Over-represented localized sequence motifs in ribosomal protein gene promoters of basal metazoans

Perina, Dragutin; Korolija, Marina; Roller, Maša; Harcet, Matija; Jeličić, Branka; Mikoč, Andreja; Ćetković, Helena

doi:10.1016/j.ygeno.2011.03.009

Cited by 15 publications

(25 citation statements)

References 43 publications

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“…Fop parameters were based on results of correspondence analysis of 224 S. domuncula genes. 17 Fgc for BtkSD was 46 %, Fop 0.287 and G + C content at silent codon position 38.2 %. Fop varies from 13.7 to 60.6 %.…”

Section: Analysis Of Btksd Genementioning

confidence: 95%

“…16 A sample of 224 coding sequences of S. domuncula (including cDNA coding BtkSD) was collected for analysis of synonymous codon usage. 17 CODONW program was used for synonymous codon usage analysis (http://codonw.sourceforge.net/) and calculated GC3S, Fgc and Fop parameters. GC3S is fraction of codons in gene which have either a guanine or cytosine at third codon position.…”

Section: Sponge Btksd Genementioning

confidence: 99%

“…17 Sponges as the oldest metazoan lineage probably provide the best possible insight into the characteristics of the genome of the metazoan ancestor. The preference for C-and G-ending codons has previously been documented in other metazoans.…”

Section: Analysis Of Btksd Genementioning

confidence: 99%

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Characterization of Bruton’s Tyrosine Kinase Gene and Protein from Marine Sponge Suberites domuncula

Perina¹,

Mikoč²,

Harcet³

et al. 2012

Croat. Chem. Acta

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Abstract. Bruton's tyrosine kinase (Btk) is a member of Tec family of protein tyrosine kinases. It is expressed in B cells and myeloid cells in humans and it is crucial for maturation of B-lineage lymphoid cells. Mutations in the gene encoding human Btk result in hereditary immunodeficiency X-linked agammaglobulinemia. Sponge proteins can probably reflect characteristics of the ancestral metazoan homologues before their diversifications and specializations in complex animals.Gene coding for sponge Btk-like protein was fully characterized and its structure was compared with homologous genes from other organisms. Kinase activity of sponge protein was compared to human Btk activity.We showed that sponge Btk-like gene is probably the most ancient member of Tec family while other members arose from the ancestral gene present in chordate ancestor. The ancestral-type protein was structurally and functionally similar to the highly sophisticated enzyme it is today, whose functions are usually associated with higher Metazoa. (doi: 10.5562/cca1862)

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Section: Analysis Of Btksd Genementioning

confidence: 95%

Section: Sponge Btksd Genementioning

confidence: 99%

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Characterization of Bruton’s Tyrosine Kinase Gene and Protein from Marine Sponge Suberites domuncula

Perina¹,

Mikoč²,

Harcet³

et al. 2012

Croat. Chem. Acta

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“…Ciona TATA-less RP genes therefore also may use a TRF2-based transcription system. Extensive analysis of overrepresented motifs in RP gene promoters have been done in many species, such as human, Drosophila, yeast, C. elegans, and basal metazoans (Tanay et al 2005;Roepcke et al 2006;Ma et al 2009;Perina et al 2011;Sleumer et al 2012). Our preliminary study of C. intestinalis RP gene promoters focused only on a polypyrimidine initiator motif and the best-characterized promoter motif, TATA box.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

et al. 2015

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The tunicate Ciona intestinalis, an invertebrate chordate, has recently emerged as a powerful model organism for gene regulation analysis. However, few studies have been conducted to identify and characterize its transcription start sites (TSSs) and promoters at the genome-wide level. Here, using TSS-seq, we identified TSSs at the genome-wide scale and characterized promoters in C. intestinalis. Specifically, we identified TSS clusters (TSCs), high-density regions of TSS-seq tags, each of which appears to originate from an identical promoter. TSCs were found not only at known TSSs but also in other regions, suggesting the existence of many unknown transcription units in the genome. We also identified candidate promoters of 79 ribosomal protein (RP) genes, each of which had the major TSS in a polypyrimidine tract and showed a sharp TSS distribution like human RP gene promoters. Ciona RP gene promoters, however, did not appear to have typical TATA boxes, unlike human RP gene promoters. In Ciona non-RP promoters, two pyrimidine-purine dinucleotides, CA and TA, were frequently used as TSSs. Despite the absence of CpG islands, Ciona TATA-less promoters showed low expression specificity like CpG-associated human TATA-less promoters. By using TSS-seq, we also predicted trans-spliced gene TSSs and found that their downstream regions had higher G+T content than those of non-trans-spliced gene TSSs. Furthermore, we identified many putative alternative promoters, some of which were regulated in a tissue-specific manner. Our results provide valuable information about TSSs and promoter characteristics in C. intestinalis and will be helpful in future analysis of transcriptional regulation in chordates.

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“…The overall sequence conservation between sponge and rat RPs is 80% or higher [29]. Furthermore, cis -regulatory architecture in promoters of RPGs appears not to be drastically changed from sponge to human [30]. Available data suggest that sponges changed little during metazoan evolution and are probably the most plausible model for studying gene/protein structure in ancestral metazoan.…”

Section: Introductionmentioning

confidence: 99%

Structural and Functional Characterization of Ribosomal Protein Gene Introns in Sponges

et al. 2012

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Ribosomal protein genes (RPGs) are a powerful tool for studying intron evolution. They exist in all three domains of life and are much conserved. Accumulating genomic data suggest that RPG introns in many organisms abound with non-protein-coding-RNAs (ncRNAs). These ancient ncRNAs are small nucleolar RNAs (snoRNAs) essential for ribosome assembly. They are also mobile genetic elements and therefore probably important in diversification and enrichment of transcriptomes through various mechanisms such as intron/exon gain/loss. snoRNAs in basal metazoans are poorly characterized. We examined 449 RPG introns, in total, from four demosponges: Amphimedon queenslandica, Suberites domuncula, Suberites ficus and Suberites pagurorum and showed that RPG introns from A. queenslandica share position conservancy and some structural similarity with “higher” metazoans. Moreover, our study indicates that mobile element insertions play an important role in the evolution of their size. In four sponges 51 snoRNAs were identified. The analysis showed discrepancies between the snoRNA pools of orthologous RPG introns between S. domuncula and A. queenslandica. Furthermore, these two sponges show as much conservancy of RPG intron positions between each other as between themselves and human. Sponges from the Suberites genus show consistency in RPG intron position conservation. However, significant differences in some of the orthologous RPG introns of closely related sponges were observed. This indicates that RPG introns are dynamic even on these shorter evolutionary time scales.

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Over-represented localized sequence motifs in ribosomal protein gene promoters of basal metazoans

Cited by 15 publications

References 43 publications

Characterization of Bruton’s Tyrosine Kinase Gene and Protein from Marine Sponge Suberites domuncula

Characterization of Bruton’s Tyrosine Kinase Gene and Protein from Marine Sponge Suberites domuncula

Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis

Structural and Functional Characterization of Ribosomal Protein Gene Introns in Sponges

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