Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization.

Abstract:

BACKGROUND:Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known about how the ultimate effectors of cell differentiation are selected and controlled. We addressed this question during late Drosophila embryogenesis, when the finely tuned expression of the TF Ovo/Shavenbaby (Svb) triggers the morphological differentiation of epidermal trichomes. RESULTS:We defined a sizeable set of genes downstream of Svb and used in vivo assays to delineate 14 enhancers driving their specific expression in trichome cells. Coupling computational modeling to functional dissection, we investigated the regulatory logic of these enhancers. Extending the repertoire of epidermal effectors using genome-wide approaches showed that the regulatory models learned from this first sample are representative of the whole set of trichome enhancers. These enhancers harbor remarkable features with respect to their functional architectures, including a weak or non-existent clustering of Svb binding sites. The in vivo function of each site relies on its intimate context, notably the flanking nucleotides. Two additional cis-regulatory motifs, present in a broad diversity of composition and positioning among trichome enhancers, critically contribute to enhancer activity. CONCLUSIONS:Our results show that Svb directly regulates a large set of terminal effectors of the remodeling of epidermal cells. Further, these data reveal that trichome formation is underpinned by unexpectedly diverse modes of regulation, providing fresh insights into the functional architecture of enhancers governing a terminal differentiation program.

journal_name

Genome Biol

journal_title

Genome biology

authors

Menoret D,Santolini M,Fernandes I,Spokony R,Zanet J,Gonzalez I,Latapie Y,Ferrer P,Rouault H,White KP,Besse P,Hakim V,Aerts S,Payre F,Plaza S

doi

10.1186/gb-2013-14-8-r86

subject

Has Abstract

pub_date

2013-08-23 00:00:00

pages

R86

issue

8

eissn

1474-7596

issn

1474-760X

pii

gb-2013-14-8-r86

journal_volume

14

pub_type

杂志文章
  • A fuzzy gene expression-based computational approach improves breast cancer prognostication.

    abstract::Early gene expression studies classified breast tumors into at least three clinically relevant subtypes. Although most current gene signatures are prognostic for estrogen receptor (ER) positive/human epidermal growth factor receptor 2 (HER2) negative breast cancers, few are informative for ER negative/HER2 negative an...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2010-11-2-r18

    authors: Haibe-Kains B,Desmedt C,Rothé F,Piccart M,Sotiriou C,Bontempi G

    更新日期:2010-01-01 00:00:00

  • Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver.

    abstract:BACKGROUND:RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2014-15-6-r79

    authors: Blanc V,Park E,Schaefer S,Miller M,Lin Y,Kennedy S,Billing AM,Ben Hamidane H,Graumann J,Mortazavi A,Nadeau JH,Davidson NO

    更新日期:2014-06-19 00:00:00

  • Nucleosome deposition and DNA methylation at coding region boundaries.

    abstract:BACKGROUND:Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation. RESULTS:Here we report a genome-wide observation of distinct peaks of nucleosomes and methylation at both ends of a pro...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-9-r89

    authors: Choi JK,Bae JB,Lyu J,Kim TY,Kim YJ

    更新日期:2009-01-01 00:00:00

  • Common gene expression strategies revealed by genome-wide analysis in yeast.

    abstract:BACKGROUND:Gene expression is a two-step synthesis process that ends with the necessary amount of each protein required to perform its function. Since the protein is the final product, the main focus of gene regulation should be centered on it. However, because mRNA is an intermediate step and the amounts of both mRNA ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-10-r222

    authors: García-Martínez J,González-Candelas F,Pérez-Ortín JE

    更新日期:2007-01-01 00:00:00

  • Dynamic systems.

    abstract::A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb-2012-13-1-312

    authors: Bakal C

    更新日期:2012-01-30 00:00:00

  • Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.

    abstract:BACKGROUND:In eukaryotic cells, oxidative phosphorylation (OXPHOS) uses the products of both nuclear and mitochondrial genes to generate cellular ATP. Interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-2-r11

    authors: Tripoli G,D'Elia D,Barsanti P,Caggese C

    更新日期:2005-01-01 00:00:00

  • Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments.

    abstract:BACKGROUND:Methods of microarray analysis that suit experimentalists using the technology are vital. Many methodologies discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly applied to multifactorial experimental design. Here we present a flexible, quantitative Bayesian framewor...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2002-3-12-research0071

    authors: Townsend JP,Hartl DL

    更新日期:2002-01-01 00:00:00

  • Alternative splicing links histone modifications to stem cell fate decision.

    abstract:BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1512-3

    authors: Xu Y,Zhao W,Olson SD,Prabhakara KS,Zhou X

    更新日期:2018-09-14 00:00:00

  • A versatile reporter system for CRISPR-mediated chromosomal rearrangements.

    abstract::Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous e...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-015-0680-7

    authors: Li Y,Park AI,Mou H,Colpan C,Bizhanova A,Akama-Garren E,Joshi N,Hendrickson EA,Feldser D,Yin H,Anderson DG,Jacks T,Weng Z,Xue W

    更新日期:2015-05-28 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

  • Investigating enhancer evolution with massively parallel reporter assays.

    abstract::A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-018-1502-5

    authors: Kwon SB,Ernst J

    更新日期:2018-08-14 00:00:00

  • Probing the yeast proteome for RNA-processing factors.

    abstract::A method has been developed to identify proteins required for the biogenesis of non-coding RNA in yeast, using a microarray to screen for aberrant patterns of RNA processing in mutant strains, and new proteins involved in the processing of ribosomal and non-coding RNAs have been found. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2003-4-10-229

    authors: Granneman S,Baserga SJ

    更新日期:2003-01-01 00:00:00

  • A computational investigation of kinetoplastid trans-splicing.

    abstract::Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, wi...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-11-r95

    authors: Gopal S,Awadalla S,Gaasterland T,Cross GA

    更新日期:2005-01-01 00:00:00

  • The circadian clock goes genomic.

    abstract::Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2013-14-6-208

    authors: Staiger D,Shin J,Johansson M,Davis SJ

    更新日期:2013-06-24 00:00:00

  • Classifying leukemia types with chromatin conformation data.

    abstract:BACKGROUND:Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. RESULTS:Here, we explore whether chromatin conformation can be used to classify human leu...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2014-15-4-r60

    authors: Rousseau M,Ferraiuolo MA,Crutchley JL,Wang XQ,Miura H,Blanchette M,Dostie J

    更新日期:2014-04-30 00:00:00

  • Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.

    abstract::Many essential transcription factors have conserved roles in regulating biological programs, yet their genomic occupancy can diverge significantly. A new study demonstrates that such variations are primarily due to cis-regulatory sequences, rather than differences between the regulators or nuclear environments. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2008-9-11-240

    authors: Zinzen RP,Furlong EE

    更新日期:2008-01-01 00:00:00

  • Mining physical protein-protein interactions from the literature.

    abstract:BACKGROUND:Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the yeast two-hybrid screening has produced an explosion in data relating to interactions. Since manual...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-s2-s12

    authors: Huang M,Ding S,Wang H,Zhu X

    更新日期:2008-01-01 00:00:00

  • The rate of the molecular clock and the cost of gratuitous protein synthesis.

    abstract:BACKGROUND:The nature of the protein molecular clock, the protein-specific rate of amino acid substitutions, is among the central questions of molecular evolution. Protein expression level is the dominant determinant of the clock rate in a number of organisms. It has been suggested that highly expressed proteins evolve...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2010-11-9-r98

    authors: Plata G,Gottesman ME,Vitkup D

    更新日期:2010-01-01 00:00:00

  • Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes.

    abstract:BACKGROUND:The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcri...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-12-r148

    authors: Schwalie PC,Ward MC,Cain CE,Faure AJ,Gilad Y,Odom DT,Flicek P

    更新日期:2013-12-31 00:00:00

  • Rapid gene isolation in barley and wheat by mutant chromosome sequencing.

    abstract::Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-016-1082-1

    authors: Sánchez-Martín J,Steuernagel B,Ghosh S,Herren G,Hurni S,Adamski N,Vrána J,Kubaláková M,Krattinger SG,Wicker T,Doležel J,Keller B,Wulff BB

    更新日期:2016-10-31 00:00:00

  • Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle.

    abstract:BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-6-r63

    authors: Jupe J,Stam R,Howden AJ,Morris JA,Zhang R,Hedley PE,Huitema E

    更新日期:2013-06-25 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

  • Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.

    abstract:BACKGROUND:The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial s...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-6-r103

    authors: Hogg JS,Hu FZ,Janto B,Boissy R,Hayes J,Keefe R,Post JC,Ehrlich GD

    更新日期:2007-01-01 00:00:00

  • Decontamination of ambient RNA in single-cell RNA-seq with DecontX.

    abstract::Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the cell suspension can be aberrantly counted along with a cell's native mRNA and result in cross-contamination of transcripts between different cell populations. DecontX is a n...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-1950-6

    authors: Yang S,Corbett SE,Koga Y,Wang Z,Johnson WE,Yajima M,Campbell JD

    更新日期:2020-03-05 00:00:00

  • Identification of cyanobacterial non-coding RNAs by comparative genome analysis.

    abstract:BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-9-r73

    authors: Axmann IM,Kensche P,Vogel J,Kohl S,Herzel H,Hess WR

    更新日期:2005-01-01 00:00:00

  • Is mouse embryonic stem cell technology obsolete?

    abstract::Injection of recombinant Cas9 protein and synthetic guide RNAs into mouse zygotes has been shown to facilitate gene disruption and knock-ins using the CRISPR system. These technologies may soon displace genetic modification using embryonic stem cells. ...

    journal_title:Genome biology

    pub_type: 评论,杂志文章

    doi:10.1186/s13059-015-0673-6

    authors: Skarnes WC

    更新日期:2015-05-27 00:00:00

  • Fine-tuning sugar content in strawberry.

    abstract::Fine-tuning quantitative traits for continuous subtle phenotypes is highly advantageous. We engineer the highly conserved upstream open reading frame (uORF) of FvebZIPs1.1 in strawberry (Fragaria vesca), using base editor A3A-PBE. Seven novel alleles are generated. Sugar content of the homozygous T1 mutant lines is 33...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02146-5

    authors: Xing S,Chen K,Zhu H,Zhang R,Zhang H,Li B,Gao C

    更新日期:2020-09-03 00:00:00

  • Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex.

    abstract:BACKGROUND:Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1701-8

    authors: Liu Z,Ran Y,Tao C,Li S,Chen J,Yang E

    更新日期:2019-05-20 00:00:00

  • Copy number variation goes clinical.

    abstract::A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...

    journal_title:Genome biology

    pub_type:

    doi:10.1186/gb-2009-10-1-301

    authors: Le Caignec C,Redon R

    更新日期:2009-01-01 00:00:00

  • iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations.

    abstract:BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-6-r69

    authors: Henry CS,Zinner JF,Cohoon MP,Stevens RL

    更新日期:2009-01-01 00:00:00