The R-spondin protein family.

Abstract:

:The four vertebrate R-spondin proteins are secreted agonists of the canonical Wnt/β-catenin signaling pathway. These proteins are approximately 35 kDa, and are characterized by two amino-terminal furin-like repeats, which are necessary and sufficient for Wnt signal potentiation, and a thrombospondin domain situated more towards the carboxyl terminus that can bind matrix glycosaminoglycans and/or proteoglycans. Although R-spondins are unable to initiate Wnt signaling, they can potently enhance responses to low-dose Wnt proteins. In humans, rare disruptions of the gene encoding R-spondin1 cause a syndrome of XX sex reversal (phenotypic male), palmoplantar keratosis (a thickening of the palms and soles caused by excess keratin formation) and predisposition to squamous cell carcinoma of the skin. Mutations in the gene encoding R-spondin4 cause anonychia (absence or hypoplasia of nails on fingers and toes). Recently, leucine-rich repeat-containing G-protein-coupled receptor (Lgr)4, Lgr5 and Lgr6, three closely related orphans of the leucine-rich repeat family of G-protein-coupled receptors, have been identified as receptors for R-spondins. Lgr5 and Lgr6 are markers for adult stem cells. Because R-spondins are potent stimulators of adult stem cell proliferation in vivo and in vitro, these findings might guide the therapeutic use of R-spondins in regenerative medicine.

journal_name

Genome Biol

journal_title

Genome biology

authors

de Lau WB,Snel B,Clevers HC

doi

10.1186/gb-2012-13-3-242

subject

Has Abstract

pub_date

2012-01-01 00:00:00

pages

242

issue

3

eissn

1474-7596

issn

1474-760X

pii

gb-2012-13-3-242

journal_volume

13

pub_type

杂志文章,评审
  • mirMark: a site-level and UTR-level classifier for miRNA target prediction.

    abstract::MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0500-5

    authors: Menor M,Ching T,Zhu X,Garmire D,Garmire LX

    更新日期:2014-01-01 00:00:00

  • Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshii OT3.

    abstract:BACKGROUND:Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-12-r98

    authors: Usui K,Katayama S,Kanamori-Katayama M,Ogawa C,Kai C,Okada M,Kawai J,Arakawa T,Carninci P,Itoh M,Takio K,Miyano M,Kidoaki S,Matsuda T,Hayashizaki Y,Suzuki H

    更新日期:2005-01-01 00:00:00

  • Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae.

    abstract:BACKGROUND:Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processe...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-5-r85

    authors: Oh Y,Donofrio N,Pan H,Coughlan S,Brown DE,Meng S,Mitchell T,Dean RA

    更新日期:2008-01-01 00:00:00

  • quantro: a data-driven approach to guide the choice of an appropriate normalization method.

    abstract::Normalization is an essential step in the analysis of high-throughput data. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation. However, these methods rely on the assumption that observed global changes across samples are due to unwanted...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0679-0

    authors: Hicks SC,Irizarry RA

    更新日期:2015-06-04 00:00:00

  • External signals shape the epigenome.

    abstract::A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3-STAT6 pathway, which causes dendritic-cell-specific DNA demethylation. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-0884-5

    authors: Lennartsson A

    更新日期:2016-02-01 00:00:00

  • Using ontologies to describe mouse phenotypes.

    abstract::The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sou...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2004-6-1-r8

    authors: Gkoutos GV,Green EC,Mallon AM,Hancock JM,Davidson D

    更新日期:2005-01-01 00:00:00

  • Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps.

    abstract:BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-12-r183

    authors: Desjardins CA,Gundersen-Rindal DE,Hostetler JB,Tallon LJ,Fadrosh DW,Fuester RW,Pedroni MJ,Haas BJ,Schatz MC,Jones KM,Crabtree J,Forberger H,Nene V

    更新日期:2008-01-01 00:00:00

  • Statistical tests for differential expression in cDNA microarray experiments.

    abstract::Extracting biological information from microarray data requires appropriate statistical methods. The simplest statistical method for detecting differential expression is the t test, which can be used to compare two conditions when there is replication of samples. With more than two conditions, analysis of variance (AN...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2003-4-4-210

    authors: Cui X,Churchill GA

    更新日期:2003-01-01 00:00:00

  • THoR: a tool for domain discovery and curation of multiple alignments.

    abstract::We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family. The entire process is designed for use via a web-browser, with simple...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-8-r52

    authors: Dickens NJ,Ponting CP

    更新日期:2003-01-01 00:00:00

  • Dramatic changes in transcription factor binding over evolutionary time.

    abstract::A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章

    doi:10.1186/gb-2010-11-6-122

    authors: Weirauch MT,Hughes TR

    更新日期:2010-01-01 00:00:00

  • Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites.

    abstract:BACKGROUND:Malaria is a one of the most important infectious diseases and is caused by parasitic protozoa of the genus Plasmodium. Previously, quantitative characterization of the P. falciparum transcriptome demonstrated that the strictly controlled progression of these parasites through their intra-erythrocytic develo...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-12-r177

    authors: Foth BJ,Zhang N,Mok S,Preiser PR,Bozdech Z

    更新日期:2008-01-01 00:00:00

  • Characterization of background noise in capture-based targeted sequencing data.

    abstract:BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1275-2

    authors: Park G,Park JK,Shin SH,Jeon HJ,Kim NKD,Kim YJ,Shin HT,Lee E,Lee KH,Son DS,Park WY,Park D

    更新日期:2017-07-21 00:00:00

  • Avianbase: a community resource for bird genomics.

    abstract::Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released ...

    journal_title:Genome biology

    pub_type: 信件

    doi:10.1186/s13059-015-0588-2

    authors: Eöry L,Gilbert MT,Li C,Li B,Archibald A,Aken BL,Zhang G,Jarvis E,Flicek P,Burt DW

    更新日期:2015-01-29 00:00:00

  • Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi.

    abstract::Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA pathway. Will these findings limit the therapeutic use of such hairpins? ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2006-7-8-231

    authors: Snøve O Jr,Rossi JJ

    更新日期:2006-01-01 00:00:00

  • The continuum of causality in human genetic disorders.

    abstract::Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare, common, benign, or deleterious based on their population frequencies. The availability of exome and genome da...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-1107-9

    authors: Katsanis N

    更新日期:2016-11-17 00:00:00

  • Dynamic diversity of the tryptophan pathway in chlamydiae: reductive evolution and a novel operon for tryptophan recapture.

    abstract:BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-9-research0051

    authors: Xie G,Bonner CA,Jensen RA

    更新日期:2002-08-29 00:00:00

  • To be or not to be a piRNA: genomic origin and processing of piRNAs.

    abstract::Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb4154

    authors: Le Thomas A,Tóth KF,Aravin AA

    更新日期:2014-01-27 00:00:00

  • Personalized and graph genomes reveal missing signal in epigenomic data.

    abstract:BACKGROUND:Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02038-8

    authors: Groza C,Kwan T,Soranzo N,Pastinen T,Bourque G

    更新日期:2020-05-25 00:00:00

  • A CRISPR design for next-generation antimicrobials.

    abstract::Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章

    doi:10.1186/s13059-014-0516-x

    authors: Beisel CL,Gomaa AA,Barrangou R

    更新日期:2014-11-08 00:00:00

  • Comparative and functional genomics reveals genetic diversity and determinants of host specificity among reference strains and a large collection of Chinese isolates of the phytopathogen Xanthomonas campestris pv. campestris.

    abstract:BACKGROUND:Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS:We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated t...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-10-r218

    authors: He YQ,Zhang L,Jiang BL,Zhang ZC,Xu RQ,Tang DJ,Qin J,Jiang W,Zhang X,Liao J,Cao JR,Zhang SS,Wei ML,Liang XX,Lu GT,Feng JX,Chen B,Cheng J,Tang JL

    更新日期:2007-01-01 00:00:00

  • Pigs taking wing with transposons and recombinases.

    abstract::Swine production has been an important part of our lives since the late Mesolithic or early Neolithic periods, and ranks number one in world meat production. Pig production also contributes to high-value-added medical markets in the form of pharmaceuticals, heart valves, and surgical materials. Genetic engineering, in...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2007-8-s1-s13

    authors: Clark KJ,Carlson DF,Fahrenkrug SC

    更新日期:2007-01-01 00:00:00

  • Molecular orchestration of the hepatic circadian symphony.

    abstract::The circadian clock determines the rhythmic expression of many different genes throughout a 24-hour period. A recent study investigating the circadian regulation of liver proteins reveals multiple levels of regulation, including transcriptional, post-transcriptional and post-translational mechanisms. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2006-7-9-234

    authors: Albrecht U

    更新日期:2006-01-01 00:00:00

  • Epigenetic prediction of complex traits and death.

    abstract:BACKGROUND:Genome-wide DNA methylation (DNAm) profiling has allowed for the development of molecular predictors for a multitude of traits and diseases. Such predictors may be more accurate than the self-reported phenotypes and could have clinical applications. RESULTS:Here, penalized regression models are used to deve...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1514-1

    authors: McCartney DL,Hillary RF,Stevenson AJ,Ritchie SJ,Walker RM,Zhang Q,Morris SW,Bermingham ML,Campbell A,Murray AD,Whalley HC,Gale CR,Porteous DJ,Haley CS,McRae AF,Wray NR,Visscher PM,McIntosh AM,Evans KL,Deary IJ,Mar

    更新日期:2018-09-27 00:00:00

  • Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

    abstract:BACKGROUND:A large fraction of the human genome is attributable to L1 retrotransposon sequences. Not only do L1s themselves make up a significant portion of the genome, but L1-encoded proteins are thought to be responsible for the transposition of other repetitive elements and processed pseudogenes. In addition, L1s ca...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-5-r30

    authors: Szak ST,Pickeral OK,Landsman D,Boeke JD

    更新日期:2003-01-01 00:00:00

  • In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants.

    abstract:BACKGROUND:mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA pro...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02236-4

    authors: Liu Z,Liu Q,Yang X,Zhang Y,Norris M,Chen X,Cheema J,Zhang H,Ding Y

    更新日期:2021-01-04 00:00:00

  • Butterfly gene flow goes berserk.

    abstract::A new study shows that genomic introgression between two Heliconius butterfly species is not solely confined to color pattern loci. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章

    doi:10.1186/s13059-016-0898-z

    authors: Ffrench-Constant RH

    更新日期:2016-02-27 00:00:00

  • Wheat chromatin architecture is organized in genome territories and transcription factories.

    abstract:BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-01998-1

    authors: Concia L,Veluchamy A,Ramirez-Prado JS,Martin-Ramirez A,Huang Y,Perez M,Domenichini S,Rodriguez Granados NY,Kim S,Blein T,Duncan S,Pichot C,Manza-Mianza D,Juery C,Paux E,Moore G,Hirt H,Bergounioux C,Crespi M,Mahfouz

    更新日期:2020-04-29 00:00:00

  • A comparison of programmed cell death between species.

    abstract::Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2000-1-3-reviews0003

    authors: Tittel JN,Steller H

    更新日期:2000-01-01 00:00:00

  • Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat.

    abstract:BACKGROUND:Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS:By investigating the whole-genome resequencing data of 93 ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1744-x

    authors: Cheng H,Liu J,Wen J,Nie X,Xu L,Chen N,Li Z,Wang Q,Zheng Z,Li M,Cui L,Liu Z,Bian J,Wang Z,Xu S,Yang Q,Appels R,Han D,Song W,Sun Q,Jiang Y

    更新日期:2019-07-12 00:00:00

  • Species-wide distribution of highly polymorphic minisatellite markers suggests past and present genetic exchanges among house mouse subspecies.

    abstract:BACKGROUND:Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in house mouse subspecies. Internal structures of alleles were determined by minisatellite variant repeat mapping PCR to produce maps of interming...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-5-r80

    authors: Bonhomme F,Rivals E,Orth A,Grant GR,Jeffreys AJ,Bois PR

    更新日期:2007-01-01 00:00:00