Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins

Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation

(2016) Sarah Nainar et al.   ACS Chemical Biology

pRNAm-PC: Predicting N6-methyladenosine sites in RNA sequences via physical–chemical properties

(2016) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

(2016) Alexander Borodavka et al.   BIOPHYSICAL JOURNAL

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database

(2016) Zhichao Miao et al.   NUCLEIC ACIDS RESEARCH

SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features

(2016) Yuan Zhou et al.   NUCLEIC ACIDS RESEARCH

SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across theXistlncRNA in living cells

(2016) Matthew J. Smola et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression

(2016) Hironori Nishitsuji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long noncoding RNAs in viral infections

(2016) Puri Fortes et al.   VIRUS RESEARCH

Detection of RNA–Protein Interactions in Living Cells with SHAPE

(2015) Matthew J. Smola et al.   BIOCHEMISTRY

Viral noncoding RNAs: more surprises

(2015) Kazimierz T. Tycowski et al.   GENES & DEVELOPMENT

Whole-Genome Sequencing of Kaposi's Sarcoma-Associated Herpesvirus from Zambian Kaposi's Sarcoma Biopsy Specimens Reveals Unique Viral Diversity

(2015) Landon N. Olp et al.   JOURNAL OF VIROLOGY

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis

(2015) Matthew J Smola et al.   Nature Protocols

The 3D structure of Kaposi sarcoma herpesvirus LANA C-terminal domain bound to DNA

(2015) Jan Hellert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

KSHV ORF57, a Protein of Many Faces

(2015) Vladimir Majerciak et al.   Viruses-Basel

HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism

(2015) Emi Sei et al.   PLoS Pathogens

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Describing the Structural Diversity within an RNA’s Ensemble

(2014) Joshua Martin   Entropy

Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli

(2014) Katsutoshi Imamura et al.   MOLECULAR CELL

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix

(2014) Jessica A Brown et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

KSHV LANA—The Master Regulator of KSHV Latency

(2014) Timsy Uppal et al.   Viruses-Basel

PAN’s Labyrinth: Molecular Biology of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) PAN RNA, a Multifunctional Long Noncoding RNA

(2014) Cyprian Rossetto et al.   Viruses-Basel

Heterogeneity and Breadth of Host Antibody Response to KSHV Infection Demonstrated by Systematic Analysis of the KSHV Proteome

(2014) Nazzarena Labo et al.   PLoS Pathogens

KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features

(2014) Carolina Arias et al.   PLoS Pathogens

Long noncoding RNAs in innate and adaptive immunity

(2013) Katherine A. Fitzgerald et al.   CURRENT OPINION IN IMMUNOLOGY

Phosphorylation of Kaposi's Sarcoma-Associated Herpesvirus Processivity Factor ORF59 by a Viral Kinase Modulates Its Ability To Associate with RTA and oriLyt

(2013) M. E. McDowell et al.   JOURNAL OF VIROLOGY

A Lytic Viral Long Noncoding RNA Modulates the Function of a Latent Protein

(2013) M. Campbell et al.   JOURNAL OF VIROLOGY

Regulation of Viral and Cellular Gene Expression by Kaposi's Sarcoma-Associated Herpesvirus Polyadenylated Nuclear RNA

(2013) C. C. Rossetto et al.   JOURNAL OF VIROLOGY

The RNAsnp web server: predicting SNP effects on local RNA secondary structure

(2013) Radhakrishnan Sabarinathan et al.   NUCLEIC ACIDS RESEARCH

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots

(2013) C. E. Hajdin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7)

(2013) R. Turner et al.   RNA

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

(2013) N. Liu et al.   RNA

Cis and Trans Acting Factors Involved in Human Cytomegalovirus Experimental and Natural Latent Infection of CD14 (+) Monocytes and CD34 (+) Cells

(2013) Cyprian C. Rossetto et al.   PLoS Pathogens

Stability of a Long Noncoding Viral RNA Depends on a 9-Nt Core Element at the RNA 5' End to Interact with Viral ORF57 and Cellular PABPC1

(2012) Maria J. Massimelli et al.   International Journal of Biological Sciences

MicroRNAs and Unusual Small RNAs Discovered in Kaposi's Sarcoma-Associated Herpesvirus Virions

(2012) X. Lin et al.   JOURNAL OF VIROLOGY

Interplay between Polyadenylate-Binding Protein 1 and Kaposi's Sarcoma-Associated Herpesvirus ORF57 in Accumulation of Polyadenylated Nuclear RNA, a Viral Long Noncoding RNA

(2012) M. J. Massimelli et al.   JOURNAL OF VIROLOGY

Latent Kaposi's Sarcoma-Associated Herpesvirus Infection of Monocytes Downregulates Expression of Adaptive Immune Response Costimulatory Receptors and Proinflammatory Cytokines

(2012) S. M. Gregory et al.   JOURNAL OF VIROLOGY

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

KSHV PAN RNA Associates with Demethylases UTX and JMJD3 to Activate Lytic Replication through a Physical Interaction with the Virus Genome

(2012) Cyprian C. Rossetto et al.   PLoS Pathogens

Kaposi's Sarcoma-Associated Herpesvirus Noncoding Polyadenylated Nuclear RNA Interacts with Virus- and Host Cell-Encoded Proteins and Suppresses Expression of Genes Involved in Immune Modulation

(2011) C. C. Rossetto et al.   JOURNAL OF VIROLOGY

Kaposi's Sarcoma-Associated Herpesvirus ORF57 Promotes Escape of Viral and Human Interleukin-6 from MicroRNA-Mediated Suppression

(2011) J.-G. Kang et al.   JOURNAL OF VIROLOGY

Delineation of a core RNA element required for Kaposi's sarcoma-associated herpesvirus ORF57 binding and activity

(2011) Emi Sei et al.   VIROLOGY

A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression

(2011) Sumit Borah et al.   PLoS Pathogens

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

(2010) R. M. Mitton-Fry et al.   SCIENCE

Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein Binds and Protects a Nuclear Noncoding RNA from Cellular RNA Decay Pathways

(2010) Brooke B. Sahin et al.   PLoS Pathogens

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

Selective Uptake of Small RNA Molecules in the Virion of Murine Gammaherpesvirus 68

(2008) A. R. Cliffe et al.   JOURNAL OF VIROLOGY

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

(2008) Kevin A Wilkinson et al.   PLOS BIOLOGY