Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication

Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame

(2017) Jules Deforges et al.   NUCLEIC ACIDS RESEARCH

HIV-1 tolerates changes in A-count in a small segment of the pol gene

(2017) Bep Klaver et al.   Retrovirology

Synonymous Codons: Choose Wisely for Expression

(2017) Christina E. Brule et al.   TRENDS IN GENETICS

Sequence-Specific Sensing of Nucleic Acids

(2017) Nicolas Vabret et al.   TRENDS IN IMMUNOLOGY

The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression

(2017) Mishi Kaushal Wasson et al.   Scientific Reports

Source of CpG Depletion in the HIV-1 Genome

(2016) Hamid Alinejad-Rokny et al.   MOLECULAR BIOLOGY AND EVOLUTION

NMR Studies of the Structure and Function of the HIV-1 5′-Leader

(2016) Sarah Keane et al.   Viruses-Basel

Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias

(2016) Dusan Kunec et al.   Cell Reports

Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection

(2016) Eleanor Gaunt et al.   eLife

HIV-1 assembly, release and maturation

(2015) Eric O. Freed   NATURE REVIEWS MICROBIOLOGY

Distinguishing the immunostimulatory properties of noncoding RNAs expressed in cancer cells

(2015) Antoine Tanne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats

(2015) Scott Sherrill-Mix et al.   Retrovirology

Translational Control of the HIV Unspliced Genomic RNA

(2015) Bárbara Rojas-Araya et al.   Viruses-Basel

Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes

(2015) Christopher A. Lavender et al.   PLoS Computational Biology

Global Changes in the RNA Binding Specificity of HIV-1 Gag Regulate Virion Genesis

(2014) Sebla B. Kutluay et al.   CELL

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

(2014) Nathan A Siegfried et al.   NATURE METHODS

The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication

(2014) Nicky J. Atkinson et al.   NUCLEIC ACIDS RESEARCH

Life of psi: How full-length HIV-1 RNAs become packaged genomes in the viral particles

(2014) Malika Kuzembayeva et al.   VIROLOGY

Microbial Sensing by Toll-Like Receptors and Intracellular Nucleic Acid Sensors

(2014) Surya Pandey et al.   Cold Spring Harbor Perspectives in Biology

Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection

(2014) Eun-Young Kim et al.   PLoS Pathogens

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

(2014) Fiona Tulloch et al.   eLife

Synonymous site conservation in the HIV-1 genome

(2013) Itay Mayrose et al.   BMC EVOLUTIONARY BIOLOGY

Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla –selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses

(2013) Peter Simmonds et al.   BMC GENOMICS

Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture

(2013) Gloria Martrus et al.   Retrovirology

Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs

(2013) Elizabeth Pollom et al.   PLoS Pathogens

Posttranscriptional regulation of retroviral gene expression: primary RNA transcripts play three roles as pre-mRNA, mRNA, and genomic RNA

(2013) Jason LeBlanc et al.   Wiley Interdisciplinary Reviews-RNA

Human Immunodeficiency Virus Reverse Transcriptase: 25 Years of Research, Drug Discovery, and Promise

(2012) Stuart F. J. Le Grice   JOURNAL OF BIOLOGICAL CHEMISTRY

The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus

(2012) Antoinette C van der Kuyl et al.   Retrovirology

Opening of the TAR hairpin in the HIV-1 genome causes aberrant RNA dimerization and packaging

(2012) Atze T Das et al.   Retrovirology

The HIV-1 major splice donor D1 is activated by splicing enhancer elements within the leader region and the p17-inhibitory sequence

(2012) Corinna Asang et al.   VIROLOGY

Structural Determinants and Mechanism of HIV-1 Genome Packaging

(2011) Kun Lu et al.   JOURNAL OF MOLECULAR BIOLOGY

Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints

(2011) Joke Snoeck et al.   Retrovirology

NMR Detection of Structures in the HIV-1 5'-Leader RNA That Regulate Genome Packaging

(2011) K. Lu et al.   SCIENCE

Alternative splicing: regulation of HIV-1 multiplication as a target for therapeutic action

(2010) Jamal Tazi et al.   FEBS Journal

RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1

(2010) E. Simon-Loriere et al.   JOURNAL OF VIROLOGY

SRp40 and SRp55 Promote the Translation of Unspliced Human Immunodeficiency Virus Type 1 RNA

(2010) C. M. Swanson et al.   JOURNAL OF VIROLOGY

Interplay between RNA Structure and Protein Evolution in HIV-1

(2010) R. Sanjuan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3

(2010) Nicolas Locker et al.   NUCLEIC ACIDS RESEARCH

Circularization of the HIV-1 genome facilitates strand transfer during reverse transcription

(2010) N. Beerens et al.   RNA

Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons

(2009) C. C. Burns et al.   JOURNAL OF VIROLOGY

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

(2009) Joseph M. Watts et al.   NATURE

A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA

(2009) Laure Weill et al.   NUCLEIC ACIDS RESEARCH

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

(2008) C. P. Keating et al.   NUCLEIC ACIDS RESEARCH

Quantitative Effect of Suboptimal Codon Usage on Translational Efficiency of mRNA Encoding HIV-1 gag in Intact T Cells

(2008) Kholiswa C. Ngumbela et al.   PLoS One

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

(2008) Nobubelo K Ngandu et al.   Virology Journal

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

Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses

(2008) Benjamin D. Greenbaum et al.   PLoS Pathogens