Short interspersed DNA elements and miRNAs: a novel hidden gene regulation layer in zebrafish?

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• 作者：Margherita Scarpato ; Claudia Angelini ; Ennio Cocca…
• 关键词：Retrotransposons ; SINEs ; miRNA ; 3′UTR
• 刊名：Chromosome Research
• 出版年：2015
• 出版时间：September 2015
• 年：2015
• 卷：23
• 期：3
• 页码：533-544
• 全文大小：1,561 KB
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• 作者单位：Margherita Scarpato (1)
  Claudia Angelini (2)
  Ennio Cocca (3)
  Maria M. Pallotta (4)
  Maria A Morescalchi (4)
  Teresa Capriglione (4)
  
  1. IGB “Adriano Buzzati-Traverso” CNR, via P. Castellino, 80131, Napoli, Italy
  2. Istituto per le Applicazioni del Calcolo “M. Picone”, CNR, via P. Castellino, 80131, Napoli, Italy
  3. IBBR-CNR, via P. Castellino, 80131, Napoli, Italy
  4. Dipartimento di Biologia, Università di Napoli Federico II, via Cinthia 21, 80126, Napoli, Italy
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Human Genetics
  Animal Genetics and Genomics
  Plant Genetics and Genomics
  
• 出版者：Springer Netherlands
• ISSN：1573-6849

文摘

In this study, we investigated by in silico analysis the possible correlation between microRNAs (miRNAs) and Anamnia V-SINEs (a superfamily of short interspersed nuclear elements), which belong to those retroposon families that have been preserved in vertebrate genomes for millions of years and are actively transcribed because they are embedded in the 3′ untranslated region (UTR) of several genes. We report the results of the analysis of the genomic distribution of these mobile elements in zebrafish (Danio rerio) and discuss their involvement in generating miRNA gene loci. The computational study showed that the genes predicted to bear V-SINEs can be targeted by miRNAs with a very high hybridization E-value. Gene ontology analysis indicates that these genes are mainly involved in metabolic, membrane, and cytoplasmic signaling pathways. Nearly all the miRNAs that were predicted to target the V-SINEs of these genes, i.e., miR-338, miR-9, miR-181, miR-724, miR-735, and miR-204, have been validated in similar regulatory roles in mammals. The large number of genes bearing a V-SINE involved in metabolic and cellular processes suggests that V-SINEs may play a role in modulating cell responses to different stimuli and in preserving the metabolic balance during cell proliferation and differentiation. Although they need experimental validation, these preliminary results suggest that in the genome of D. rerio, as in other TE families in vertebrates, the preservation of V-SINE retroposons may also have been favored by their putative role in gene network modulation.