Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus.

Autor: Ghosh A; Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA., Platt RN 2nd; Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA., Vandewege MW; Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA; Department of Biology, Eastern New Mexico University, Portales, NM, USA., Tabassum R; Charles Darwin University, Australia., Hsu CY; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA., Isberg SR; Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia; The Centre for Crocodile Research, Darwin, NT, Australia., Peterson DG; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA., Finger JW Jr; Department of Environmental Health Science, University of Georgia, Athens, GA, USA; Department of Biological Sciences, Auburn University, Auburn, AL, USA., Kieran TJ; Department of Environmental Health Science, University of Georgia, Athens, GA, USA., Glenn TC; Department of Environmental Health Science, University of Georgia, Athens, GA, USA., Gongora J; Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia., Ray DA; Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA. Electronic address: david.4.ray@gmail.com.
Jazyk: angličtina
Zdroj: Analytical biochemistry [Anal Biochem] 2020 Aug 01; Vol. 602, pp. 113781. Date of Electronic Publication: 2020 May 30.
DOI: 10.1016/j.ab.2020.113781
Abstrakt: MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with >78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.
Competing Interests: Declaration of competing interest None.
(Copyright © 2020 Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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