Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Mol Biol Rep
2012 Mar 01;393:2633-44. doi: 10.1007/s11033-011-1016-7.
Show Gene links
Show Anatomy links
In silico characterization of the neural alpha tubulin gene promoter of the sea urchin embryo Paracentrotus lividus by phylogenetic footprinting.
Ragusa MA
,
Longo V
,
Emanuele M
,
Costa S
,
Gianguzza F
.
???displayArticle.abstract???
During Paracentrotus lividus sea urchin embryo development one alpha and one beta tubulin genes are expressed specifically in the neural cells and they are early end output of the gene regulatory network that specifies the neural commitment. In this paper we have used a comparative genomics approach to identify conserved regulatory elements in the P. lividus neural alpha tubulin gene. To this purpose, we have first isolated a genomic clone containing the entire gene plus 4.5 Kb of 5'' upstream sequences. Then, we have shown by gene transfer experiments that its non-coding region drives the spatio-temporal gene expression corresponding substantially to that of the endogenous gene. In addition, we have identified by genome and EST sequence analysis the S. purpuratus alpha tubulin orthologous gene and we propose a revised annotation of some tubulin family members. Moreover, by computational techniques we delineate at least three putative regulatory regions located both in the upstream region and in the first intron containing putative binding sites for Forkhead and Nkx transcription factor families.
Arnone,
Using reporter genes to study cis-regulatory elements.
2004, Pubmed,
Echinobase
Arnone,
Using reporter genes to study cis-regulatory elements.
2004,
Pubmed
,
Echinobase
Arnone,
Genetic organization and embryonic expression of the ParaHox genes in the sea urchin S. purpuratus: insights into the relationship between clustering and colinearity.
2006,
Pubmed
,
Echinobase
Ben-Tabou de-Leon,
Deciphering the underlying mechanism of specification and differentiation: the sea urchin gene regulatory network.
2006,
Pubmed
,
Echinobase
Berezikov,
CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.
2004,
Pubmed
Bonnet,
Differential binding regulation of microtubule-associated proteins MAP1A, MAP1B, and MAP2 by tubulin polyglutamylation.
2001,
Pubmed
Brooke,
The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster.
1998,
Pubmed
Brown,
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.
2005,
Pubmed
Burke,
A genomic view of the sea urchin nervous system.
2006,
Pubmed
,
Echinobase
Calzone,
Gene regulatory factors of the sea urchin embryo. I. Purification by affinity chromatography and cloning of P3A2, a novel DNA-binding protein.
1991,
Pubmed
,
Echinobase
Cameron,
A sea urchin genome project: sequence scan, virtual map, and additional resources.
2000,
Pubmed
,
Echinobase
Cameron,
SpBase: the sea urchin genome database and web site.
2009,
Pubmed
,
Echinobase
Cameron,
Unusual gene order and organization of the sea urchin hox cluster.
2006,
Pubmed
,
Echinobase
Casano,
Spatial expression of alpha and beta tubulin genes in the late embryogenesis of the sea urchin Paracentrotus lividus.
1996,
Pubmed
,
Echinobase
Cheesman,
Zebrafish and fly Nkx6 proteins have similar CNS expression patterns and regulate motoneuron formation.
2004,
Pubmed
Coffman,
SpMyb functions as an intramodular repressor to regulate spatial expression of CyIIIa in sea urchin embryos.
1997,
Pubmed
,
Echinobase
Costa,
Sea urchin neural alpha2 tubulin gene: isolation and promoter analysis.
2004,
Pubmed
,
Echinobase
Davidson,
Network design principles from the sea urchin embryo.
2009,
Pubmed
,
Echinobase
Dibb,
Evidence that introns arose at proto-splice sites.
1989,
Pubmed
Dubchak,
VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes.
2006,
Pubmed
Duboc,
Nodal and BMP2/4 signaling organizes the oral-aboral axis of the sea urchin embryo.
2004,
Pubmed
,
Echinobase
Duboc,
Left-right asymmetry in the sea urchin embryo is regulated by nodal signaling on the right side.
2005,
Pubmed
,
Echinobase
Dunn,
Molecular paleoecology: using gene regulatory analysis to address the origins of complex life cycles in the late Precambrian.
2007,
Pubmed
,
Echinobase
Elnitski,
Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques.
2006,
Pubmed
Frazer,
VISTA: computational tools for comparative genomics.
2004,
Pubmed
Garcia-Fernàndez,
Hox, ParaHox, ProtoHox: facts and guesses.
2005,
Pubmed
Gianguzza,
DNA sequence and pattern of expression of the sea urchin (Paracentrotus lividus) alpha-tubulin genes.
1989,
Pubmed
,
Echinobase
Gianguzza,
Alpha-tubulin marker gene of neural territory of sea urchin embryos detected by whole-mount in situ hybridization.
1995,
Pubmed
,
Echinobase
Grumbling,
FlyBase: anatomical data, images and queries.
2006,
Pubmed
Hatano,
Ncx, a Hox11 related gene, is expressed in a variety of tissues derived from neural crest cells.
1997,
Pubmed
Huang,
On global sequence alignment.
1994,
Pubmed
Khodiyar,
A revised nomenclature for the human and rodent alpha-tubulin gene family.
2007,
Pubmed
Larkin,
Clustal W and Clustal X version 2.0.
2007,
Pubmed
Lassmann,
Kalign--an accurate and fast multiple sequence alignment algorithm.
2005,
Pubmed
McMahon,
Neural patterning: the role of Nkx genes in the ventral spinal cord.
2000,
Pubmed
McMahon,
Introduction of cloned DNA into sea urchin egg cytoplasm: replication and persistence during embryogenesis.
1985,
Pubmed
,
Echinobase
Morris,
Analysis of cytoskeletal and motility proteins in the sea urchin genome assembly.
2006,
Pubmed
,
Echinobase
Otim,
SpHnf6, a transcription factor that executes multiple functions in sea urchin embryogenesis.
2004,
Pubmed
,
Echinobase
Pattyn,
Complementary roles for Nkx6 and Nkx2 class proteins in the establishment of motoneuron identity in the hindbrain.
2003,
Pubmed
Perumal,
Intron position conservation across eukaryotic lineages in tubulin genes.
2005,
Pubmed
Phillips,
The virtuoso of versatility: POU proteins that flex to fit.
2000,
Pubmed
Poustka,
Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters.
2003,
Pubmed
,
Echinobase
Poustka,
A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks.
2007,
Pubmed
,
Echinobase
Rebeiz,
GenePalette: a universal software tool for genome sequence visualization and analysis.
2004,
Pubmed
Rosenbaum,
Cytoskeleton: functions for tubulin modifications at last.
2000,
Pubmed
Sasaki,
Specification process of animal plate in the sea urchin embryo.
2008,
Pubmed
,
Echinobase
Shirasawa,
Enx (Hox11L1)-deficient mice develop myenteric neuronal hyperplasia and megacolon.
1997,
Pubmed
Smolenicka,
Sequence of a conserved region of a new sea urchin homeobox gene from the NK family.
2003,
Pubmed
,
Echinobase
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Stöbe,
Multifactorial regulation of a hox target gene.
2009,
Pubmed
Su,
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo.
2009,
Pubmed
,
Echinobase
Takacs,
Expression of an NK2 homeodomain gene in the apical ectoderm defines a new territory in the early sea urchin embryo.
2004,
Pubmed
,
Echinobase
Tu,
Sea urchin Forkhead gene family: phylogeny and embryonic expression.
2006,
Pubmed
,
Echinobase
Yaguchi,
Specification of ectoderm restricts the size of the animal plate and patterns neurogenesis in sea urchin embryos.
2006,
Pubmed
,
Echinobase
Yaguchi,
Sp-Smad2/3 mediates patterning of neurogenic ectoderm by nodal in the sea urchin embryo.
2007,
Pubmed
,
Echinobase
Yuh,
Patchy interspecific sequence similarities efficiently identify positive cis-regulatory elements in the sea urchin.
2002,
Pubmed
,
Echinobase
