Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

scientific article published on January 2006

Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage is …
instance of (P31):
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1045362207
P356DOI10.1186/GB-2006-7-7-R56
P932PMC publication ID1779573
P698PubMed publication ID16859531
P5875ResearchGate publication ID6925618

P50authorElia StupkaQ30089912
Remo SangesQ39597138
P2093author name stringMaria D'Amato
Pamela Claudiani
Eva Kalmar
Ferenc Muller
P2860cites workHighly conserved non-coding sequences are associated with vertebrate developmentQ21092819
Fast and sensitive multiple alignment of large genomic sequencesQ21284293
Ultraconserved Elements in the Human GenomeQ22065813
Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripesQ22065831
Gene ontology: tool for the unification of biologyQ23781406
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomesQ24534193
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammalsQ24630840
Improved tools for biological sequence comparisonQ24652199
EMBL Nucleotide Sequence Database: developments in 2005Q25256713
Ensembl 2006.Q25256782
Basic local alignment search toolQ25938991
DAVID: Database for Annotation, Visualization, and Integrated DiscoveryQ27499374
Prediction of complete gene structures in human genomic DNAQ27860780
Stages of embryonic development of the zebrafishQ27860947
New human and mouse microRNA genes found by homology searchQ28301238
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNAQ28775786
Aligning multiple genomic sequences with the threaded blockset alignerQ29547490
A greedy algorithm for aligning DNA sequencesQ29547622
dbEST--database for "expressed sequence tags"Q29547785
VISTA : visualizing global DNA sequence alignments of arbitrary lengthQ29614270
GOstat: find statistically overrepresented Gene Ontologies within a group of genesQ29618721
Activator effect of coinjected enhancers on the muscle-specific expression of promoters in zebrafish embryos.Q52193396
Numerous potentially functional but non-genic conserved sequences on human chromosome 21Q57161881
Migration of promoter elements between genes: a role in transcriptional regulation and evolutionQ68317014
A gene expression screen in zebrafish embryogenesis.Q30772929
Long-range interactions between three transcriptional enhancers, active Vkappa gene promoters, and a 3' boundary sequence spanning 46 kilobasesQ33724374
Effects of stuffer DNA on transgene expression from helper-dependent adenovirus vectors.Q33818929
Evidence for stabilizing selection in a eukaryotic enhancer element.Q33890254
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequencesQ33910867
The RNA polymerase II core promoterQ33965089
Evolution of transcriptional regulationQ34026971
Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.Q34085680
Glocal alignment: finding rearrangements during alignmentQ34213425
Differential induction of four msx homeobox genes during fin development and regeneration in zebrafishQ34311992
In vivo characterization of a vertebrate ultraconserved enhancerQ34417560
Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripesQ34646248
Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elementsQ34732972
GALA, a database for genomic sequence alignments and annotationsQ34994777
A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regionsQ35076931
Comparative genomics at the vertebrate extremesQ35778678
The spatial organization of the genome in mammalian cellsQ35804631
Conserved non-genic sequences - an unexpected feature of mammalian genomesQ36045183
The identification and functional characterisation of conserved regulatory elements in developmental genesQ36090792
Conserved sequences and the evolution of gene regulatory signalsQ36268623
A floor plate enhancer of the zebrafish netrin1 gene requires Cyclops (Nodal) signalling and the winged helix transcription factor FoxA2.Q38360484
The Zebrafish Information Network (ZFIN): the zebrafish model organism databaseQ38523014
Faithful expression of a tagged Fugu WT1 protein from a genomic transgene in zebrafish: efficient splicing of pufferfish genes in zebrafish but not miceQ39758710
Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis.Q40451574
Intronic sequences flanking alternatively spliced exons are conserved between human and mouseQ40830190
Every enhancer works with every promoter for all the combinations tested: could new regulatory pathways evolve by enhancer shuffling?Q41690369
A novel approach to identifying regulatory motifs in distantly related genomesQ42059367
Fog1 is required for cardiac looping in zebrafishQ42940077
The discovery, positioning and verification of a set of transcription-associated motifs in vertebratesQ43251324
TBP is not universally required for zygotic RNA polymerase II transcription in zebrafishQ43543191
Inducible expression of an hsp68-lacZ hybrid gene in transgenic miceQ44484787
Going the distance: a current view of enhancer actionQ46076458
Megabase deletions of gene deserts result in viable miceQ46272102
Promoter shuffling has occurred during the evolution of the vertebrate growth hormone geneQ46397654
Expression analysis of jagged genes in zebrafish embryos.Q47074002
Intronic enhancers control expression of zebrafish sonic hedgehog in floor plate and notochord.Q47971112
Zebrafish mab21l2 is specifically expressed in the presumptive eye and tectum from early somitogenesis onwardsQ48733539
P433issue7
P921main subjectcis-regulatory elementQ1093165
P304page(s)R56
P577publication date2006-01-01
P1433published inGenome BiologyQ5533480
P1476titleShuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage
P478volume7

Reverse relations

cites work (P2860)
Q21267236Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend
Q84866811Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos
Q41410676C2H2 zinc finger proteins greatly expand the human regulatory lexicon
Q33296096CONDOR: a database resource of developmentally associated conserved non-coding elements
Q37209981Conservation of core gene expression in vertebrate tissues
Q47112088Conserved non-coding elements: developmental gene regulation meets genome organization
Q30577485Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics
Q49358577Conserved noncoding sequences conserve biological networks and influence genome evolution
Q38161887Deep conservation of cis-regulatory elements in metazoans
Q42124559Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
Q36961266Dispensability of mammalian DNA
Q41955907Evolution of the mammalian transcription factor binding repertoire via transposable elements
Q35980467Fishing for function: zebrafish BAC transgenics for functional genomics
Q38606028Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction
Q39596997Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development
Q33281754Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers
Q28592776Identification and analysis of a conserved Tcfap2a intronic enhancer element required for expression in facial and limb bud mesenchyme
Q37201438Identification of direct T-box target genes in the developing zebrafish mesoderm
Q33282668Multiple non-collinear TF-map alignments of promoter regions
Q37087609Organization of conserved elements near key developmental regulators in vertebrate genomes
Q35751638Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
Q33307647TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
Q47073478The words of the regulatory code are arranged in a variable manner in highly conserved enhancers.
Q34261528Transcriptional enhancers in protein-coding exons of vertebrate developmental genes
Q42129929Uncovering cis regulatory codes using synthetic promoter shuffling

Search more.