A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza a viruses.

Abstract:

BACKGROUND:RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA editing in animals. The roles of RNA editing events have been implicated in important biological pathways. Cellular RNA editing activity in response to influenza A virus infection has not been fully characterized in human and avian hosts. This study was designed as a big data analysis to investigate the role and response of RNA editing in epithelial cells during the course of infection with various subtypes of influenza A viruses. RESULTS:Using a bioinformatics pipeline modified from our previous study, we characterized the profiles of A-to-I and C-to-U RNA editing events in human epithelial cells during the course of influenza A virus infection. Our results revealed a striking diversity of A-to-I RNA editing activities in human epithelial cells in responses to different subtypes of influenza A viruses. The infection of H1N1 and H3N2 significantly up-regulated normalized A-to-I RNA editing levels in human epithelial cells, whereas that of H5N1 did not change it and H7N9 infection significantly down-regulated normalized A-to-I editing level in A549 cells. Next, the expression levels of ADAR and APOBEC enzymes responsible for A-to-I and C-to-U RNA editing during the course of virus infection were examined. The increase of A-to-I RNA editing activities in infections with some influenza A viruses (H1N1 and H3N2) is linked to the up-regulation of ADAR1 but not ADAR2. Further, the pattern recognition receptors of human epithelial cells infected with H1N1, H3N2, H5N1 and H7N9 were examined. Variable responsive changes in gene expression were observed with RIG-I like receptors and Toll like receptors. Finally, the effect of influenza A virus infection on cellular RNA editing activity was also analyzed in avian hosts. CONCLUSION:This work represents the first comprehensive study of cellular RNA editing activity in response to different influenza A virus infections in human and avian hosts, highlighting the critical role of RNA editing in innate immune response and the pathogenicity of different subtypes of influenza A viruses.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Cao Y,Cao R,Huang Y,Zhou H,Liu Y,Li X,Zhong W,Hao P

doi

10.1186/s12864-017-4330-1

subject

Has Abstract

pub_date

2018-01-19 00:00:00

pages

925

issue

Suppl 1

issn

1471-2164

pii

10.1186/s12864-017-4330-1

journal_volume

19

pub_type

杂志文章
  • ACEP: improving antimicrobial peptides recognition through automatic feature fusion and amino acid embedding.

    abstract:BACKGROUND:Antimicrobial resistance is one of our most serious health threats. Antimicrobial peptides (AMPs), effecter molecules of innate immune system, can defend host organisms against microbes and most have shown a lowered likelihood for bacteria to form resistance compared to many conventional drugs. Thus, AMPs ar...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06978-0

    authors: Fu H,Cao Z,Li M,Wang S

    更新日期:2020-08-28 00:00:00

  • Transcriptome profiling provides insights into dormancy release during cold storage of Lilium pumilum.

    abstract:BACKGROUND:Bulbs of the ornamental flower Lilium pumilum enter a period of dormancy after flowering in spring, and require exposure to cold for a period of time in order to release dormancy. Previous studies focused mainly on anatomical, physiological and biochemical changes during dormancy release. There are no dorman...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4536-x

    authors: Wang W,Su X,Tian Z,Liu Y,Zhou Y,He M

    更新日期:2018-03-14 00:00:00

  • P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads.

    abstract:BACKGROUND:Obtaining complete gene structures is one major goal of genome assembly. Some gene regions are fragmented in low quality and high-quality assemblies. Therefore, new approaches are needed to recover gene regions. Genomes are widely transcribed, generating messenger and non-coding RNAs. These widespread transc...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4567-3

    authors: Zhu BH,Xiao J,Xue W,Xu GC,Sun MY,Li JT

    更新日期:2018-03-02 00:00:00

  • A new approach for efficient genotype imputation using information from relatives.

    abstract:BACKGROUND:Genotype imputation can help reduce genotyping costs particularly for implementation of genomic selection. In applications entailing large populations, recovering the genotypes of untyped loci using information from reference individuals that were genotyped with a higher density panel is computationally chal...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-478

    authors: Sargolzaei M,Chesnais JP,Schenkel FS

    更新日期:2014-06-17 00:00:00

  • Improvement of the clinical applicability of the Genomic Grade Index through a qRT-PCR test performed on frozen and formalin-fixed paraffin-embedded tissues.

    abstract:BACKGROUND:Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be re...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-424

    authors: Toussaint J,Sieuwerts AM,Haibe-Kains B,Desmedt C,Rouas G,Harris AL,Larsimont D,Piccart M,Foekens JA,Durbecq V,Sotiriou C

    更新日期:2009-09-10 00:00:00

  • A hybrid expectation maximisation and MCMC sampling algorithm to implement Bayesian mixture model based genomic prediction and QTL mapping.

    abstract:BACKGROUND:Bayesian mixture models in which the effects of SNP are assumed to come from normal distributions with different variances are attractive for simultaneous genomic prediction and QTL mapping. These models are usually implemented with Monte Carlo Markov Chain (MCMC) sampling, which requires long compute times ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-3082-7

    authors: Wang T,Chen YP,Bowman PJ,Goddard ME,Hayes BJ

    更新日期:2016-09-21 00:00:00

  • Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality.

    abstract:BACKGROUND:Infectious salmon anemia virus (ISAV) causes a multisystemic disease responsible for severe losses in salmon aquaculture. Better understanding of factors that explain variations in resistance between individuals and families is essential for development of strategies for disease control. To approach this, we...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-179

    authors: Jørgensen SM,Afanasyev S,Krasnov A

    更新日期:2008-04-18 00:00:00

  • How many human genes can be defined as housekeeping with current expression data?

    abstract:BACKGROUND:Housekeeping (HK) genes are ubiquitously expressed in all tissue/cell types and constitute a basal transcriptome for the maintenance of basic cellular functions. Partitioning transcriptomes into HK and tissue-specific (TS) genes relatively is fundamental for studying gene expression and cellular differentiat...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-172

    authors: Zhu J,He F,Song S,Wang J,Yu J

    更新日期:2008-04-16 00:00:00

  • Transcriptomic analyses of Aedes aegypti cultured cells and ex vivo midguts in response to an excess or deficiency of heme: a quest for transcriptionally-regulated heme transporters.

    abstract:BACKGROUND:Aedes aegypti is the principle vector of many arboviruses, including dengue virus and Zika virus, which are transmitted when an infected female mosquito takes a blood meal in order to initiate vitellogenesis. During blood digestion, ~ 10 mM heme-iron is ingested into the midgut lumen. While heme acts as both...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06981-5

    authors: Eggleston H,Adelman ZN

    更新日期:2020-08-31 00:00:00

  • Integrative analysis of transcriptomic data related to the liver of laying hens: from physiological basics to newly identified functions.

    abstract:BACKGROUND:At sexual maturity, the liver of laying hens undergoes many metabolic changes to support vitellogenesis. In published transcriptomic approaches, hundreds of genes were reported to be overexpressed in laying hens and functional gene annotation using gene ontology tools have essentially revealed an enrichment ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6185-0

    authors: Gloux A,Duclos MJ,Brionne A,Bourin M,Nys Y,Réhault-Godbert S

    更新日期:2019-11-07 00:00:00

  • Comparison of feature selection and classification for MALDI-MS data.

    abstract:INTRODUCTION:In the classification of Mass Spectrometry (MS) proteomics data, peak detection, feature selection, and learning classifiers are critical to classification accuracy. To better understand which methods are more accurate when classifying data, some publicly available peak detection algorithms for Matrix assi...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-S1-S3

    authors: Liu Q,Sung AH,Qiao M,Chen Z,Yang JY,Yang MQ,Huang X,Deng Y

    更新日期:2009-07-07 00:00:00

  • Role of chromatin and transcriptional co-regulators in mediating p63-genome interactions in keratinocytes.

    abstract:BACKGROUND:The Transcription Factor (TF) p63 is a master regulator of epidermal development and differentiation as evident from the remarkable skin phenotype of p63 mouse knockouts. Furthermore, ectopic expression of p63 alone is sufficient to convert simple epithelium into stratified epithelial tissues in vivo and p63...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1042

    authors: Sethi I,Sinha S,Buck MJ

    更新日期:2014-11-29 00:00:00

  • Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens.

    abstract:BACKGROUND:Duplication, followed by fixation or random loss of novel genes, contributes to genome evolution. Particular outcomes of duplication events are possibly associated with pathogenic life histories in fungi. To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, de...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-147

    authors: Powell AJ,Conant GC,Brown DE,Carbone I,Dean RA

    更新日期:2008-03-28 00:00:00

  • Comprehensive analysis of genetic and evolutionary features of the hepatitis E virus.

    abstract:BACKGROUND:The hepatitis E virus (HEV) is the causative pathogen of hepatitis E, a global public health concern. HEV comprises 8 genotypes with a wide host range and geographic distribution. This study aims to determine the genetic factors influencing the molecular adaptive changes of HEV open reading frames (ORFs) and...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6100-8

    authors: Baha S,Behloul N,Liu Z,Wei W,Shi R,Meng J

    更新日期:2019-10-29 00:00:00

  • Large scale genome-wide association and LDLA mapping study identifies QTLs for boar taint and related sex steroids.

    abstract:BACKGROUND:Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androstenone is a steroid produced in the testis in parallel with biosynthesis of other sex steroids like tes...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-362

    authors: Grindflek E,Lien S,Hamland H,Hansen MH,Kent M,van Son M,Meuwissen TH

    更新日期:2011-07-13 00:00:00

  • Analysis of salivary transcripts and antigens of the sand fly Phlebotomus arabicus.

    abstract:BACKGROUND:Sand fly saliva plays an important role in blood feeding and Leishmania transmission as it was shown to increase parasite virulence. On the other hand, immunity to salivary components impedes the establishment of infection. Therefore, it is most desirable to gain a deeper insight into the composition of sali...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-282

    authors: Hostomská J,Volfová V,Mu J,Garfield M,Rohousová I,Volf P,Valenzuela JG,Jochim RC

    更新日期:2009-06-25 00:00:00

  • Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum.

    abstract:BACKGROUND:Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis-associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1517-1

    authors: Guo Y,Tang K,Rowe LA,Li N,Roellig DM,Knipe K,Frace M,Yang C,Feng Y,Xiao L

    更新日期:2015-04-18 00:00:00

  • Inferring linkage disequilibrium from non-random samples.

    abstract:BACKGROUND:Linkage disequilibrium (LD) plays a fundamental role in population genetics and in the current surge of studies to screen for subtle genetic variants affecting complex traits. Methods widely implemented in LD analyses require samples to be randomly collected, which, however, are usually ignored and thus rais...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-328

    authors: Wang M,Jia T,Jiang N,Wang L,Hu X,Luo Z

    更新日期:2010-05-26 00:00:00

  • Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.

    abstract:BACKGROUND:Development of the soil amoeba Dictyostelium discoideum is triggered by starvation. When placed on a solid substrate, the starving solitary amoebae cease growth, communicate via extracellular cAMP, aggregate by tens of thousands and develop into multicellular organisms. Early phases of the developmental prog...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1491-7

    authors: Rosengarten RD,Santhanam B,Fuller D,Katoh-Kurasawa M,Loomis WF,Zupan B,Shaulsky G

    更新日期:2015-04-13 00:00:00

  • Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus.

    abstract:BACKGROUND:Leaf blight caused by Calonectria spp. is one of the most destructive diseases to affect Eucalyptus nurseries and plantations. These pathogens mainly attack Eucalyptus, a tree with a diversity of secondary metabolites employed as defense-related phytoalexins. To unravel the fungal adaptive mechanisms to vari...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4739-1

    authors: Ye X,Zhong Z,Liu H,Lin L,Guo M,Guo W,Wang Z,Zhang Q,Feng L,Lu G,Zhang F,Chen Q

    更新日期:2018-05-10 00:00:00

  • Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

    abstract:BACKGROUND:New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-501

    authors: Stubben CJ,Duffield ML,Cooper IA,Ford DC,Gans JD,Karlyshev AV,Lingard B,Oyston PC,de Rochefort A,Song J,Wren BW,Titball RW,Wolinsky M

    更新日期:2009-10-29 00:00:00

  • Development of a relevant strategy using de novo transcriptome assembly method for transcriptome comparisons between Muscovy and common duck species and their reciprocal inter-specific mule and hinny hybrids fed ad libitum and overfed.

    abstract:BACKGROUND:Common Pekin and Muscovy ducks and their intergeneric hinny and mule hybrids have different abilities for fatty liver production. RNA-Seq analyses from the liver of these different genetic types fed ad libitum or overfed would help to identify genes with different response to overfeeding between them. Howeve...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-07099-4

    authors: Liu X,Hérault F,Diot C,Corre E

    更新日期:2020-10-02 00:00:00

  • Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer.

    abstract:BACKGROUND:Genome-scale metabolic models (GSMM) integrating transcriptomics have been widely used to study cancer metabolism. This integration is achieved through logical rules that describe the association between genes, proteins, and reactions (GPRs). However, current gene-to-reaction formulation lacks the stoichiome...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5979-4

    authors: Marín de Mas I,Torrents L,Bedia C,Nielsen LK,Cascante M,Tauler R

    更新日期:2019-08-15 00:00:00

  • Genomic comparison of serogroups O159 and O170 with other Vibrio cholerae serogroups.

    abstract:BACKGROUND:Of the hundreds of Vibrio cholerae serogroups, O1 and O139 are the main epidemic-causing ones. Although non-O1/non-O139 serogroups rarely cause epidemics, the possibility exists for strains within them to have pathogenic potential. RESULTS:We selected 25 representative strains within 16 V. cholerae serogrou...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5603-7

    authors: Li Z,Lu X,Wang D,Liang WL,Zhang J,Li J,Xu J,Pang B,Kan B

    更新日期:2019-03-25 00:00:00

  • Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability.

    abstract:BACKGROUND:Intellectual Disability (ID) is among the most common global disorders, yet etiology is unknown in ~30% of patients despite clinical assessment. Whole genome sequencing (WGS) is able to interrogate the entire genome, providing potential to diagnose idiopathic patients. METHODS:We conducted WGS on eight chil...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3671-0

    authors: Zahir FR,Mwenifumbo JC,Chun HE,Lim EL,Van Karnebeek CDM,Couse M,Mungall KL,Lee L,Makela N,Armstrong L,Boerkoel CF,Langlois SL,McGillivray BM,Jones SJM,Friedman JM,Marra MA

    更新日期:2017-05-24 00:00:00

  • PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities.

    abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, mos...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-5497-4

    authors: Pyfrom SC,Luo H,Payton JE

    更新日期:2019-02-15 00:00:00

  • Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations.

    abstract:BACKGROUND:Ancestry informative markers (AIMs) are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs), the materials ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-346

    authors: Yang HC,Wang PL,Lin CW,Chen CH,Chen CH

    更新日期:2012-07-28 00:00:00

  • Tracing the genetic history of the 'Cañaris' from Ecuador and Peru using uniparental DNA markers.

    abstract:BACKGROUND:According to history, in the pre-Hispanic period, during the conquest and Inka expansion in Ecuador, many Andean families of the Cañar region would have been displaced to several places of Tawantinsuyu, including Kañaris, a Quechua-speaking community located at the highlands of the Province of Ferreñafe, Lam...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06834-1

    authors: Sandoval JR,Lacerda DR,Jota MMS,Robles-Ruiz P,Danos P,Paz-Y-Miño C,Wells S,Santos FR,Fujita R

    更新日期:2020-09-10 00:00:00

  • Genes to predict VO2max trainability: a systematic review.

    abstract:BACKGROUND:Cardiorespiratory fitness (VO2max) is an excellent predictor of chronic disease morbidity and mortality risk. Guidelines recommend individuals undertake exercise training to improve VO2max for chronic disease reduction. However, there are large inter-individual differences between exercise training responses...

    journal_title:BMC genomics

    pub_type: 杂志文章,评审

    doi:10.1186/s12864-017-4192-6

    authors: Williams CJ,Williams MG,Eynon N,Ashton KJ,Little JP,Wisloff U,Coombes JS

    更新日期:2017-11-14 00:00:00

  • The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.

    abstract:BACKGROUND:Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-686

    authors: Natali L,Cossu RM,Barghini E,Giordani T,Buti M,Mascagni F,Morgante M,Gill N,Kane NC,Rieseberg L,Cavallini A

    更新日期:2013-10-06 00:00:00