ArticleJournal of virology2006
Effects of random mutations in the human immunodeficiency virus type 1 transcriptional promoter on viral fitness in different host cell environments.
Article in Journal of virology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed, 55 citations in OpenAlex.
- Dynamic Pneumococcal Genetic Adaptations Support Bacterial Growth and Inflammation during Coinfection with Influenza.Infection and immunity · 2021Article
- Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions.Journal of medical virology · 2021Article
- Transposon Insertion Sequencing, a Global Measure of Gene Function.Annual review of genetics · 2020Review
- Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes.Nature communications · 2019Article
- On the stability of sequences inserted into viral genomes.Virus evolution · 2019Review
- Cat and Mouse: HIV Transcription in Latency, Immune Evasion and Cure/Remission Strategies.Viruses · 2019Review
- Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria.Cell reports · 2017Article
- Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome.PLoS pathogens · 2016Article
- Distribution of mutational fitness effects and of epistasis in the 5' untranslated region of a plant RNA virus.BMC evolutionary biology · 2015Article
- Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events.Journal of virology · 2014Article
- Variability in mutational fitness effects prevents full lethal transitions in large quasispecies populations.Scientific reports · 2014Article
- Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms.Nature reviews. Microbiology · 2013Review
- Extreme genetic fragility of the HIV-1 capsid.PLoS pathogens · 2013Article
- A fine scale phenotype-genotype virulence map of a bacterial pathogen.Genome research · 2012Article
- Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus.Heredity · 2012Article
- Control of virulence by small RNAs in Streptococcus pneumoniae.PLoS pathogens · 2012Article
- Effect of host species on the distribution of mutational fitness effects for an RNA virus.PLoS genetics · 2011Article
- Pervasive sign epistasis between conjugative plasmids and drug-resistance chromosomal mutations.PLoS genetics · 2011Article
- Fitness ranking of individual mutants drives patterns of epistatic interactions in HIV-1.PloS one · 2011Article
- Quasispecies spatial models for RNA viruses with different replication modes and infection strategies.PloS one · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A mutation's effect on fitness or phenotype may in part depend on the interaction of the mutation with the environment. The resulting phenotype or fitness is important, since it determines the adaptive potential of a species. To date, most studies have focused on alterations to protein-coding regions of the genome and their consequential fitness effects. Non-protein-coding regulatory regions have been largely neglected, although they make up a large and important part of an organism's genome. Here, we use human immunodeficiency virus type 1 as a model system to investigate fitness effects of random mutations in noncoding DNA-binding sites of the transcriptional promoter. We determined 242 fitness values for 35 viral promoter mutants with one, two, or three mutations across seven distinct cellular environments and identified that (i) all mutants have an effect in at least one cellular environment; (ii) fitness effects are highly dependent on the cellular environment; (iii) disadvantageous and advantageous mutations occur at high and similar frequencies; and (iv) epistatic effects of multiple mutations are rare. Our results underline the evolutionary potential of regulatory regions and indicate that DNA-binding sites evolve under strong selection, while at the same time, they are very plastic to environmental change.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.