraded slower in H3K56A compared to wildtype. Finally, we show that post-transcriptional buffering of Puf5 targets is widespread and does not occur only in an H3K56A mutant, but also in an H3K4R background, which leads to a global increase in nascent transcription. Our data suggest that Puf5 determines the fate of its mRNA targets in a context-dependent manner acting as an mRNA surveillance hub balancing de-regulated nascent transcription to maintain physiological mRNA levels.

scholarly journals Yeast RNA-Binding Protein Nab3 Regulates Genes Involved in Nitrogen Metabolism

2017 ◽  
Vol 37 (18) ◽  
Author(s):  
Jonathan Merran ◽  
Jeffry L. Corden
Keyword(s):  
Rna Polymerase Ii ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Content Type ◽  
Alternative Pathways ◽  
Mrna Transcripts ◽  
Cleavage And Polyadenylation ◽  
Nuclear Exosome

ABSTRACT Termination of Saccharomyces cerevisiae RNA polymerase II (Pol II) transcripts occurs through two alternative pathways. Termination of mRNAs is coupled to cleavage and polyadenylation while noncoding transcripts are terminated through the Nrd1-Nab3-Sen1 (NNS) pathway in a process that is linked to RNA degradation by the nuclear exosome. Some mRNA transcripts are also attenuated through premature termination directed by the NNS complex. In this paper we present the results of nuclear depletion of the NNS component Nab3. As expected, many noncoding RNAs fail to terminate properly. In addition, we observe that nitrogen catabolite-repressed genes are upregulated by Nab3 depletion.

scholarly journals Sequence diversity in the 3’ untranslated region of alphavirus modulates IFIT2-dependent restriction in a cell type-dependent manner

2021 ◽  
Author(s):  
Sarah E. Hickson ◽  
Eden Brekke ◽  
Johannes Schwerk ◽  
Indraneel Saluhke ◽  
Shivam Zaver ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Rna Binding ◽  
Structural Features ◽  
Differential Sensitivity ◽  
Restriction Factor ◽  
Dependent Manner ◽  
Tetratricopeptide Repeats ◽  
Rna Interaction

ABSTRACTAlphaviruses (family Togaviridae) are a diverse group of positive-sense RNA (+ssRNA) viruses that are transmitted by arthropods and are the causative agent of several significant human and veterinary diseases. Interferon (IFN)-induced proteins with tetratricopeptide repeats (IFITs) are a family of RNA-binding IFN stimulated genes (ISGs) that are highly upregulated following viral infection, and have been identified as potential restrictors of alphaviruses. The mechanism by which IFIT1 restricts RNA viruses is dependent on self and non-self-discrimination of RNA, and alphaviruses evade this recognition via their 5’UTR. However, the role of IFIT2 during alphavirus replication and the mechanism of viral replication inhibition is unclear. In this study, we identify IFIT2 as a restriction factor for Venezuelan equine encephalitis virus (VEEV) and show that IFIT2 binds the 3’ untranslated region (3’UTR) of the virus. We investigated the potential role of variability in the 3’UTR of the virus affecting IFIT2 antiviral activity by studying infection with VEEV. Comparison of recombinant VEEV clones containing 3’UTR sequences derived from epizootic and enzootic isolates exhibited differential sensitivity to IFIT2 restriction in vitro infection studies, suggesting that the alphavirus 3’UTR sequence may function in part to evade IFIT2 restriction. In vitro binding assays demonstrate that IFIT2 binds to the VEEV 3’UTR, however in contrast to previous studies VEEV restriction did not appear to be dependent on the ability of IFIT2 to inhibit translation of viral RNA, suggesting a novel mechanism of IFIT2 restriction. Our study demonstrates that IFIT2 is a restriction factor for alphaviruses and variability in the 3’UTR of VEEV can modulate viral restriction by IFIT2. Ongoing studies are exploring the biological consequences of IFIT2-VEEV RNA interaction in viral pathogenesis and defining sequence and structural features of RNAs that regulate IFIT2 recognition.

scholarly journals RNA-Binding Protein Musashi-2 Inhibits Aldosterone Production

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A815-A815
Author(s):  
Kathryn Bartholomay ◽  
Amber Baldwin ◽  
Neelanjan Mukherjee
Keyword(s):  
Molecular Mechanism ◽  
Transcriptional Control ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Steroid Hormone ◽  
Mrna Levels ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Hormone Synthesis ◽  
Aldosterone Production

Abstract The adrenal cortex is the site of steroid hormone synthesis. These hormones control important physiological processes like metabolism, blood pressure and volume, and sexual characteristic development. While the signaling pathways, transcription factors, and steroidogenic enzymes are well-characterized, surprisingly little is known about the contribution RNA-binding proteins (RBPs). RBPs exert post-transcriptional control by interacting with specific elements within target mRNAs. Here we focus on the RBP, Mushashi-2 (MSI2), which binds to UAG sequences in the 3’UTR of its target transcripts. MSI2 is required for development of steroidogenic tissues which is consistent with its higher mRNA levels in human ovaries and testis. MSI2 also exhibits high expression levels in human adrenal tissue and the immortalized human adrenocortical cell line (H295R). Based on the compelling MSI2 expression pattern, we set out to determine the role of MSI2 on aldosterone production. Depletion of MSI2 using siRNA led to significantly lower aldosterone levels in H295R cells stimulated with AngII. We also employed an orthogonal loss-of-function approach by co-treating cells with AngII and increasing concentrations of Ro-08-2750 (Ro), a direct and selective inhibitor of MSI2-RNA interactions. Ro inhibited aldosterone production in a dose-dependent manner at 1 µM with almost complete inhibition at 5 µM. The molecular mechanism by which MSI2 regulates target RNA translation and/or decay is unknown. Moreover, whether MSI2 acts as a repressor or activator appears to be context dependent. Our goal is to determine the precise molecular mechanism by which MSI2 promotes aldosterone production. Specifically, we will identify MSI2 targets, temporally resolved consequences of MSI2 inhibition, and protein interaction partners. This work will impact our understanding of fundamental principles of RBP-mediated regulation, as well as novel regulatory mechanisms underlying human steroid hormone synthesis. Indeed, Ro (or further optimized compounds) may represent new therapeutic avenues for adrenal disease.

scholarly journals Control of noncoding RNA production and histone levels by a 5′ tRNA fragment

2018 ◽  
Author(s):  
Ana Boskovic ◽  
Xin Yang Bing ◽  
Ebru Kaymak ◽  
Oliver J Rando
Keyword(s):  
Transcriptional Repression ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Noncoding Rnas ◽  
Cajal Body ◽  
Mrna Levels ◽  
Histone 3 ◽  
Rna Biogenesis ◽  
Mechanistic Basis

Small RNAs derived from mature tRNAs, referred to as tRNA fragments or "tRFs", are an emerging class of regulatory RNAs with poorly understood functions in cellular regulation. We recently identified a role for one specific tRF - 5′ tRF-Gly-GCC, or tRF-GG - in repression of genes associated with the endogenous retroelement MERVL, but the mechanistic basis for this regulation was unknown. Here, we show that tRF-GG plays a role in production of a wide variety of noncoding RNAs normally synthesized in Cajal bodies. Among these noncoding RNAs, tRF-GG regulation of the U7 snRNA modulates heterochromatin-mediated transcriptional repression of MERVL elements by supporting an adequate supply of histone proteins. Importantly, the effects of inhibiting tRF-GG on histone mRNA levels, activity of a histone 3′ UTR reporter, and ultimately on MERVL regulation could all be suppressed by the U7 RNA. We show that the related RNA-binding proteins hnRNPF and H bind directly to tRF-GG, and are required for Cajal body biogenesis. Together, our data reveal a conserved mechanism for 5′ tRNA fragment control of noncoding RNA biogenesis and, consequently, in global chromatin organization.

scholarly journals c-Myc-activated USP2-AS1 suppresses senescence and promotes tumor progression via stabilization of E2F1 mRNA

2021 ◽  
Vol 12 (11) ◽  
Author(s):  
Bingyan Li ◽  
Guang Zhang ◽  
Zhongyu Wang ◽  
Yang Yang ◽  
Chenfeng Wang ◽  
...  
Keyword(s):  
Cellular Senescence ◽  
Messenger Rna ◽  
Untranslated Region ◽  
Rna Binding ◽  
Noncoding Rnas ◽  
Negative Regulator ◽  
Cancer Initiation ◽  
Important Player ◽  
Oncogenic Function ◽  
Transcriptional Target

AbstractThe c-Myc oncoprotein plays a prominent role in cancer initiation, progression, and maintenance. Long noncoding RNAs (lncRNAs) are recently emerging as critical regulators of the c-Myc signaling pathway. Here, we report the lncRNA USP2-AS1 as a direct transcriptional target of c-Myc. Functionally, USP2-AS1 inhibits cellular senescence and acts as an oncogenic molecule by inducing E2F1 expression. Mechanistically, USP2-AS1 associates with the RNA-binding protein G3BP1 and facilitates the interaction of G3BP1 to E2F1 3′-untranslated region, thereby leading to the stabilization of E2F1 messenger RNA. Furthermore, USP2-AS1 is shown as a mediator of the oncogenic function of c-Myc via the regulation of E2F1. Together, these findings suggest that USP2-AS1 is a negative regulator of cellular senescence and also implicates USP2-AS1 as an important player in mediating c-Myc function.

scholarly journals Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi

2017 ◽  
Vol 114 (52) ◽  
pp. E11208-E11217 ◽  
Author(s):  
Takuya Kajitani ◽  
Hiroaki Kato ◽  
Yuji Chikashige ◽  
Chihiro Tsutsumi ◽  
Yasushi Hiraoka ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Chromatin Structure ◽  
Molecular Basis ◽  
Rna Binding ◽  
Noncoding Rnas ◽  
Transcriptional Silencing ◽  
Binding Activity ◽  
Dependent Manner ◽  
Heterochromatin Formation ◽  
A Subunit

Some long noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (RNAPII) are retained on chromatin, where they regulate RNAi and chromatin structure. The molecular basis of this retention remains unknown. We show that in fission yeast serine 7 (Ser7) of the C-terminal domain (CTD) of RNAPII is required for efficient siRNA generation for RNAi-dependent heterochromatin formation. Surprisingly, Ser7 facilitates chromatin retention of nascent heterochromatic RNAs (hRNAs). Chromatin retention of hRNAs and siRNA generation requires both Ser7 and an RNA-binding activity of the chromodomain of Chp1, a subunit of the RNA-induced transcriptional silencing (RITS) complex. Furthermore, RITS associates with RNAPII in a Ser7-dependent manner. We propose that Ser7 promotes cotranscriptional chromatin retention of hRNA by recruiting the RNA-chromatin connector protein Chp1, which facilitates RNAi-dependent heterochromatin formation. Our findings reveal a function of the CTD code: linking ncRNA transcription to RNAi for heterochromatin formation.

scholarly journals Mta Has Properties of an RNA Export Protein and Increases Cytoplasmic Accumulation of Epstein-Barr Virus Replication Gene mRNA

1998 ◽  
Vol 72 (12) ◽  
pp. 9526-9534 ◽  
Author(s):  
O. John Semmes ◽  
Lin Chen ◽  
Robert T. Sarisky ◽  
Zhigang Gao ◽  
Ling Zhong ◽  
...  
Keyword(s):  
Rna Processing ◽  
Nuclear Export ◽  
Epstein Barr Virus ◽  
Rna Binding ◽  
Mrna Levels ◽  
Transfected Cells ◽  
Barr Virus ◽  
Replication Gene ◽  
Cytoplasmic Accumulation ◽  
Epstein Barr

ABSTRACT The Epstein-Barr virus (EBV) Zta and Mta regulatory proteins were previously found to be required for efficient replication of oriLyt in cotransfection-replication assays, but the contribution of Mta to the replication process was unknown. We now demonstrate that Mta regulates replication gene expression. Using the polymerase processivity factor BMRF1 as an example, we found that in transfected cells, total BMRF1 mRNA levels were unaffected by Mta but that the amounts of cytoplasmic BMRF1 RNA and protein were greatly increased in the presence of Mta. Mta also increased cytoplasmic accumulation of the BALF2, BALF5, BSLF1, and BBLF4 replication gene mRNAs but did not affect cytoplasmic levels of BBLF2/3 mRNA. Thus, five of the six core replication genes require Mta for efficient accumulation of cytoplasmic RNA. The contribution of Mta to posttranscriptional RNA processing was examined. Examination of Mta localization in transfected cells by indirect immunofluorescence revealed that Mta colocalized with the splicing factor SC35. We also found that Mta has RNA binding activity. GlutathioneS-transferase–Mta bound to BMRF1 and BMLF1 transcripts but not to a control cellular gene RNA. Mta contains a consensus leucine-rich nuclear export signal. Such signal sequences are characteristic of proteins that undergo nuclear export. Examination of Mta localization in a heterokaryon assay provided evidence that Mta shuttles between the nucleus and the cytoplasm. Our experiments indicate that Mta functions in RNA processing and transport and mediates cytoplasmic accumulation of a number of EBV early mRNAs.

scholarly journals 7SL RNA represses p53 translation by competing with HuR

2014 ◽  
Vol 42 (15) ◽  
pp. 10099-10111 ◽  
Author(s):  
Kotb Abdelmohsen ◽  
Amaresh C Panda ◽  
Min-Ju Kang ◽  
Rong Guo ◽  
Jiyoung Kim ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Untranslated Region ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Noncoding Rnas ◽  
Transcriptional Regulators ◽  
Tumor Suppressor P53 ◽  
P53 Expression ◽  
7Sl Rna ◽  
Partial Hybrid

Abstract Noncoding RNAs (ncRNAs) and RNA-binding proteins are potent post-transcriptional regulators of gene expression. The ncRNA 7SL is upregulated in cancer cells, but its impact upon the phenotype of cancer cells is unknown. Here, we present evidence that 7SL forms a partial hybrid with the 3′-untranslated region (UTR) of TP53 mRNA, which encodes the tumor suppressor p53. The interaction of 7SL with TP53 mRNA reduced p53 translation, as determined by analyzing p53 expression levels, nascent p53 translation and TP53 mRNA association with polysomes. Silencing 7SL led to increased binding of HuR to TP53 mRNA, an interaction that led to the promotion of p53 translation and increased p53 abundance. We propose that the competition between 7SL and HuR for binding to TP53 3′UTR contributes to determining the magnitude of p53 translation, in turn affecting p53 levels and the growth-suppressive function of p53. Our findings suggest that targeting 7SL may be effective in the treatment of cancers with reduced p53 levels.

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