Hyeshik Chang

The selective tRNA aminoacylation mechanism based on a single G•U pair

Nature 510, 7506 (2014). doi:10.1038/nature13440

Authors: Masahiro Naganuma, Shun-ichi Sekine, Yeeting Esther Chong, Min Guo, Xiang-Lei Yang, Howard Gamper, Ya-Ming Hou, Paul Schimmel & Shigeyuki Yokoyama

Ligation of tRNAs with their cognate amino acids, by aminoacyl-tRNA synthetases, establishes the genetic code. Throughout evolution, tRNAAla selection by alanyl-tRNA synthetase (AlaRS) has depended predominantly on a single wobble base pair in the acceptor stem, G3•U70, mainly on the kcat

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism.

EMBO J. 2014 Jun 23;

Authors: Stoeckius M, Grün D, Kirchner M, Ayoub S, Torti F, Piano F, Herzog M, Selbach M, Rajewsky N

Abstract
The oocyte-to-embryo transition (OET) is thought to be mainly driven by post-transcriptional gene regulation. However, expression of both RNAs and proteins during the OET has not been comprehensively assayed. Furthermore, specific molecular mechanisms that regulate gene expression during OET are largely unknown. Here, we quantify and analyze transcriptome-wide, expression of mRNAs and thousands of proteins in Caenorhabditis elegans oocytes, 1-cell, and 2-cell embryos. This represents a first comprehensive gene expression atlas during the OET in animals. We discovered a first wave of degradation in which thousands of mRNAs are cleared shortly after fertilization. Sequence analysis revealed a statistically highly significant presence of a polyC motif in the 3' untranslated regions of most of these degraded mRNAs. Transgenic reporter assays demonstrated that this polyC motif is required and sufficient for mRNA degradation after fertilization. We show that orthologs of human polyC-binding protein specifically bind this motif. Our data suggest a mechanism in which the polyC motif and binding partners direct degradation of maternal mRNAs. Our data also indicate that endogenous siRNAs but not miRNAs promote mRNA clearance during the OET.

PMID: 24957527 [PubMed - as supplied by publisher]

Nature Reviews Molecular Cell Biology 15, 431 (2014). doi:10.1038/nrm3817

Author: Frank Uhlmann

Frank Uhlmann discusses how biophysics and electron microscopy studies have shed light on what lies inside chromosomes.

Nature Reviews Molecular Cell Biology 15, 453 (2014). doi:10.1038/nrm3821

Authors: Michal Breker & Maya Schuldiner

During the lifetime of a cell proteins can change their localization, alter their abundance and undergo modifications, all of which cannot be assayed by tracking mRNAs alone. Methods to study proteomes directly are coming of age, thereby opening new perspectives on the role of post-translational

Nature Reviews Molecular Cell Biology 15, 429 (2014). doi:10.1038/nrm3833

Author: Eytan Zlotorynski

Single-cell protein analysis techniques lack resolution, sensitivity or specificity, or require protein tagging. Western blotting avoids these pitfalls but is not amenable to single-cell analysis. Hughes et al. now couple western blotting with single-cell analysis, which enables the simultaneous analysis of ∼2,000 individual cells.

Related Articles

Global microRNA depletion suppresses tumor angiogenesis.

Genes Dev. 2014 May 15;28(10):1054-67

Authors: Chen S, Xue Y, Wu X, Le C, Bhutkar A, Bell EL, Zhang F, Langer R, Sharp PA

Abstract
MicroRNAs delicately regulate the balance of angiogenesis. Here we show that depletion of all microRNAs suppresses tumor angiogenesis. We generated microRNA-deficient tumors by knocking out Dicer1. These tumors are highly hypoxic but poorly vascularized, suggestive of deficient angiogenesis signaling. Expression profiling revealed that angiogenesis genes were significantly down-regulated as a result of the microRNA deficiency. Factor inhibiting hypoxia-inducible factor 1 (HIF-1), FIH1, is derepressed under these conditions and suppresses HIF transcription. Knocking out FIH1 using CRISPR/Cas9-mediated genome engineering reversed the phenotypes of microRNA-deficient cells in HIF transcriptional activity, VEGF production, tumor hypoxia, and tumor angiogenesis. Using multiplexed CRISPR/Cas9, we deleted regions in FIH1 3' untranslated regions (UTRs) that contain microRNA-binding sites, which derepresses FIH1 protein and represses hypoxia response. These data suggest that microRNAs promote tumor responses to hypoxia and angiogenesis by repressing FIH1.

PMID: 24788094 [PubMed - indexed for MEDLINE]

Related Articles

Site-Directed RNA Editing with Antagomir Deaminases - A Tool to Study Protein and RNA Function.

ChemMedChem. 2014 Jun 20;

Authors: Vogel P, Stafforst T

Abstract
RNA-guided machineries perfectly satisfy the demand for rationally programmable tools that manipulate gene function inside the cell. Over the last ten years, various natural machineries have been harnessed, with RNA interference being among the most prominent examples. It is now time to tackle the engineering of novel RNA-guided tools not provided by nature. In this respect, we highlight RNA-guided site-directed RNA editing as a new concept for the manipulation of RNA and protein function. In contrast to currently available techniques, RNA editing allows for the introduction of selected point mutations into the transcriptome without the need for genomic manipulation. In particular, the approach described using chemically stabilized, antagomir-like guideRNAs may offer advantages over others, such as specificity and circumvention of immunogenicity. These new tools have significant potential for the advancement of both basic science and medicinal application, especially in the treatment of genetic diseases.

PMID: 24954543 [PubMed - as supplied by publisher]

The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and have revealed multiple mechanisms of tolerance, but it remains difficult to separate the direct and indirect effects of ethanol. We...

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It is demonstrated, using NMR spectroscopy, that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch.

Genome-wide identification and functional analysis of Apobec-1 mediated C-to-U RNA editing in mouse small intestine and liver.

Genome Biol. 2014 Jun 19;15(6):R79

Authors: Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Ben Hamidane H, Graumann J, Mortazavi A, Nadeau JH, Davidson NO

Abstract
BACKGROUND: RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoproteinB mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1 mediated C-to-U RNA editing remain incompletely explored.
RESULTS: Deep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1 deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3[prime] untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels in 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1 deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1 deficient mice, demonstrating that Apobec-1 is required.
CONCLUSIONS: These studies define selective, tissue-specific targets of Apobec-1 dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.

PMID: 24946870 [PubMed - as supplied by publisher]

Does the ORF in the control region of Mytilus mtDNA code for a protein product?

Gene. 2014 Jun 17;

Authors: Kyriakou E, Chatzoglou E, Rodakis GC, Zouros E

Abstract
The control region of the mtDNA of Mytilus is known to contain sequences that determine whether the genome will be paternally or maternally transmitted. An open reading frame (ORF) in this region raised suspicion that it may code for a protein involved in this mechanism. An analysis of the mtDNA transcriptome failed to produce evidence for this hypothesis.

PMID: 24950231 [PubMed - as supplied by publisher]

Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation.

Brief Funct Genomics. 2014 Jun 20;

Authors: Kloetgen A, Münch PC, Borkhardt A, Hoell JI, McHardy AC

Abstract
Our understanding of transcriptional gene regulation has dramatically increased over the past decades, and many regulators of gene expression, such as transcription factors, have been analyzed extensively. Additionally, in recent years, deeper insights into the physiological roles of RNA have been obtained. More precisely, splicing, polyadenylation, various modifications, localization and the translation of messenger RNAs (mRNAs) are regulated by their interaction with RNA-binding proteins (RBPs). New technologies now enable the analysis of this regulation at different levels. A technique known as ultraviolet (UV) cross-linking and immunoprecipitation (CLIP) allows us to determine physical protein-RNA interactions on a genome-wide scale. UV cross-linking introduces covalent bonds between interacting RBPs and RNAs. In combination with immunoprecipitation and deep sequencing techniques, tens of millions of short reads (representing bound RNAs by an RBP of interest) are generated and are used to characterize the regulatory network mediated by an RBP. Other methods, such as mass spectrometry, can also be used for characterization of cross-linked RBPs and RNAs instead of CLIP methods. In this review, we discuss experimental and computational methods for the generation and analysis of CLIP data. The computational methods include short-read alignment, annotation and RNA-binding motif discovery. We describe the challenges of analyzing CLIP data and indicate areas where improvements are needed.

PMID: 24951655 [PubMed - as supplied by publisher]

Publication date: 10 July 2014
Source:Cell Reports, Volume 8, Issue 1
Author(s): Simone Backes , Ryan A. Langlois , Sonja Schmid , Andrew Varble , Jaehee V. Shim , David Sachs , Benjamin R. tenOever
A successful cellular response to virus infection is essential for evolutionary survival. In plants, arthropods, and nematodes, cellular antiviral defenses rely on RNAi. Interestingly, the mammalian response to virus is predominantly orchestrated through interferon (IFN)-mediated induction of antiviral proteins. Despite the potency of the IFN system, it remains unclear whether mammals also have the capacity to employ antiviral RNAi. Here, we investigated this by disabling IFN function, small RNA function, or both activities in the context of virus infection. We find that loss of small RNAs in the context of an in vivo RNA virus infection lowers titers due to reduced transcriptional repression of the host antiviral response. In contrast, enabling a virus with the capacity to inhibit the IFN system results in increased titers. Taken together, these results indicate that small RNA silencing is not a physiological contributor to the IFN-mediated cellular response to virus infection.

Graphical abstract

Teaser

Bacteria, plants, and many invertebrates utilize small RNAs to guide effector molecules to microbial threats in a sequence-specific manner. In vertebrates, the response to virus is protein-based and is more general in nature. However, many have speculated about the evolutionary retention of antiviral small RNAs. Backes et al. now investigate this idea by comparing virus replication in the presence and absence of both systems, and they find that small RNA-mediated silencing is not a physiological contributor to our antiviral defenses.

Publication date: 19 June 2014
Source:Cell, Volume 157, Issue 7
Author(s): Neva Caliskan , Vladimir I. Katunin , Riccardo Belardinelli , Frank Peske , Marina V. Rodnina
Programmed –1 ribosomal frameshifting (−1PRF) is an mRNA recoding event utilized by cells to enhance the information content of the genome and to regulate gene expression. The mechanism of –1PRF and its timing during translation elongation are unclear. Here, we identified the steps that govern –1PRF by following the stepwise movement of the ribosome through the frameshifting site of a model mRNA derived from the IBV 1a/1b gene in a reconstituted in vitro translation system from Escherichia coli. Frameshifting occurs at a late stage of translocation when the two tRNAs are bound to adjacent slippery sequence codons of the mRNA. The downstream pseudoknot in the mRNA impairs the closing movement of the 30S subunit head, the dissociation of EF-G, and the release of tRNA from the ribosome. The slippage of the ribosome into the –1 frame accelerates the completion of translocation, thereby further favoring translation in the new reading frame.

Graphical abstract

Teaser

Programmed ribosomal frameshifting is an mRNA recoding process that allows cells to maximize gene expression. Kinetic deconstruction of this process reveals that the binding of tRNAs to adjacent slippery sequence codons of the mRNA and the resulting pseudoknot impair movement of the 30S ribosome and slip it to the −1 position into a new translational frame.

Publication date: 17 July 2014
Source:Molecular Cell, Volume 55, Issue 2
Author(s): Moe Yokoshi , Quan Li , Munetaka Yamamoto , Hitomi Okada , Yutaka Suzuki , Yukio Kawahara
It has been proposed that Ataxin-2, a member of the like-Sm (LSm) protein family, participates in the regulation of RNA metabolism through interaction with PABPC1. However, the exact biological mechanism and in vivo targets remain unknown. Here, we report that Ataxin-2 binds directly to RNAs in a PABPC1-independent manner. High-throughput sequencing of Ataxin-2-bound RNAs prepared by PAR-CLIP revealed that Ataxin-2 binds predominantly to uridine-rich elements, including well-characterized cis-regulatory AU-rich elements, in the 3′ UTRs of target mRNAs. Gene expression analysis after Ataxin-2 depletion or overexpression revealed that Ataxin-2 stabilizes target mRNAs and increases the abundance of the corresponding proteins. A tethering assay demonstrated that Ataxin-2 elicits this effect by direct interaction with mRNAs. We also found that disease-associated polyglutamine expansion downregulates the physiological activity of Ataxin-2. These findings suggest that Ataxin-2 is an RNA-binding protein that targets cis-regulatory elements in 3′ UTRs to stabilize a subset of mRNAs and increase protein expression.

Graphical abstract

Teaser

Yokoshi et al. show that Ataxin-2 binds uridine-rich elements within 3′ UTRs of mRNAs to promote mRNA stability and protein expression. This function is inhibited by neurodegeneration-associated polyglutamine expansions in Ataxin-2.

Publication date: 19 June 2014
Source:Molecular Cell, Volume 54, Issue 6
Author(s): Katsutoshi Imamura , Naoto Imamachi , Gen Akizuki , Michiko Kumakura , Atsushi Kawaguchi , Kyosuke Nagata , Akihisa Kato , Yasushi Kawaguchi , Hiroki Sato , Misako Yoneda , Chieko Kai , Tetsushi Yada , Yutaka Suzuki , Toshimichi Yamada , Takeaki Ozawa , Kiyomi Kaneki , Tsuyoshi Inoue , Mika Kobayashi , Tatsuhiko Kodama , Youichiro Wada , Kazuhisa Sekimizu , Nobuyoshi Akimitsu

This article analyzes the mechanism by which Pumilio represses the translation of its targets. The results show, rather surprisingly, that promotion of deadenylation is not required for expression. Instead, Pumilio interacts with poly(A) binding protein and somehow interferes with its activity.

This article describes recently evolved testis-specific miRNAs in Drosophila. Evidence is provided that these miRNAs are expressed at much higher levels than non-testis-specific miRNAs of similar age. They also appear to have greater regulatory capacity than do other young miRNAs.

Identification of primary microRNA (miRNA) gene targets is critical for developing miRNA-based therapeutics and understanding their mechanisms of action. However, disentangling primary target derepression induced by miRNA inhibition from secondary effects on the transcriptome remains a technical challenge. Here, we utilized RNA immunoprecipitation (RIP) combined with competitive binding assays to identify novel primary targets of miR-122. These transcripts physically dissociate from AGO2-miRNA complexes when anti-miR is spiked into liver lysates. mRNA target displacement strongly correlated with expression changes in these genes following in vivo anti-miR dosing, suggesting that derepression of these targets directly reflects changes in AGO2 target occupancy. Importantly, using a metric based on weighted miRNA expression, we found that the most responsive mRNA target candidates in both RIP competition assays and expression profiling experiments were those with fewer alternative seed sites for highly expressed non-inhibited miRNAs. These data strongly suggest that miRNA co-regulation modulates the transcriptomic response to anti-miR. We demonstrate the practical utility of this ‘miR-target impact’ model, and encourage its incorporation, together with the RIP competition assay, into existing target prediction and validation pipelines.

U12-type introns are a rare class of introns in the genomes of diverse eukaryotes. In the human genome, they number over 700. A subset of these introns has been shown to be spliced at a slower rate compared to the major U2-type introns. This suggests a rate-limiting regulatory function for the minor spliceosome in the processing of transcripts containing U12-type introns. However, both the generality of slower splicing and the subsequent fate of partially processed pre-mRNAs remained unknown. Here, we present a global analysis of the nuclear retention of transcripts containing U12-type introns and provide evidence for the nuclear decay of such transcripts in human cells. Using SOLiD RNA sequencing technology, we find that, in normal cells, U12-type introns are on average 2-fold more retained than the surrounding U2-type introns. Furthermore, we find that knockdown of RRP41 and DIS3 subunits of the exosome stabilizes an overlapping set of U12-type introns. RRP41 knockdown leads to slower decay kinetics of U12-type introns and globally upregulates the retention of U12-type, but not U2-type, introns. Our results indicate that U12-type introns are spliced less efficiently and are targeted by the exosome. These characteristics support their role in the regulation of cellular mRNA levels.

Publication date: July 2014
Source:Trends in Biochemical Sciences, Volume 39, Issue 7
Author(s): Michael L. Gleghorn , Lynne E. Maquat
The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.

Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease.

Front Genet. 2014;5:164

Authors: Clark BS, Blackshaw S

Abstract
Comprehensive analysis of the mammalian transcriptome has revealed that long non-coding RNAs (lncRNAs) may make up a large fraction of cellular transcripts. Recent years have seen a surge of studies aimed at functionally characterizing the role of lncRNAs in development and disease. In this review, we discuss new findings implicating lncRNAs in controlling development of the central nervous system (CNS). The evolution of the higher vertebrate brain has been accompanied by an increase in the levels and complexities of lncRNAs expressed within the developing nervous system. Although a limited number of CNS-expressed lncRNAs are now known to modulate the activity of proteins important for neuronal differentiation, the function of the vast majority of neuronal-expressed lncRNAs is still unknown. Topics of intense current interest include the mechanism by which CNS-expressed lncRNAs might function in epigenetic and transcriptional regulation during neuronal development, and how gain and loss of function of individual lncRNAs contribute to neurological diseases.

PMID: 24936207 [PubMed - as supplied by publisher]

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Nature 510, 7505 (2014). doi:10.1038/nature13437

Authors: Alex K. Shalek, Rahul Satija, Joe Shuga, John J. Trombetta, Dave Gennert, Diana Lu, Peilin Chen, Rona S. Gertner, Jellert T. Gaublomme, Nir Yosef, Schraga Schwartz, Brian Fowler, Suzanne Weaver, Jing Wang, Xiaohui Wang, Ruihua Ding, Raktima Raychowdhury, Nir Friedman, Nir Hacohen, Hongkun Park, Andrew P. May & Aviv Regev

High-throughput single-cell transcriptomics offers an unbiased approach for understanding the extent, basis and function of gene expression variation between seemingly identical cells. Here we sequence single-cell RNA-seq libraries prepared from over 1,700 primary mouse bone-marrow-derived dendritic cells spanning several experimental conditions. We find substantial variation

Timed regulation of PIWI-interacting RNAs expression during rat liver regeneration.

Hepatology. 2014 Jun 16;

Authors: Rizzo F, Hashim A, Marchese G, Ravo M, Tarallo R, Nassa G, Giurato G, Rinaldi A, Cordella A, Persico M, Sulas P, Perra A, Ledda-Columbano GM, Columbano A, Weisz A

Abstract
Small non-coding RNAs comprise a growing family of molecules that regulate key cellular processes including mRNA degradation, translational repression and transcriptional gene silencing. PIWI-interacting RNAs (piRNAs) represent a class of small RNAs initially identified in the germline of a variety of species, where they contribute to maintenance of genome stability, and recently found expressed also in stem and somatic cells, where their role and responsiveness to physiopathological signals remain elusive. We investigated here piRNA expression in rat liver and its response to the stimuli exerted by regenerative proliferation of this organ. Q-PCR analysis identify in the liver the RNAs encoding PIWIL2/HILI, PIWIL4/HIWI2 and other components of the piRNA biogenesis pathways, suggesting that this is indeed functional. RNA sequencing before, during and after the wave of cell proliferation that follows partial hepatectomy (PH) identified ~1400 mammalian germline piRNAs expressed in rat liver, including 72 showing timed changes in expression 24-48h post-PH, a timing that corresponds to cell transition through the S phase, returning to basal levels by 168h, when organ regeneration is completed and hepatocytes reach quiescence. Conclusion: These results demonstrate for the first time that the piRNA pathway is active in somatic cells of the liver and, more important, that it is subject to regulation during the pathophysiological process of organ regeneration, when these molecules are thus available to exert their regulatory functions on the cell genome and transcriptome, as demonstrated by the identification of several liver mRNAs representing candidate targets of these regulatory RNAs. (Hepatology 2014;).

PMID: 24930433 [PubMed - as supplied by publisher]

Summary: Non-coding RNAs (ncRNAs) play a vital role in many cellular processes such as RNA splicing, translation, gene regulation. However the vast majority of ncRNAs still have no functional annotation. One prominent approach for putative function assignment is clustering of transcripts according to sequence and secondary structure. However sequence information is changed by post-transcriptional modifications, and secondary structure is only a proxy for the true 3D conformation of the RNA polymer. A different type of information that does not suffer from these issues and that can be used for the detection of RNA classes, is the pattern of processing and its traces in small RNA-seq reads data. Here we introduce BlockClust, an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. We perform both unsupervised clustering and develop family specific discriminative models; finally we show how the proposed approach is scalable, accurate and robust across different organisms, tissues and cell lines.

Availability: The whole BlockClust galaxy workflow including all tool dependencies is available at http://toolshed.g2.bx.psu.edu/view/rnateam/blockclust_workflow.

Contact: backofen@informatik.uni-freiburg.de; costa@informatik.uni-freiburg.de

Supplementary information: Supplementary data are available at Bioinformatics online.

dsRNA-dependent protein kinase R (PKR) is a ubiquitously expressed enzyme well known for its roles in immune response. Upon binding to viral dsRNA, PKR undergoes autophosphorylation, and the phosphorylated PKR (pPKR) regulates translation and multiple signaling pathways in infected cells. Here, we found that PKR is activated in uninfected cells, specifically during mitosis, by binding to dsRNAs formed by inverted Alu repeats (IRAlus). While PKR and IRAlu-containing RNAs are segregated in the cytosol and nucleus of interphase cells, respectively, they interact during mitosis when nuclear structure is disrupted. Once phosphorylated, PKR suppresses global translation by phosphorylating the α subunit of eukaryotic initiation factor 2 (eIF2α). In addition, pPKR acts as an upstream kinase for c-Jun N-terminal kinase and regulates the levels of multiple mitotic factors such as CYCLINS A and B and POLO-LIKE KINASE 1 and phosphorylation of HISTONE H3. Disruption of PKR activation via RNAi or expression of a transdominant-negative mutant leads to misregulation of the mitotic factors, delay in mitotic progression, and defects in cytokinesis. Our study unveils a novel function of PKR and endogenous dsRNAs as signaling molecules during the mitosis of uninfected cells.

Related Articles

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs.

Nat Struct Mol Biol. 2014 Jun 15;

Authors: Zheng GX, Do BT, Webster DE, Khavari PA, Chang HY

Abstract
Long noncoding RNAs (lncRNAs) are important regulators of cell fate, yet little is known about mechanisms controlling lncRNA expression. Here we show that transcription is quantitatively different for lncRNAs and mRNAs-as revealed by deficiency of Dicer (Dcr), a key RNase that generates microRNAs (miRNAs). Dcr loss in mouse embryonic stem cells led unexpectedly to decreased levels of hundreds of lncRNAs. The canonical Dgcr8-Dcr-miRNA pathway is required for robust lncRNA transcriptional initiation and elongation. Computational and genetic epistasis analyses demonstrated that Dcr activation of the oncogenic transcription factor cMyc is partly responsible for lncRNA expression. A quantitative metric of mRNA-lncRNA decoupling revealed that Dcr and cMyc differentially regulate lncRNAs versus mRNAs in diverse cell types and in vivo. Thus, numerous lncRNAs may be modulated as a class in development and disease, notably where Dcr and cMyc act.

PMID: 24929436 [PubMed - as supplied by publisher]

Emerging mechanisms of mRNP remodeling regulation.

Wiley Interdiscip Rev RNA. 2014 Jun 12;

Authors: Chen CY, Shyu AB

Abstract
The assembly and remodeling of the components of messenger ribonucleoprotein particles (mRNPs) are important in determining the fate of a messenger RNA (mRNA). A combination of biochemical and cell biology research, recently complemented by genome-wide high-throughput approaches, has led to significant progress on understanding the formation, dynamics, and function of mRNPs. These studies also advanced the challenging process of identifying the evolving constituents of individual mRNPs at various stages during an mRNA's lifetime. While research on mRNP remodeling in general has been gaining momentum, there has been relatively little attention paid to the regulatory aspect of mRNP remodeling. Here, we discuss the results of some new studies and potential mechanisms for regulation of mRNP remodeling. For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.

PMID: 24923990 [PubMed - as supplied by publisher]

Related Articles

Certain Adenylated Non-Coding RNAs, Including 5' Leader Sequences of Primary MicroRNA Transcripts, Accumulate in Mouse Cells following Depletion of the RNA Helicase MTR4.

PLoS One. 2014;9(6):e99430

Authors: Dorweiler JE, Ni T, Zhu J, Munroe SH, Anderson JT

Abstract
RNA surveillance plays an important role in posttranscriptional regulation. Seminal work in this field has largely focused on yeast as a model system, whereas exploration of RNA surveillance in mammals is only recently begun. The increased transcriptional complexity of mammalian systems provides a wider array of targets for RNA surveillance, and, while many questions remain unanswered, emerging data suggest the nuclear RNA surveillance machinery exhibits increased complexity as well. We have used a small interfering RNA in mouse N2A cells to target the homolog of a yeast protein that functions in RNA surveillance (Mtr4p). We used high-throughput sequencing of polyadenylated RNAs (PA-seq) to quantify the effects of the mMtr4 knockdown (KD) on RNA surveillance. We demonstrate that overall abundance of polyadenylated protein coding mRNAs is not affected, but several targets of RNA surveillance predicted from work in yeast accumulate as adenylated RNAs in the mMtr4KD. microRNAs are an added layer of transcriptional complexity not found in yeast. After Drosha cleavage separates the pre-miRNA from the microRNA's primary transcript, the byproducts of that transcript are generally thought to be degraded. We have identified the 5' leading segments of pri-miRNAs as novel targets of mMtr4 dependent RNA surveillance.

PMID: 24926684 [PubMed - as supplied by publisher]