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Adaptation of A-to-I RNA editing in Drosophila.
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5365144
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5 April 2020
title
Adaptation of A-to-I RNA editing in Drosophila
(English)
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5365144
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5 April 2020
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Drosophila
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Shengqian Dou
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2
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5365144
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5 April 2020
Jian Lu
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5
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5365144
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5 April 2020
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Yuange Duan
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1
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5 April 2020
Shiqi Luo
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3
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5 April 2020
Hong Zhang
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4
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5 April 2020
publication date
10 March 2017
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5365144
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5 April 2020
published in
PLOS Genetics
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5 April 2020
volume
13
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5 April 2020
issue
3
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5 April 2020
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e1006648
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5 April 2020
copyright license
Creative Commons Attribution 4.0 International
start time
10 March 2017
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April 2022 Public Data File from Crossref
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0 references
describes a project that uses
edgeR
object named as
edgeR
1 reference
stated in
CZ Software Mentions: A large dataset of software mentions in the biomedical literature
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Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing.
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The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection
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Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications
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Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster
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Genetic mapping uncovers cis-regulatory landscape of RNA editing
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Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates.
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The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing
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30 September 2017
Dynamic response of RNA editing to temperature in Drosophila.
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In search of beneficial coding RNA editing
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Profiling the RNA editomes of wild-type C. elegans and ADAR mutants
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Estimating genotype error rates from high-coverage next-generation sequence data
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Robustly detecting differential expression in RNA sequencing data using observation weights
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RNA editome in rhesus macaque shaped by purifying selection
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Human coding RNA editing is generally nonadaptive
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30 September 2017
Identification of evolutionarily meaningful information within the mammalian RNA editing landscape
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A biochemical landscape of A-to-I RNA editing in the human brain transcriptome.
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30 September 2017
Mammalian conserved ADAR targets comprise only a small fragment of the human editosome
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30 September 2017
A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes
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30 September 2017
Deciphering the functions and regulation of brain-enriched A-to-I RNA editing
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30 September 2017
RADAR: a rigorously annotated database of A-to-I RNA editing
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30 September 2017
PAMLX: a graphical user interface for PAML.
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30 September 2017
Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly
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30 September 2017
Identifying RNA editing sites using RNA sequencing data alone
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The ADAR protein family
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Adar is essential for optimal presynaptic function
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30 September 2017
STAR: ultrafast universal RNA-seq aligner
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The genomic landscape and evolutionary resolution of antagonistic pleiotropy in yeast
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A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
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Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila
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Auto-regulatory RNA editing fine-tunes mRNA re-coding and complex behaviour in Drosophila
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High levels of RNA-editing site conservation amongst 15 laboratory mouse strains
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Systematic identification of edited microRNAs in the human brain
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".
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30 September 2017
Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
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30 September 2017
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome
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30 September 2017
RNA editing underlies temperature adaptation in K+ channels from polar octopuses
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30 September 2017
Very few RNA and DNA sequence differences in the human transcriptome
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30 September 2017
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
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30 September 2017
Editing of neurotransmitter receptor and ion channel RNAs in the nervous system
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30 September 2017
Widespread RNA and DNA sequence differences in the human transcriptome.
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30 September 2017
The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms.
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30 September 2017
A-to-I RNA editing is induced upon hypoxia
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30 September 2017
The developmental transcriptome of Drosophila melanogaster
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30 September 2017
Engineered alterations in RNA editing modulate complex behavior in Drosophila: regulatory diversity of adenosine deaminase acting on RNA (ADAR) targets
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30 September 2017
One hundred years of pleiotropy: a retrospective
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30 September 2017
The heat shock response: life on the verge of death
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30 September 2017
Adenosine-to-inosine RNA editing
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30 September 2017
Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats
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30 September 2017
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
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30 September 2017
Evolution of the mutation rate
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30 September 2017
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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30 September 2017
Functions and regulation of RNA editing by ADAR deaminases
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30 September 2017
Rate, molecular spectrum, and consequences of human mutation
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30 September 2017
Adenosine deamination in human transcripts generates novel microRNA binding sites
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30 September 2017
RNA editing: a driving force for adaptive evolution?
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30 September 2017
Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing
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30 September 2017
Fast and accurate short read alignment with Burrows-Wheeler transform
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30 September 2017
Large-scale mRNA sequencing determines global regulation of RNA editing during brain development.
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30 September 2017
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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
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30 September 2017
Mapping and quantifying mammalian transcriptomes by RNA-Seq
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30 September 2017
RNA editing in regulating gene expression in the brain
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30 September 2017
RNA editing and alternative splicing of the insect nAChR subunit alpha6 transcript: evolutionary conservation, divergence and regulation
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30 September 2017
Editing modifies the GABA(A) receptor subunit alpha3
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30 September 2017
RNA-editing-mediated exon evolution
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
Hypothesis: RNA editing of microRNA target sites in humans?
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
Editor meets silencer: crosstalk between RNA editing and RNA interference
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
RNA editing by ADAR2 is metabolically regulated in pancreatic islets and beta-cells.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Developmentally regulated, combinatorial RNA processing modulates AMPA receptor biogenesis.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
Toward a molecular understanding of pleiotropy
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Evolutionarily conserved human targets of adenosine to inosine RNA editing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Evidence that RNA editing modulates splice site selection in the 5-HT2C receptor gene
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Synthetic polynucleotides and the amino acid code. VI.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
The human genome browser at UCSC
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
RNA editing by adenosine deaminases that act on RNA
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
The many roles of an RNA editor.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Mutation in pre-mRNA adenosine deaminase markedly attenuates neuronal tolerance to O2 deprivation in Drosophila melanogaster
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
The evolution of mutation rates: separating causes from consequences
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
dADAR, a Drosophila double-stranded RNA-specific adenosine deaminase is highly developmentally regulated and is itself a target for RNA editing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
RNA editing of the Drosophila para Na(+) channel transcript. Evolutionary conservation and developmental regulation
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
EMBOSS: the European Molecular Biology Open Software Suite
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
The genome sequence of Drosophila melanogaster
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Regulation of alternative splicing by RNA editing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
Inosine exists in mRNA at tissue-specific levels and is most abundant in brain mRNA
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
RNA editing of AMPA receptor subunit GluR-B: a base-paired intron-exon structure determines position and efficiency
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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30 September 2017
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
RNA editing in brain controls a determinant of ion flow in glutamate-gated channels
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
30 September 2017
The C-terminal domain of RNA Pol II helps ensure that editing precedes splicing of the GluR-B transcript
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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29 June 2018
Tuning of RNA editing by ADAR is required in Drosophila
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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29 June 2018
Molecular determinants and guided evolution of species-specific RNA editing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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29 June 2018
Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
29 June 2018
A-to-I pre-mRNA editing in Drosophila is primarily involved in adult nervous system function and integrity
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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29 June 2018
Genome-wide analysis of A-to-I RNA editing by single-molecule sequencing in Drosophila.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
22 September 2018
Reduction of RNA A-to-I editing in Drosophila acclimated to heat shock.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
22 September 2018
Comment on "Widespread RNA and DNA sequence differences in the human transcriptome".
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
22 September 2018
A-to-I editing sites are a genomically encoded G: implications for the evolutionary significance and identification of novel editing sites
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
22 September 2018
Early life stress alters adult serotonin 2C receptor pre-mRNA editing and expression of the alpha subunit of the heterotrimeric G-protein G q.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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22 September 2018
How stress and fluoxetine modulate serotonin 2C receptor pre-mRNA editing.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
retrieved
22 September 2018
A standardized nomenclature for adenosine deaminases that act on RNA.
1 reference
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5365144
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22 September 2018
Pleiotropy, Natural Selection, and the Evolution of Senescence
1 reference
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https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1006648
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21 January 2018
Differential impact of simultaneous migration on coevolving hosts and parasites
1 reference
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https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1006648
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21 January 2018
The Relative Rates of Evolution of Sex Chromosomes and Autosomes
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1006648
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21 January 2018
ViennaRNA Package 2.0
1 reference
stated in
Crossref
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https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1006648
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21 January 2018
BLAST+: architecture and applications
1 reference
stated in
Crossref
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https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1006648
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21 January 2018
How epigenetic mutations can affect genetic evolution: model and mechanism
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/28282384
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Comment on "Widespread RNA and DNA sequence differences in the human transcriptome"
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/28282384
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1371/JOURNAL.PGEN.1006648
1 reference
stated in
Europe PubMed Central
PMC publication ID
5365144
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28282384%20AND%20SRC:MED&resulttype=core&format=json
retrieved
5 April 2020
PMC publication ID
5365144
1 reference
stated in
Europe PubMed Central
PMC publication ID
5365144
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28282384%20AND%20SRC:MED&resulttype=core&format=json
retrieved
5 April 2020
PubMed publication ID
28282384
1 reference
stated in
Europe PubMed Central
PMC publication ID
5365144
reference URL
https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28282384%20AND%20SRC:MED&resulttype=core&format=json
retrieved
5 April 2020
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