Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters

Poustka, Albert J.; Groth, Detlef; Hennig, Steffen; Thamm, Sabine; Cameron, R. Andrew; Beck, Alfred; Reinhardt, Richard; Herwig, Ralf; Panopoulou, Georgia; Lehrach, Hans

doi:10.1101/gr.1674103

Cited by 46 publications

(26 citation statements)

References 35 publications

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“…The 5Ј-RACE sequence was confirmed with a partial SpNodal 5Ј sequence (SpNodal5; Fig. 6B) obtained from an S. purpuratus "unigene screen" (Poustka et al, 1999(Poustka et al, , 2003. A genomic Southern using SpNodal cDNA as probe and genomic DNA from three individuals indicate a single nodal-related gene is present in the S. purpuratus genome (data not shown).…”

Section: Cloning Of Sea Urchin Nodalmentioning

confidence: 65%

“…Seminested RACE was performed twice using the 5Ј Nested GeneRacer primer and the same gene-specific primer as in the first round of amplification. In addition, a partial SpNodal sequence was identified in a "unigene" screen (Poustka et al, 1999(Poustka et al, , 2003 that encoded 615 bp of coding sequence and a portion of the 5Ј-UTR. This 5Ј clone (SpNodal5; Fig.…”

Section: Pcr Cloning and Macroarray Screeningmentioning

confidence: 99%

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Nodal/activin signaling establishes oral–aboral polarity in the early sea urchin embryo

Flowers

Courteau

Poustka

et al. 2004

Developmental Dynamics

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Components of the Wnt signaling pathway are involved in patterning the sea urchin primary or animal-vegetal (AV) axis, but the molecular cues that pattern the secondary embryonic axis, the aboral/oral (AO) axis, are not known. In an analysis of signaling molecules that influence patterning along the sea urchin embryonic axes, we found that members of the activin subfamily of transforming growth factor-␤ (

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Section: Cloning Of Sea Urchin Nodalmentioning

confidence: 65%

Section: Pcr Cloning and Macroarray Screeningmentioning

confidence: 99%

Nodal/activin signaling establishes oral–aboral polarity in the early sea urchin embryo

Flowers

Courteau

Poustka

et al. 2004

Developmental Dynamics

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“…Second, the high number of ESTs associated with housekeeping processes such as metabolism and ribosomal proteins was to be expected, due to the energy production and protein synthesis requirements in both normal and regenerating organs (45). These results are in accordance with Agü ero and coworkers (3), who found an even larger percentage (17.4%) of ribosomal protein in Trypanosoma cruzi total ESTs, and Chaudhuri and Lieberman (13), who showed a rise in liver ribosome and protein synthesis after partial hepatectomy.…”

Section: Discussionmentioning

confidence: 99%

“…Sequences were also queried against those at the NCBI for the Holothuroidea and against a custom database of all known Strongylocentrotus purpuratus (NCBI, taxonomy ID: 7668), sequences extracted from GenBank (8) with the NCBI taxonomy Browser (62). The sea urchin S. purpuratus was selected because of its phylogenetically proximity and the extent of the sequencing efforts in this organism (45).…”

Section: Methodsmentioning

confidence: 99%

Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumberHolothuria glaberrima

Rojas‐Cartagena

Ortíz-Pineda

Ramírez-Gómez

et al. 2007

Physiological Genomics

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Repair and regeneration are key processes for tissue maintenance, and their disruption may lead to disease states. Little is known about the molecular mechanisms that underline the repair and regeneration of the digestive tract. The sea cucumber Holothuria glaberrima represents an excellent model to dissect and characterize the molecular events during intestinal regeneration. To study the gene expression profile, cDNA libraries were constructed from normal, 3-day, and 7-day regenerating intestines of H. glaberrima. Clones were randomly sequenced and queried against the nonredundant protein database at the National Center for Biotechnology Information. RT-PCR analyses were made of several genes to determine their expression profile during intestinal regeneration. A total of 5,173 sequences from three cDNA libraries were obtained. About 46.2, 35.6, and 26.2% of the sequences for the normal, 3-days, and 7-days cDNA libraries, respectively, shared significant similarity with known sequences in the protein database of GenBank but only present 10% of similarity among them. Analysis of the libraries in terms of functional processes, protein domains, and most common sequences suggests that a differential expression profile is taking place during the regeneration process. Further examination of the expressed sequence tag dataset revealed that 12 putative genes are differentially expressed at significant level ( R > 6). Experimental validation by RT-PCR analysis reveals that at least three genes (unknown C-4677-1, melanotransferrin, and centaurin) present a differential expression during regeneration. These findings strongly suggest that the gene expression profile varies among regeneration stages and provide evidence for the existence of differential gene expression.

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“…From these scaffolds we extracted putative coding sequences with unique 3 0 UTR and these sequences were used as query to verify them and to find correlate 5 0 UTR sequences. Performing BLAST search in NCBI (S. purpuratus EST database [22]) we selected EST sequences with high similarity (C98%) in coding sequence and in 3 0 UTR. In this way we were able not only to construct in silico mRNA (coding and untranslated regions) alpha tubulin sequences, but also to find for three of them (scaffold_v2_18119, scaffold_v2_86155, scaffold_v2_61 948) 5 0 UTR sequences in the genome.…”

Section: Neural Alpha Tubulin Ortholog Identificationmentioning

confidence: 99%

In silico characterization of the neural alpha tubulin gene promoter of the sea urchin embryo Paracentrotus lividus by phylogenetic footprinting

et al. 2011

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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 0 upstream sequences. Then, we have shown by gene transfer experiments that its non-coding region drives the spatiotemporal 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.

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Generation, Annotation, Evolutionary Analysis, and Database Integration of 20,000 Unique Sea Urchin EST Clusters

Cited by 46 publications

References 35 publications

Nodal/activin signaling establishes oral–aboral polarity in the early sea urchin embryo

Nodal/activin signaling establishes oral–aboral polarity in the early sea urchin embryo

Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumberHolothuria glaberrima

In silico characterization of the neural alpha tubulin gene promoter of the sea urchin embryo Paracentrotus lividus by phylogenetic footprinting

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