Identification of sensory hair-cell transcripts by thiouracil-tagging in zebrafish.


BACKGROUND:Sensory hair cells are exquisitely sensitive to mechanical stimuli and as such, are prone to damage and apoptosis during dissections or in vitro manipulations. Thiouracil (TU)-tagging is a noninvasive method to label cell type-specific transcripts in an intact organism, thereby meeting the challenge of how to analyze gene expression in hair cells without the need to sort cells. We adapted TU-tagging to zebrafish to identify novel transcripts expressed in the sensory hair cells of the developing acoustico-lateralis organs. METHODS:We created a transgenic line of zebrafish expressing the T.gondii uracil phospho-ribosyltransferase (UPRT) enzyme specifically in the hair cells of the inner ear and lateral line organ. RNA was labeled by exposing 3 days post-fertilization (dpf) UPRT transgenic larvae to 2.5 mM 4-thiouracil (4TU) for 15 hours. Following total RNA isolation, poly(A) mRNA enrichment, and purification of TU-tagged RNA, deep sequencing was performed on the input and TU-tagged RNA samples. RESULTS:Analysis of the RNA sequencing data revealed the expression of 28 transcripts that were significantly enriched (adjusted p-value < 0.05) in the UPRT TU-tagged RNA relative to the input sample. Of the 25 TU-tagged transcripts with mammalian homologs, the expression of 18 had not been previously demonstrated in zebrafish hair cells. The hair cell-restricted expression for 17 of these transcripts was confirmed by whole mount mRNA in situ hybridization in 3 dpf larvae. CONCLUSIONS:The hair cell-restricted pattern of expression of these genes offers insight into the biology of this receptor cell type and may serve as useful markers to study the development and function of sensory hair cells. In addition, our study demonstrates the utility of TU-tagging to study nascent transcripts in specific cell types that are relatively rare in the context of the whole zebrafish larvae.


BMC Genomics


BMC genomics


Erickson T,Nicolson T




Has Abstract


2015-10-23 00:00:00










  • Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil.

    abstract:BACKGROUND:Sclerotinia Stem Rot (SSR), caused by the fungal pathogen Sclerotinia sclerotiorum, is ubiquitous in cooler climates where soybean crops are grown. Breeding for resistance to SSR remains challenging in crops like soybean, where no single gene provides strong resistance, but instead, multiple genes work toget...

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    pub_type: 杂志文章


    authors: Wei W,Mesquita ACO,Figueiró AA,Wu X,Manjunatha S,Wickland DP,Hudson ME,Juliatti FC,Clough SJ

    更新日期:2017-11-07 00:00:00

  • Comparative transcriptomics reveals suppressed expression of genes related to auxin and the cell cycle contributes to the resistance of cucumber against Meloidogyne incognita.

    abstract:BACKGROUND:Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infection, the exact regulation mechanism of M. incognita-resistance in cucumber remains elusive. Ver...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang X,Cheng C,Zhang K,Tian Z,Xu J,Yang S,Lou Q,Li J,Chen JF

    更新日期:2018-08-03 00:00:00

  • A comparison of the transcriptome of Drosophila melanogaster in response to entomopathogenic fungus, ionizing radiation, starvation and cold shock.

    abstract:BACKGROUND:The molecular mechanisms that determine the organism's response to a variety of doses and modalities of stress factors are not well understood. RESULTS:We studied effects of ionizing radiation (144, 360 and 864 Gy), entomopathogenic fungus (10 and 100 CFU), starvation (16 h), and cold shock (+4, 0 and -4°C)...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Moskalev A,Zhikrivetskaya S,Krasnov G,Shaposhnikov M,Proshkina E,Borisoglebsky D,Danilov A,Peregudova D,Sharapova I,Dobrovolskaya E,Solovev I,Zemskaya N,Shilova L,Snezhkina A,Kudryavtseva A

    更新日期:2015-01-01 00:00:00

  • The transcriptome of the invasive eel swimbladder nematode parasite Anguillicola crassus.

    abstract:BACKGROUND:Anguillicola crassus is an economically and ecologically important parasitic nematode of eels. The native range of A. crassus is in East Asia, where it infects Anguilla japonica, the Japanese eel. A. crassus was introduced into European eels, Anguilla anguilla, 30 years ago. The parasite is more pathogenic i...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Heitlinger E,Bridgett S,Montazam A,Taraschewski H,Blaxter M

    更新日期:2013-02-08 00:00:00

  • Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

    abstract:BACKGROUND:Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.)...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Straub SC,Fishbein M,Livshultz T,Foster Z,Parks M,Weitemier K,Cronn RC,Liston A

    更新日期:2011-05-04 00:00:00

  • Genomics of sex allocation in the parasitoid wasp Nasonia vitripennis.

    abstract:BACKGROUND:Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, perhaps the b...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pannebakker BA,Cook N,van den Heuvel J,van de Zande L,Shuker DM

    更新日期:2020-07-20 00:00:00

  • Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes.

    abstract:BACKGROUND:Gibberella ear rot (GER) is one of the most economically important fungal diseases of maize in the temperate zone due to moldy grain contaminated with health threatening mycotoxins. To develop resistant genotypes and control the disease, understanding the host-pathogen interaction is essential. RESULTS:RNA-...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kebede AZ,Johnston A,Schneiderman D,Bosnich W,Harris LJ

    更新日期:2018-02-09 00:00:00

  • Spread of avian pathogenic Escherichia coli ST117 O78:H4 in Nordic broiler production.

    abstract:BACKGROUND:Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in gener...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ronco T,Stegger M,Olsen RH,Sekse C,Nordstoga AB,Pohjanvirta T,Lilje B,Lyhs U,Andersen PS,Pedersen K

    更新日期:2017-01-03 00:00:00

  • Identification of candidate genes for human pituitary development by EST analysis.

    abstract:BACKGROUND:The pituitary is a critical neuroendocrine gland that is comprised of five hormone-secreting cell types, which develops in tandem during the embryonic stage. Some essential genes have been identified in the early stage of adenohypophysial development, such as PITX1, FGF8, BMP4 and SF-1. However, it is likely...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ma Y,Qi X,Du J,Song S,Feng D,Qi J,Zhu Z,Zhang X,Xiao H,Han Z,Hao X

    更新日期:2009-03-15 00:00:00

  • Comparative mitochondrial proteomic, physiological, biochemical and ultrastructural profiling reveal factors underpinning salt tolerance in tetraploid black locust (Robinia pseudoacacia L.).

    abstract:BACKGROUND:Polyploidy is an important phenomenon in plants because of its roles in agricultural and forestry production as well as in plant tolerance to environmental stresses. Tetraploid black locust (Robinia pseudoacacia L.) is a polyploid plant and a pioneer tree species due to its wide ranging adaptability to adver...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Luo Q,Peng M,Zhang X,Lei P,Ji X,Chow W,Meng F,Sun G

    更新日期:2017-08-22 00:00:00

  • Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

    abstract:BACKGROUND:Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomi...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Butler JB,Vaillancourt RE,Potts BM,Lee DJ,King GJ,Baten A,Shepherd M,Freeman JS

    更新日期:2017-05-22 00:00:00

  • Cell population-specific expression analysis of human cerebellum.

    abstract:BACKGROUND:Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kuhn A,Kumar A,Beilina A,Dillman A,Cookson MR,Singleton AB

    更新日期:2012-11-12 00:00:00

  • Recurrence-associated pathways in hepatitis B virus-positive hepatocellular carcinoma.

    abstract:BACKGROUND:Despite the recent identification of several prognostic gene signatures, the lack of common genes among experimental cohorts has posed a considerable challenge in uncovering the molecular basis underlying hepatocellular carcinoma (HCC) recurrence for application in clinical purposes. To overcome the limitati...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kim BY,Choi DW,Woo SR,Park ER,Lee JG,Kim SH,Koo I,Park SH,Han CJ,Kim SB,Yeom YI,Yang SJ,Yu A,Lee JW,Jang JJ,Cho MH,Jeon WK,Park YN,Suh KS,Lee KH

    更新日期:2015-04-10 00:00:00

  • Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides.

    abstract:BACKGROUND:Vinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: McMurdie PJ,Hug LA,Edwards EA,Holmes S,Spormann AM

    更新日期:2011-06-02 00:00:00

  • Alpha tubulin genes from Leishmania braziliensis: genomic organization, gene structure and insights on their expression.

    abstract:BACKGROUND:Alpha tubulin is a fundamental component of the cytoskeleton which is responsible for cell shape and is involved in cell division, ciliary and flagellar motility and intracellular transport. Alpha tubulin gene expression varies according to the morphological changes suffered by Leishmania in its life cycle. ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ramírez CA,Requena JM,Puerta CJ

    更新日期:2013-07-06 00:00:00

  • The genetic organisation of prokaryotic two-component system signalling pathways.

    abstract:BACKGROUND:Two-component systems (TCSs) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. TCS gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and m...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Williams RH,Whitworth DE

    更新日期:2010-12-20 00:00:00

  • Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.

    abstract:BACKGROUND:Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes der...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Park KD,Park J,Ko J,Kim BC,Kim HS,Ahn K,Do KT,Choi H,Kim HM,Song S,Lee S,Jho S,Kong HS,Yang YM,Jhun BH,Kim C,Kim TH,Hwang S,Bhak J,Lee HK,Cho BW

    更新日期:2012-09-12 00:00:00

  • Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis.

    abstract:BACKGROUND:Flammulina filiformis (previously known as Asian F. velutipes) is a popular commercial edible mushroom. Many bioactive compounds with medicinal effects, such as polysaccharides and sesquiterpenoids, have been isolated and identified from F. filiformis, but their biosynthesis and regulation at the molecular l...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen J,Li JM,Tang YJ,Ma K,Li B,Zeng X,Liu XB,Li Y,Yang ZL,Xu WN,Xie BG,Liu HW,Guo SX

    更新日期:2020-10-17 00:00:00

  • Comparative transcriptomic analysis unveils interactions between the regulatory CarS protein and light response in Fusarium.

    abstract:BACKGROUND:The orange pigmentation of the agar cultures of many Fusarium species is due to the production of carotenoids, terpenoid pigments whose synthesis is stimulated by light. The genes of the carotenoid pathway and their regulation have been investigated in detail in Fusarium fujikuroi. In this and other Fusarium...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ruger-Herreros M,Parra-Rivero O,Pardo-Medina J,Romero-Campero FJ,Limón MC,Avalos J

    更新日期:2019-01-21 00:00:00

  • Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds.

    abstract:BACKGROUND:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Huang X,Otecko NO,Peng M,Weng Z,Li W,Chen J,Zhong M,Zhong F,Jin S,Geng Z,Luo W,He D,Ma C,Han J,Ommeh SC,Zhang Y,Zhang X,Du B

    更新日期:2020-04-20 00:00:00

  • Comparative genomics and concerted evolution of beta-tubulin paralogs in Leishmania spp.

    abstract:BACKGROUND:Tubulin isotypes and expression patterns are highly regulated in diverse organisms. The genome sequence of the protozoan parasite Leishmania major contains three distinct beta-tubulin loci. To investigate the diversity of beta-tubulin genes, we have compared the published genome sequence to draft genome sequ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Jackson AP,Vaughan S,Gull K

    更新日期:2006-06-06 00:00:00

  • Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury.

    abstract:BACKGROUND:Spinal cord injury leads to neurological dysfunctions affecting the motor, sensory as well as the autonomic systems. Increased excitability of motor neurons has been implicated in injury-induced spasticity, where the reappearance of self-sustained plateau potentials in the absence of modulatory inputs from t...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ryge J,Winther O,Wienecke J,Sandelin A,Westerdahl AC,Hultborn H,Kiehn O

    更新日期:2010-06-09 00:00:00

  • A Caenorhabditis motif compendium for studying transcriptional gene regulation.

    abstract:BACKGROUND:Controlling gene expression is fundamental to biological complexity. The nematode Caenorhabditis elegans is an important model for studying principles of gene regulation in multi-cellular organisms. A comprehensive parts list of putative regulatory motifs was yet missing for this model system. In this study,...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dieterich C,Sommer RJ

    更新日期:2008-01-23 00:00:00

  • Genomic analysis of nontypeable pneumococci causing invasive pneumococcal disease in South Africa, 2003-2013.

    abstract:BACKGROUND:The capsular polysaccharide is the principal virulence factor of Streptococcus pneumoniae and a target for current pneumococcal vaccines. However, some pathogenic pneumococci are serologically nontypeable [nontypeable pneumococci (NTPn)]. Due to their relative rarity, NTPn are poorly characterized, and, as s...

    journal_title:BMC genomics

    pub_type: 历史文章,杂志文章


    authors: Mohale T,Wolter N,Allam M,Ndlangisa K,Crowther-Gibson P,du Plessis M,von Gottberg A

    更新日期:2016-06-22 00:00:00

  • High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species.

    abstract:BACKGROUND:Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hyb...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dawson DA,Ball AD,Spurgin LG,Martín-Gálvez D,Stewart IR,Horsburgh GJ,Potter J,Molina-Morales M,Bicknell AW,Preston SA,Ekblom R,Slate J,Burke T

    更新日期:2013-03-15 00:00:00

  • Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species.

    abstract:BACKGROUND:Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high throughput sequencing is a relatively low cost means of expression profiling with deep coverage. Howe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Voelckel C,Gruenheit N,Biggs P,Deusch O,Lockhart P

    更新日期:2012-07-19 00:00:00

  • "Integrative genomic analysis of the bioprospection of regulators and accessory enzymes associated with cellulose degradation in a filamentous fungus (Trichoderma harzianum)".

    abstract:BACKGROUND:Unveiling fungal genome structure and function reveals the potential biotechnological use of fungi. Trichoderma harzianum is a powerful CAZyme-producing fungus. We studied the genomic regions in T. harzianum IOC3844 containing CAZyme genes, transcription factors and transporters. RESULTS:We used bioinformat...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Ferreira Filho JA,Horta MAC,Dos Santos CA,Almeida DA,Murad NF,Mendes JS,Sforça DA,Silva CBC,Crucello A,de Souza AP

    更新日期:2020-11-02 00:00:00

  • OMGene: mutual improvement of gene models through optimisation of evolutionary conservation.

    abstract:BACKGROUND:The accurate determination of the genomic coordinates for a given gene - its gene model - is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, frequentl...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Dunne MP,Kelly S

    更新日期:2018-04-27 00:00:00

  • Altered microRNA expression in frontotemporal lobar degeneration with TDP-43 pathology caused by progranulin mutations.

    abstract:BACKGROUND:Frontotemporal lobar degeneration (FTLD) is a progressive neurodegenerative disorder that can be triggered through genetic or sporadic mechanisms. MicroRNAs (miRNAs) have become a major therapeutic focus as their pervasive expression and powerful regulatory roles in disease pathogenesis become increasingly a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kocerha J,Kouri N,Baker M,Finch N,DeJesus-Hernandez M,Gonzalez J,Chidamparam K,Josephs KA,Boeve BF,Graff-Radford NR,Crook J,Dickson DW,Rademakers R

    更新日期:2011-10-27 00:00:00

  • Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet.

    abstract:BACKGROUND:Efforts towards utilisation of diets without fish meal (FM) or fish oil (FO) in finfish aquaculture have been being made for more than two decades. Metabolic responses to substitution of fishery products have been shown to impact growth performance and immune system of fish as well as their subsequent nutrit...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Geay F,Ferraresso S,Zambonino-Infante JL,Bargelloni L,Quentel C,Vandeputte M,Kaushik S,Cahu CL,Mazurais D

    更新日期:2011-10-23 00:00:00