Analysis of co-transcriptional RNA processing by RNA-ChIP assay

Long noncoding RNA TUG1 regulates smooth muscle cell differentiation via KLF4-myocardin axis

Abdominal aortic aneurysms (AAAs) are asymptomatic vascular diseases that have life-threatening outcomes. Smooth muscle cell (SMC) dysfunction plays an important role in AAA development. The contribution of non-coding genome, specifically the role of long non-coding RNAs (lncRNAs) in SMC dysfunction, is relatively unexplored. We investigated the role of lncRNA TUG1 in SMC dysfunction. To identify potential lncRNAs relevant to SMC functionality, lncRNA profiling was performed in angiotensin-II-treated SMCs. AAA was induced by angiotensin-II treatment in mice. Transcriptional regulation of TUG1 was studied using promoter luciferase and chromatin-immuno-precipitation experiments. Gain-or-loss-of-function experiments were performed in vitro to investigate TUG1-mediated regulation of SMC function. Immunoprecipitation experiments were conducted to elucidate the mechanism underlying TUG1-mediated SMC dysfunction. TUG1 was upregulated in SMCs following angiotensin-II treatment. Similarly, TUG1 levels were elevated in abdominal aorta in a mouse model of angiotensin-II-induced AAA. Further investigations showed that angiotensin-II-induced TUG1 expression could be suppressed by inhibiting Notch-signaling pathway, both in vitro and in mouse AAA model and that TUG1 is a direct transcriptional target of the Notch pathway. In aneurysmal tissues, TUG1 expression was inversely correlated with the expression of SMC contractile genes. Overexpression of TUG1 repressed SMC differentiation in vitro, whereas siRNA/shRNA-mediated TUG1 knockdown showed an opposite effect. Mechanistically, TUG1 interacts with transcriptional repressor KLF4 and facilitates its recruitment to myocardin promoter ultimately leading to the repression of SMC differentiation. In summary, our study uncovers a novel role for the lncRNA TUG1 wherein it modulates SMC differentiation via the KLF4-myocardin axis, which may have potential implications in AAA development.NEW & NOTEWORTHY TUG1 is an angiotensin-II-induced long noncoding RNA that mediates smooth muscle cell (SMC) dysfunction through interaction with transcriptional repressor KLF4.

Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae

Nuclear degradation of aberrant mRNAs in Saccharomyces cerevisiae is accomplished by the nuclear exosome and its cofactors TRAMP/CTEXT. Evidence from this investigation establishes a universal role of the Nrd1p-Nab3p-Sen1p (NNS) complex in the nuclear decay of all categories of aberrant mRNAs. In agreement with this, both nrd1-1 and nrd1-2 mutations impaired the decay of all classes of aberrant messages. This phenotype is similar to that displayed by GAL::RRP41 and rrp6-Δ mutant yeast strains. Remarkably, however, nrd1ΔCID mutation (lacking the C-terminal domain required for interaction of Nrd1p with RNAPII) only diminished the decay of aberrant messages with defects occurring during the early stage of mRNP biogenesis, without affecting other messages with defects generated later in the process. Co-transcriptional recruitment of Nrd1p on the aberrant mRNAs was vital for their concomitant decay. Strikingly, this recruitment on to mRNAs defective in the early phases of biogenesis is solely dependent upon RNAPII. In contrast, Nrd1p recruitment onto export-defective transcripts with defects occurring in the later stage of biogenesis is independent of RNAPII and dependent on the CF1A component, Pcf11p, which explains the observed characteristic phenotype of nrd1ΔCID mutation. Consistently, pcf11-2 mutation displayed a selective impairment in the degradation of only the export-defective messages.

Argonaute2 attenuates active transcription by limiting RNA Polymerase II elongation in Drosophila melanogaster

Increasing lines of evidence support that Argonaute2 (AGO2) harbors several nuclear functions in metazoa. In particular, Drosophila AGO2 modulates transcription of developmentally regulated genes; however, the molecular mechanisms behind AGO2 recruitment into chromatin and its function in transcription have not been deeply explored. In this study, we show that Drosophila AGO2 chromatin association depends on active transcription. In order to gain insight into how AGO2 controls transcription, we performed differential ChIP-seq analysis for RNA Polymerase II (Pol II) upon depletion of AGO2. Remarkably, we find specific accumulation of the elongating but not initiating form of Pol II after AGO2 knockdown, suggesting that AGO2 impairs transcription elongation. Finally, AGO2 also affects Negative Elongation Factor (NELF) chromatin association but not the Cyclin Dependent Kinase 9 (CDK9). Altogether, these results provide key insights into the molecular role of AGO2 in attenuating elongation of certain actively transcribed genes.

Nuclear RNA surveillance complexes silence HIV-1 transcription

Expression from the HIV-1 LTR can be repressed in a small population of cells, which contributes to the latent reservoir. The factors mediating this repression have not been clearly elucidated. We have identified a network of nuclear RNA surveillance factors that act as effectors of HIV-1 silencing. RRP6, MTR4, ZCCHC8 and ZFC3H1 physically associate with the HIV-1 TAR region and repress transcriptional output and recruitment of RNAPII to the LTR. Knock-down of these factors in J-Lat cells increased the number of GFP-positive cells, with a concomitant increase in histone marks associated with transcriptional activation. Loss of these factors increased HIV-1 expression from infected PBMCs and led to reactivation of HIV-1 from latently infected PBMCs. These findings identify a network of novel transcriptional repressors that control HIV-1 expression and which could open new avenues for therapeutic intervention.

Following integration into the host genome, HIV-1 expression is silenced in a small population of cells, largely via epigenetic mechanisms that repress LTR-mediated transcription. This repression creates a reservoir of cells that prevent an effective cure. It is unclear how and why integrated HIV-1 becomes transcriptionally silenced. Here, we identify a network of nuclear RNA surveillance factors that repress HIV transcription and whose loss increases virus expression in latently infected J-Lat and PBMCs. These findings advance the understanding of transcriptional repression of HIV-1.

MicroRNAs in Cardiovascular Disease: Perspectives and Reality

Since the discovery of the first noncoding RNA decades ago, the transcriptomics evolution has made a great leap reaching to the detection and recognition of microRNAs (miRNAs) in the early 1990s. Thereafter, numerous miRNAs were reported in different species, with a great body of literature focusing on their role in human health and in pathophysiological processes. miRNAs play a significant role in the cardiovascular system, not only in physiology and normal development but also in disease processes and evolution. Further studies on miRNAs have highlighted their participation in several expressions of cardiovascular disease, such as atherosclerosis, acute and chronic syndromes of coronary artery disease, heart failure, and cardiac arrhythmias. To date, the challenge remains to understand the underlying mechanisms of miRNAs that drive their expression profile so as to use them as innovative diagnostic tools or therapeutic targets in cardiovascular disease.

RNA Chromatin Immunoprecipitation (RNA-ChIP) in Caenorhabditis elegans

The RNA chromatin immunoprecipitation assay (RNA-ChIP) allows detection and quantification of RNA-protein interactions using in vivo cross-linking with formaldehyde followed by immunoprecipitation of the RNA-protein complexes. Here we describe the RNA-ChIP protocol that we have adapted for Caenorhabditis elegans (C. elegans) to detect interaction between the nuclear Argonaute CSR-1 (chromosome segregation and RNAi deficient) protein and its target nascent RNAs. We have used a transgenic strain expressing a recombinant long isoform of CSR-1 protein fused with N-terminal 3x FLAG epitope.

PI3K/AKT pathway mediates induction of IL-1RA by TSH in fibrocytes: modulation by PTEN

CONTEXT

TSH provokes expression of inflammatory genes in CD34(+) fibrocytes. These cells appear to infiltrate the orbit in Graves' disease (GD), where they putatively become the CD34(+) orbital fibroblast subset (GD-OF). This may have importance in solving the pathogenesis of thyroid-associated ophthalmopathy. The IL-1 family is targeted by TSH in fibrocytes and OFs by inducing secreted IL-1 receptor antagonist (IL-1RA) and intracellular IL-1RA in a cell-specific pattern. Phosphoinositide 3-kinase (PI3K) mediates several TSH actions in thyroid. This pathway is modulated by phosphatase and tensin homolog deleted on chromosome 10 (PTEN). Vanishingly little is known currently about TSHR signaling to IL-1RA expression in nonthyroidal cells. Furthermore, factors modulating TSH action in these cells are largely unexplored.

OBJECTIVES

To characterize intermediate signaling between TSHR and IL-1RA in fibrocytes and GD-OFs and to begin to identify the proximate regulators of TSHR signaling in nonepithelial, extrathyroidal cells as a strategy for developing therapies for thyroid-associated ophthalmopathy.

DESIGN/SETTING/PARTICIPANTS

Fibrocytes and GD-OFs were collected and analyzed from healthy individuals and those with GD in an academic clinical practice.

MAIN OUTCOME MEASURES

Real-time PCR, Western blot analysis, cell transfections, and chromatin immunoprecipitation analysis.

RESULTS

TSH induces IL-1RA in fibrocytes and GD-OFs by activating the PI3K/AKT pathway. Interrupting either PI3K or AKT with small molecule inhibitors or by knocking down their expression with targeting small interfering RNA attenuates the actions of TSH. OFs exhibit greater basal PTEN activity and lower constitutive AKT phosphorylation than do fibrocytes. Patterns of PTEN induction diverge in the two cell types.

CONCLUSIONS

The current findings identify the PI3K/AKT pathway as critical to the induction by TSH of IL-1RA in fibrocytes and GD-OFs. Furthermore, PTEN modulates the amplitude of the induction. In GD-OFs, relatively high basal PTEN levels prevent secreted IL-1RA expression or release. Knocking down PTEN allows GD-OFs to exhibit a pattern of IL-1RA expression resembling fibrocytes.

Regulation of IL-1 receptor antagonist by TSH in fibrocytes and orbital fibroblasts

CONTEXT

The IL-1 family plays important roles in normal physiology and mediates inflammation. The actions of IL-1 are modulated by multiple IL-1 receptor antagonists (IL-1RA), including intracellular and secreted forms. IL-1 has been implicated in autoimmunity, such as that occurring in Graves' disease (GD) and its inflammatory orbital manifestation, thyroid-associated ophthalmopathy (TAO). We have previously reported that CD34(+) fibrocytes, monocyte-lineage bone marrow-derived cells, express functional TSH receptor, the central antigen in GD. When activated by TSH, they produce IL-6, IL-8, and TNF-α. Moreover, they infiltrate the orbit in TAO in which they transition into CD34(+) fibroblasts and comprise a population of orbital fibroblasts (OFs). Little is known currently about any relationship between TSH, TSH receptor, and the IL-1 pathway.

OBJECTIVE

The objective of the study was to determine whether TSH regulates IL-1RA in fibrocytes and OFs.

DESIGN/SETTING/PARTICIPANTS

Fibrocytes and OFs were collected and analyzed from healthy individuals and those with GD in an academic clinical practice.

MAIN OUTCOME MEASURES

Real-time PCR, Western blot analysis, reporter gene assays, and cell transfections were performed.

RESULTS

TSH induces the expression of IL-1RA in fibrocytes and GD-OFs. The patterns of induction diverge quantitatively and qualitatively in the two cell types. This results from relatively small effects on gene transcription-related events but a greater influence on secreted IL-1RA and intracellular IL-1RA mRNA stabilities. These actions of TSH are dependent on the intermediate induction of IL-1α and IL-1β.

CONCLUSIONS

Our findings for the first time directly link activities of the TSH and IL-1 pathways. Furthermore, they identify novel molecular interactions that could be targeted as therapy for TAO.

Non-coding RNAs: the "dark matter" of cardiovascular pathophysiology

Large-scale analyses of mammalian transcriptomes have identified a significant number of different RNA molecules that are not translated into protein. In fact, the use of new sequencing technologies has identified that most of the genome is transcribed, producing a heterogeneous population of RNAs which do not encode for proteins (ncRNAs). Emerging data suggest that these transcripts influence the development of cardiovascular disease. The best characterized non-coding RNA family is represented by short highly conserved RNA molecules, termed microRNAs (miRNAs), which mediate a process of mRNA silencing through transcript degradation or translational repression. These microRNAs (miRNAs) are expressed in cardiovascular tissues and play key roles in many cardiovascular pathologies, such as coronary artery disease (CAD) and heart failure (HF). Potential links between other ncRNAs, like long non-coding RNA, and cardiovascular disease are intriguing but the functions of these transcripts are largely unknown. Thus, the functional characterization of ncRNAs is essential to improve the overall understanding of cellular processes involved in cardiovascular diseases in order to define new therapeutic strategies. This review outlines the current knowledge of the different ncRNA classes and summarizes their role in cardiovascular development and disease.

Divergent expression of IL-1 receptor antagonists in CD34⁺ fibrocytes and orbital fibroblasts in thyroid-associated ophthalmopathy: contribution of fibrocytes to orbital inflammation

CONTEXT

Thyroid-associated ophthalmopathy (TAO) manifests as inflammation of orbital connective tissue. Bone marrow-derived CD34⁺ fibrocytes infiltrate the orbit in TAO where they become CD34⁺ orbital fibroblasts. They express thyroid-specific antigens and thus may contribute to inflammation. Evidence suggests that orbital susceptibility to TAO may involve IL-1, which is modulated by IL-1 receptor antagonists, designated secreted (sIL-1RA) and intracellular (icIL-1RA).

OBJECTIVE

We sought to characterize the expression of sIL-1RA and icIL-1RA in TAO orbital fibroblasts compared to CD34⁺ fibrocytes.

DESIGN/SETTING/PARTICIPANTS

Patients with TAO and healthy donors were recruited from an academic medical center clinical practice.

MAIN OUTCOME MEASURES

Real-time PCR, cytokine-specific ELISA, gene promoter activities, transcriptional analysis, mRNA stability, and cytometric cell sorting were performed.

RESULTS

Orbital fibroblasts treated with IL-1β exhibit greater inductions of IL-1α, IL-1β, and prostaglandin endoperoxide H synthase-2 transcripts than do fibrocytes. Fibrocytes express dramatically higher basal levels of both icIL-1RA and sIL-1RA. When treated with IL-1β, icIL-1RA is induced in orbital fibroblasts but not sIL-1RA, whereas in fibrocytes, sIL-1RA is dominantly up-regulated. These inductions result from increased steady-state levels of respective mRNAs, enhanced transcript stabilities, and modestly increased gene transcription.

CONCLUSIONS

Robust responses of TAO orbital fibroblasts to IL-1β are a consequence of low-level sIL-1RA expression. This results in poorly opposed actions of IL-1β. In contrast, circulating fibrocytes express high levels of sIL-1RA, which are diminished as these cells transition to orbital fibroblasts. These findings identify an explanation for the inflammatory phenotype exhibited by TAO orbital fibroblasts and provide a potential target for altering disease susceptibility.

CTD serine-2 plays a critical role in splicing and termination factor recruitment to RNA polymerase II in vivo

Co-transcriptional pre-mRNA processing relies on reversible phosphorylation of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNA polymerase II (RNAP II). In this study, we replaced in live cells the endogenous Rpb1 by S2A Rpb1, where the second serines (Ser2) in the CTD heptapeptide repeats were switched to alanines, to prevent phosphorylation. Although slower, S2A RNAP II was able to transcribe. However, it failed to recruit splicing components such as U2AF65 and U2 snRNA to transcription sites, although the recruitment of U1 snRNA was not affected. As a consequence, co-transcriptional splicing was impaired. Interestingly, the magnitude of the S2A RNAP II splicing defect was promoter dependent. In addition, S2A RNAP II showed an impaired recruitment of the cleavage factor PCF11 to pre-mRNA and a defect in 3'-end RNA cleavage. These results suggest that CTD Ser2 plays critical roles in co-transcriptional pre-mRNA maturation in vivo: It likely recruits U2AF65 to ensure an efficient co-transcriptional splicing and facilitates the recruitment of pre-mRNA 3'-end processing factors to enhance 3'-end cleavage.

The RNA helicase DDX5/p68 is a key factor promoting c-fos expression at different levels from transcription to mRNA export

It is widely accepted that pre-mRNA maturation, including splicing, is tightly coupled to both transcription and mRNA export, but factors linking the three processes are less understood. By analysing the estrogen-regulated expression of the c-fos mRNA that is processed during transcription, we show that the ddx5 RNA helicase, is required throughout the major nuclear steps of the expression of the c-fos gene, from transcription to mRNA export. Indeed, ddx5, whose recruitment on the c-fos gene was increased upon estrogen treatment, was required for the full transcriptional activation of the c-fos gene. In addition, ddx5 was required for c-fos co-transcriptional RNA splicing. When splicing occurred post-transcriptionally in the absence of ddx5, the c-fos mRNA was poorly exported into the cytosol because of inefficient recruitment of the TAP mRNA export receptor. Finally, ddx5 was present in the c-fos messenger ribonucleoprotein together with mRNA export factors, which further supports that ddx5 is a key operator in the c-fos ‘mRNA factory’.

In vitro and in vivo analysis of the interaction between RNA helicase A and HIV-1 RNA

RNA helicase A (RHA) promotes multiple steps of HIV-1 RNA metabolism during viral replication, including transcription, translation, and the annealing of primer tRNA(3)(Lys) to the viral RNA. RHA is a member of the DExH subclass of RNA helicases that uniquely contains two double-stranded RNA binding domains (dsRBDs) at its N terminus. Here, we performed a genome-wide analysis of the interaction of RHA with HIV-1 RNA both in vitro, using fluorescence polarization, and during viral replication, using an RNA-protein coprecipitation assay. In vitro, RHA binds to all the isolated regions of the HIV-1 RNA genome tested, with K(d) (equilibrium dissociation constant) values ranging from 44 to 178 nM. In contrast, during viral replication, RNA-protein coprecipitation assays detected only a major interaction of RHA with the 5'-untranslated region (5'-UTR) and a minor interaction with the Rev response element (RRE) of HIV-1 RNA. Since RHA does not associate well with all the highly structured regions of HIV-1 RNA tested in vivo, the results suggest that other viral or cellular factors not present in vitro may modulate the direct interaction of RHA with HIV-1 RNA during virus replication. Nevertheless, a role for duplex RNA as a target for RHA binding in vivo is suggested by the fact that the deletion of either one or both dsRBDs eliminates the in vivo interaction of RHA with HIV-1 RNA. Furthermore, these mutant RHAs do not promote the in vivo annealing of tRNA(3)(Lys) to viral RNA, nor are they packaged into virions, demonstrating that the dsRBDs are essential for the role of RHA in HIV-1 replication.

The role of RNA structure in posttranscriptional regulation of gene expression

As more information is gathered on the mechanisms of transcription and translation, it is becoming apparent that these processes are highly regulated. The formation of mRNA secondary and tertiary structures is one such regulatory process that until recently it has not been analysed in depth. Formation of these mRNA structures has the potential to enhance and inhibit alternative splicing of transcripts, and regulate rates and amount of translation. As this regulatory mechanism potentially impacts at both the transcriptional and translational level, while also potentially utilising the vast array of non-coding RNAs, it warrants further investigation. Currently, a variety of high-throughput sequencing techniques including parallel analysis of RNA structure (PARS), fragmentation sequencing (FragSeq) and selective 2-hydroxyl acylation analysed by primer extension (SHAPE) lead the way in the genome-wide identification and analysis of mRNA structure formation. These new sequencing techniques highlight the diversity and complexity of the transcriptome, and demonstrate another regulatory mechanism that could become a target for new therapeutic approaches.