Hyeshik Chang

Video game training enhances cognitive control in older adults

Nature 501, 7465 (2013). doi:10.1038/nature12486

Authors: J. A. Anguera, J. Boccanfuso, J. L. Rintoul, O. Al-Hashimi, F. Faraji, J. Janowich, E. Kong, Y. Larraburo, C. Rolle, E. Johnston & A. Gazzaley

Cognitive control is defined by a set of neural processes that allow us to interact with our complex environment in a goal-directed manner. Humans regularly challenge these control processes when attempting to simultaneously accomplish multiple goals (multitasking), generating interference as the result of fundamental information processing limitations. It is clear that multitasking behaviour has become ubiquitous in today’s technologically dense world, and substantial evidence has accrued regarding multitasking difficulties and cognitive control deficits in our ageing population. Here we show that multitasking performance, as assessed with a custom-designed three-dimensional video game (NeuroRacer), exhibits a linear age-related decline from 20 to 79 years of age. By playing an adaptive version of NeuroRacer in multitasking training mode, older adults (60 to 85 years old) reduced multitasking costs compared to both an active control group and a no-contact control group, attaining levels beyond those achieved by untrained 20-year-old participants, with gains persisting for 6 months. Furthermore, age-related deficits in neural signatures of cognitive control, as measured with electroencephalography, were remediated by multitasking training (enhanced midline frontal theta power and frontal–posterior theta coherence). Critically, this training resulted in performance benefits that extended to untrained cognitive control abilities (enhanced sustained attention and working memory), with an increase in midline frontal theta power predicting the training-induced boost in sustained attention and preservation of multitasking improvement 6 months later. These findings highlight the robust plasticity of the prefrontal cognitive control system in the ageing brain, and provide the first evidence, to our knowledge, of how a custom-designed video game can be used to assess cognitive abilities across the lifespan, evaluate underlying neural mechanisms, and serve as a powerful tool for cognitive enhancement.

Genetics: A library of human knockouts

Nature 501, 7465 (2013). doi:10.1038/501009d

The functions of all 20,000 human protein-coding genes are still not known, partly because large gene-knockout libraries are not available for human cells.One strategy for making such a library is to use a retroviral gene trap that disrupts gene expression when inserted into different

The origin of life is believed to have progressed through an RNA world, in which RNA acted as both genetic material and functional molecules. The structure of the evolutionary fitness landscape of RNA would determine natural selection for the first functional sequences. Fitness landscapes are the subject of much speculation,...

Nature Methods 10, 1003 (2013). doi:10.1038/nmeth.2633

Authors: Christopher M Hindson, John R Chevillet, Hilary A Briggs, Emily N Gallichotte, Ingrid K Ruf, Benjamin J Hindson, Robert L Vessella & Muneesh Tewari

Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased 37–86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer.

Article

The nuclear protein HMGB1 is involved in muscle fibre formation. Here, Dormoy-Raclet et al. show that during muscle cell differentiation, the RNA-binding protein HuR promotes HMGB1 mRNA translation by preventing its repression by miR-1192.

Nature Communications doi: 10.1038/ncomms3388

Authors: Virginie Dormoy-Raclet, Anne Cammas, Barbara Celona, Xian Jin Lian, Kate van der Giessen, Marija Zivojnovic, Silvia Brunelli, Francesca Riuzzi, Guglielmo Sorci, Brian T. Wilhelm, Sergio Di Marco, Rosario Donato, Marco E. Bianchi, Imed-Eddine Gallouzi

Article

Messenger RNAs and their associated proteins are transported from the nucleus through highly selective nuclear pore complexes. Using ultrahigh resolution single-molecule imaging, the authors visualise the path taken by each messenger RNA as it negotiates the pore’s selectivity filter.

Nature Communications doi: 10.1038/ncomms3414

Authors: Jiong Ma, Zhen Liu, Nicole Michelotti, Sethuramasundaram Pitchiaya, Ram Veerapaneni, John R. Androsavich, Nils G. Walter, Weidong Yang

Nature Structural & Molecular Biology 20, 1022 (2013). doi:10.1038/nsmb.2657

Authors: Patricia Richard & James L. Manley

High-throughput RNA sequencing has unveiled the existence of a large number of noncoding antisense RNAs derived from bidirectional promoters; unlike sense transcripts, these RNAs are often unstable. Two recent reports investigate why downstream transcription is productive, whereas upstream transcripts are prone to degradation, revealing that an asymmetric distribution of polyadenylation signals and U1 snRNP–binding sites surrounding transcription start sites control the outcome of bidirectional transcription.

Nature Structural & Molecular Biology 20, 1019 (2013). doi:10.1038/nsmb.2661

Authors: John Achenbach & Knud H Nierhaus

Translocation is an essential step of protein synthesis in which the large tRNA2–mRNA complex inside the ribosome moves from the A and P sites to the P and E sites, respectively, bringing a new mRNA codon into the decoding center. This process is catalyzed by the elongation factor EF-G–GTP (eEF2 in eukaryotes) and is the least understood stage of peptide elongation. Four new reports describe the crystal structures of translocation intermediates, illustrating important details of the translocation reaction.

Background: Polyadenylation is a key regulatory step in eukaryotic gene expression and one of the major contributors of transcriptome diversity. Aberrant polyadenylation often associates with expression defects and leads to human diseases. Results: To better understand global polyadenylation regulation, we have developed a polyadenylation sequencing (PA-seq) approach. By profiling polyadenylation events in 13 human tissues, we found that alternative cleavage and polyadenylation (APA) is prevalent in both protein-coding and noncoding genes. In addition, APA usage, similar to gene expression profiling, exhibits tissue-specific signatures and is sufficient for determining tissue origin. A 3[prime] untranslated region shortening index (USI) was further developed for genes with tandem APA sites. Strikingly, the results showed that different tissues exhibit distinct patterns of shortening and/or lengthening of 3[prime] untranslated regions, suggesting the intimate involvement of APA in establishing tissue or cell identity. Conclusions: This study provides a comprehensive resource to uncover regulated polyadenylation events in human tissues and to characterize the underlying regulatory mechanism.

Background: HIV-1 translation is modulated by the activation of the interferon (IFN)-inducible Protein Kinase RNA-activated (PKR). PKR phosphorylates its downstream targets, including the alpha subunit of the eukaryotic translation Initiation Factor 2 (eIF2α), which decreases viral replication. The PKR Activator (PACT) is known to activate PKR after a cellular stress. In lymphocytic cell lines, HIV-1 activates PKR only transiently and not when cells replicate the virus at high levels. The regulation of this activation is due to a combination of viral and cellular factors that have been only partially identified. Results: PKR is transiently induced and activated in peripheral blood mononuclear cells after HIV-1 infection. The addition of IFN reduces viral replication, and induces both the production and phosphorylation of PKR. In lymphocytic Jurkat cells infected by HIV-1, a multiprotein complex around PKR contains the double-stranded RNA binding proteins (dsRBPs), adenosine deaminase acting on RNA (ADAR)1 and PACT. In HEK 293T cells transfected with an HIV-1 molecular clone, PACT unexpectedly inhibited PKR and eIF2α phosphorylation and increased HIV-1 protein expression and virion production in the presence of either endogenous PKR alone or overexpressed PKR. The comparison between different dsRBPs showed that ADAR1, TAR RNA Binding Protein (TRBP) and PACT inhibit PKR and eIF2α phosphorylation in HIV-infected cells, whereas Staufen1 did not. Individual or a combination of short hairpin RNAs against PACT or ADAR1 decreased HIV-1 protein expression. In the astrocytic cell line U251MG, which weakly expresses TRBP, PACT mediated an increased HIV-1 protein expression and a decreased PKR phosphorylation. In these cells, a truncated PACT, which constitutively activates PKR in non-infected cells showed no activity on either PKR or HIV-1 protein expression. Finally, PACT and ADAR1 interact with each other in the absence of RNAs. Conclusion: In contrast to its previously described activity, PACT contributes to PKR dephosphorylation during HIV-1 replication. This activity is in addition to its heterodimer formation with TRBP and could be due to its binding to ADAR1. HIV-1 has evolved to replicate in cells with high levels of TRBP, to induce the expression of ADAR1 and to change the function of PACT for PKR inhibition and increased replication.

Nature Reviews Cancer 13, 682 (2013). doi:10.1038/nrc3604

Author: Isabel Lokody

A novel in vivo genome-wide RNAi screening method in mice provides insights into the biology of skin growth and skin carcinogenesis.

Transcriptome and genome sequencing uncovers functional variation in humans

Nature 501, 7468 (2013). doi:10.1038/nature12531

Authors: Tuuli Lappalainen, Michael Sammeth, Marc R. Friedländer, Peter A. C. ‘t Hoen, Jean Monlong, Manuel A. Rivas, Mar Gonzàlez-Porta, Natalja Kurbatova, Thasso Griebel, Pedro G. Ferreira, Matthias Barann, Thomas Wieland, Liliana Greger, Maarten van Iterson, Jonas Almlöf, Paolo Ribeca, Irina Pulyakhina, Daniela Esser, Thomas Giger, Andrew Tikhonov, Marc Sultan, Gabrielle Bertier, Daniel G. MacArthur, Monkol Lek, Esther Lizano, Henk P. J. Buermans, Ismael Padioleau, Thomas Schwarzmayr, Olof Karlberg, Halit Ongen, Helena Kilpinen, Sergi Beltran, Marta Gut, Katja Kahlem, Vyacheslav Amstislavskiy, Oliver Stegle, Matti Pirinen, Stephen B. Montgomery, Peter Donnelly, Mark I. McCarthy, Paul Flicek, Tim M. Strom, The Geuvadis Consortium, Hans Lehrach, Stefan Schreiber, Ralf Sudbrak, Ángel Carracedo, Stylianos E. Antonarakis, Robert Häsler, Ann-Christine Syvänen, Gert-Jan van Ommen, Alvis Brazma, Thomas Meitinger, Philip Rosenstiel, Roderic Guigó, Ivo G. Gut, Xavier Estivill & Emmanouil T. Dermitzakis

Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. Here we report sequencing and deep analysis of messenger RNA and microRNA from lymphoblastoid cell lines

Background: Pluripotency is characterized by a unique transcriptional state, in which lineage-specification genes are poised for transcription upon exposure to appropriate stimuli, via a bivalency mechanism involving the simultaneous presence of activating and repressive methylation marks at promoter-associated histones. Recent evidence suggests that other mechanisms, such as RNA polymerase II pausing, might be operational in this process, but their regulation remains poorly understood. Results: Here we identify the non-coding snRNA 7SK as a multifaceted regulator of transcription in embryonic stem cells. We find that 7SK represses a specific cohort of transcriptionally poised genes with bivalent or activating chromatin marks in these cells, suggesting a novel poising mechanism independent of Polycomb activity. Genome-wide analysis shows that 7SK also prevents transcription downstream of polyadenylation sites at several active genes, indicating that 7SK is required for normal transcriptional termination or control of 3[prime]-UTR length. In addition, 7SK suppresses divergent upstream antisense transcription at more than 2,600 loci, including many that encode divergent long non-coding RNAs, a finding that implicates the 7SK snRNA in the control of transcriptional bidirectionality. Conclusions: Our study indicates that a single non-coding RNA, the snRNA 7SK, is a gatekeeper of transcriptional termination and bidirectional transcription in embryonic stem cells and mediates transcriptional poising through a mechanism independent of chromatin bivalency.

Molecular Systems Biology 9, (2013). doi:10.1038/msb.2013.47

Authors: Anders R Kristensen, Joerg Gsponer & Leonard J Foster

Related Articles

Long noncoding RNAs and the genetics of cancer.

Br J Cancer. 2013 Jun 25;108(12):2419-25

Authors: Cheetham SW, Gruhl F, Mattick JS, Dinger ME

Abstract
Cancer is a disease of aberrant gene expression. While the genetic causes of cancer have been intensively studied, it is becoming evident that a large proportion of cancer susceptibility cannot be attributed to variation in protein-coding sequences. This is highlighted by genome-wide association studies in cancer that reveal that more than 80% of cancer-associated SNPs occur in noncoding regions of the genome. In this review, we posit that a significant fraction of the genetic aetiology of cancer is exacted by noncoding regulatory sequences, particularly by long noncoding RNAs (lncRNAs). Recent studies indicate that several cancer risk loci are transcribed into lncRNAs and these transcripts play key roles in tumorigenesis. We discuss the epigenetic and other mechanisms through which lncRNAs function and how they contribute to each stage of cancer progression, understanding of which will be crucial for realising new opportunities in cancer diagnosis and treatment. Long noncoding RNAs play important roles in almost every aspect of cell biology from nuclear organisation and epigenetic regulation to post-transcriptional regulation and splicing, and we link these processes to the hallmarks and genetics of cancer. Finally, we highlight recent progress and future potential in the application of lncRNAs as therapeutic targets and diagnostic markers.

PMID: 23660942 [PubMed - indexed for MEDLINE]

Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates.

Methods. 2013 Sep 6;

Authors: Schapire AL, Bologna NG, Moro B, Zhai J, Meyers BC, Palatnik JF

Abstract
MicroRNAs (miRNAs) are small RNAs that derive from endogenous precursors harboring foldback structures. Plant miRNA precursors are quite variable in their size and shape. Still, the miRNA processing machinery, consisting of DICER-LIKE1 (DCL1) and accessory proteins recognize structural features on the precursors to cleave them at specific places releasing the mature miRNAs. The identification of miRNA processing intermediates in plants has mostly relied on a modified 5' RACE method, designed to detect the 5' end of uncapped RNAs. However, this method is time consuming and is, therefore, only practical for the analysis of a handful miRNAs. Here, we present a modification of this approach in order to perform genome-wide analysis of miRNA processing intermediates. Briefly, a reverse transcription is performed with a mixture of specific primers designed against all known miRNA precursors. miRNA processing intermediates are then specifically amplified to generate a library and subjected to deep sequencing. This method, called SPARE (Specific Parallel Amplification of 5' RNA Ends) allows the identification of processing intermediates for most of the Arabidopsis miRNAs. The results enable the determination of the DCL1 processing direction and the cleavage sites introduced by miRNA processing machinery in the precursors. The SPARE method can be easily adapted to detect miRNA-processing intermediates in other systems.

PMID: 24018204 [PubMed - as supplied by publisher]

The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

by Julia Salzman, Raymond E. Chen, Mari N. Olsen, Peter L. Wang, Patrick O. Brown

Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.

Ribozymes, including group I introns, have mostly been studied as free RNAs. This article shows that a group II intron within its cellular environment associates strongly with ribosomes. This association may protect the group II intron from degradative nucleases.

Toeprinting is a technique that was developed in the translation field to measure precisely the position of ribosomes (or ribosomal subunits) on mRNAs. It relies on the fact that reverse transcriptase is "stopped" when it encounters a blocking complex (ribonucleoprotein or protein) on the RNA. The length of the primer extension product produced when the RNA is occupied by such a complex compared to the full-length primer extension product indicates the 3' position of the complex of interest. Although primarily used in measuring ribosome occupancy and position, toeprinting can be used in a variety of other contexts. The procedure described here was developed to measure the position (and presence) of the exon junction complex deposited on mRNAs as a consequence of splicing. Toeprinting can, in principle, be used whenever the complex of interest is bound stably enough to withstand displacement of transcribing reverse transcriptase.

Ramin Shiekhattar. Enhancer RNAs (eRNAs) have emerged as an important component of transcriptional activation. In this issue, Mousavi et al. (2013) have uncovered a critical role for eRNAs in regulation of myogenic ....

Yang Zhang, Xiao-Ou Zhang, Tian Chen, Jian-Feng Xiang, Qing-Fei Yin, Yu-Hang Xing, Shanshan Zhu, Li Yang, Ling-Ling Chen. We describe the identification and characterization of circular intronic long noncoding RNAs in human cells, which accumulate owing to a failure in debranching. The formation of such circular intr....

Ivan Olovnikov, Ken Chan, Ravi Sachidanandam, Dianne K. Newman, Alexei A. Aravin. Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and ....

Cristina Migliore, Silvia Giordano.

Francesca C. Norris, Michael D. Wong, Nicholas D.E. Greene, Peter J. Scambler, Tom Weaver, Wolfgang J. Weninger, Timothy J. Mohun, R. Mark Henkelman, Mark F. Lythgoe.

Ulf Andersson Ørom, Ramin Shiekhattar. Enhancer-associated long noncoding RNAs act over long distances and across chromosomes to activate transcription at distal promoters. Here, we address the latest advances made toward understanding....

Bacterial argonaute samples the transcriptome to identify foreign DNA.

Mol Cell. 2013 Sep 12;51(5):594-605

Authors: Olovnikov I, Chan K, Sachidanandam R, Newman DK, Aravin AA

Abstract
Eukaryotic Argonautes bind small RNAs and use them as guides to find complementary RNA targets and induce gene silencing. Though homologs of eukaryotic Argonautes are present in many bacteria and archaea, their small RNA partners and functions are unknown. We found that the Argonaute of Rhodobacter sphaeroides (RsAgo) associates with 15-19 nt RNAs that correspond to the majority of transcripts. RsAgo also binds single-stranded 22-24 nt DNA molecules that are complementary to the small RNAs and enriched in sequences derived from exogenous plasmids as well as genome-encoded foreign nucleic acids such as transposons and phage genes. Expression of RsAgo in the heterologous E. coli system leads to formation of plasmid-derived small RNA and DNA and plasmid degradation. In a R. sphaeroides mutant lacking RsAgo, expression of plasmid-encoded genes is elevated. Our results indicate that RNAi-related processes found in eukaryotes are also conserved in bacteria and target foreign nucleic acids.

PMID: 24034694 [PubMed - in process]

Learning the language of post-transcriptional gene regulation.

Genome Biol. 2013 Aug 23;14(8):130

Authors: Gerstberger S, Hafner M, Tuschl T

Abstract
A large-scale RNA in vitro selection study systematically identified RNA recognition elements for 205 RNA-binding proteins belonging to families conserved in most eukaryotes.

PMID: 23998708 [PubMed - as supplied by publisher]

Digital imprinting of RNA recognition and processing on a self-assembled nucleic Acid matrix.

Sci Rep. 2013 Aug 30;3:2550

Authors: Redhu SK, Castronovo M, Nicholson AW

Abstract
The accelerating progress of research in nanomedicine and nanobiotechnology has included initiatives to develop highly-sensitive, high-throughput methods to detect biomarkers at the single-cell level. Current sensing approaches, however, typically involve integrative instrumentation that necessarily must balance sensitivity with rapidity in optimizing biomarker detection quality. We show here that laterally-confined, self-assembled monolayers of a short, double-stranded(ds)[RNA-DNA] chimera enable permanent digital detection of dsRNA-specific inputs. The action of ribonuclease III and the binding of an inactive, dsRNA-binding mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA], as measured by atomic force microscopy, provides a distinct digital output for each dsRNA-specific input. These findings provide the basis for developing imprinting-based bio-nanosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale.

PMID: 23989631 [PubMed - in process]