RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa
| Autor: | Viravuth P. Yin, Christina A. Dykeman, Benjamin L. King, Michael C. Rosenstein, Ashley M. Smith, Grace A. Smith |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Regulation of gene expression Database Microarray Regeneration (biology) lcsh:R Biomedical Engineering Medicine (miscellaneous) lcsh:Medicine Cell Biology Biology computer.software_genre biology.organism_classification Non-coding RNA Article 03 medical and health sciences 030104 developmental biology Gene expression Gene computer Zebrafish Organism Developmental Biology |
| Zdroj: | npj Regenerative Medicine, Vol 3, Iss 1, Pp 1-13 (2018) NPJ Regenerative Medicine |
| ISSN: | 2057-3995 |
| Popis: | Regeneration is an endogenous process of tissue repair that culminates in complete restoration of tissue and organ function. While regenerative capacity in mammals is limited to select tissues, lower vertebrates like zebrafish and salamanders are endowed with the capacity to regenerate entire limbs and most adult tissues, including heart muscle. Numerous profiling studies have been conducted using these research models in an effort to identify the genetic circuits that accompany tissue regeneration. Most of these studies, however, are confined to an individual injury model and/or research organism and focused primarily on protein encoding transcripts. Here we describe RegenDbase, a new database with the functionality to compare and contrast gene regulatory pathways within and across tissues and research models. RegenDbase combines pipelines that integrate analysis of noncoding RNAs in combination with protein encoding transcripts. We created RegenDbase with a newly generated comprehensive dataset for adult zebrafish heart regeneration combined with existing microarray and RNA-sequencing studies on multiple injured tissues. In this current release, we detail microRNA–mRNA regulatory circuits and the biological processes these interactions control during the early stages of heart regeneration. Moreover, we identify known and putative novel lncRNAs and identify their potential target genes based on proximity searches. We postulate that these candidate factors underscore robust regenerative capacity in lower vertebrates. RegenDbase provides a systems-level analysis of tissue regeneration genetic circuits across injury and animal models and addresses the growing need to understand how noncoding RNAs influence these changes in gene expression. Software: Online tool allows cross-species comparisons of regeneration A new online resource allows researchers to probe the genomic circuitry that underpins tissue regeneration across a range of injury and animal models. A team led by Benjamin King from the University of Maine in Orono and Viravuth Yin from the MDI Biological Laboratory in Bar Harbor, Maine, USA, created a tool called RegenDbase, the Comparative Models of Regeneration Database. It incorporates gene expression datasets for protein-coding genes and regulatory RNA molecules from zebrafish, axolotl salamanders and mice. As a proof of principle, the researchers used RegenDbase to find RNAs common to heart regeneration in both neonatal mice and zebrafish using an extensive new zebrafish dataset. Twenty-eight new zebrafish regulatory RNA molecules were identified using those data. Future incorporation of datasets from other organisms and human tissues will enable broader cross-species comparisons of regenerative biology. |
| Databáze: | OpenAIRE |
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