Identification and characterization of microRNAs involved in scale biomineralization in the naked carp Gymnocypris przewalskii

Arola, 2018, The limiting layer of fish scales: structure and properties, Acta Biomater., 67, 319, 10.1016/j.actbio.2017.12.011 Bizuayehu, 2014, MicroRNA in teleost fish, Genome Biol. Evol., 6, 1911, 10.1093/gbe/evu151 Blanchette, 2009, Characterization and purification of polydisperse reconstituted lipoproteins and nanolipoprotein particles, Int. J. Mol. Sci., 10, 2958, 10.3390/ijms10072958 Cao, 2010, MicroRNAs play a critical role in tooth development, J. Dent. Res., 89, 779, 10.1177/0022034510369304 Cohen, 2011, Phosphate biomineralization in mid-Neoproterozoic protists, Geology, 39, 539, 10.1130/G31833.1 Cordero, 2015, Skin mucus proteome map of European sea bass (Dicentrarchus labrax), Proteomics, 15, 4007, 10.1002/pmic.201500120 Cozza, 2017, Fam20C is under the control of sphingolipid signaling in human cell lines, FEBS J., 284, 1246, 10.1111/febs.14052 Ehrlich, 2015, Fish scales as mineral-based composites, 213 Eulalio, 2008, Getting to the root of miRNA-mediated gene silencing, Cell, 132, 9, 10.1016/j.cell.2007.12.024 Friedman, 2009, Most mammalian mRNAs are conserved targets of microRNAs, Genome Res., 19, 92, 10.1101/gr.082701.108 Gil-Duran, 2016, Effect of chemical composition and microstructure on the mechanical behavior of fish scales from Megalops Atlanticus, J. Mech. Behav. Biomed., 56, 134, 10.1016/j.jmbbm.2015.11.028 Holland, 2017, Receptors grease the metabolic wheels, Nature, 544, 42, 10.1038/nature21900 Hou, 2017, Ecotoxicological effects and mechanism of CuO nanoparticles to individual organisms, Environ. Pollut., 221, 209, 10.1016/j.envpol.2016.11.066 Jiao, 2014, Identification and characterization of microRNAs in pearl oyster Pinctada martensii by solexa deep sequencing, Mar. Biotechnol., 16, 54, 10.1007/s10126-013-9528-x Jiao, 2015, MicroRNA, Pm-miR-2305, participates in nacre formation by targeting Pearlin in pearl oyster Pinctada martensii, Int. J. Mol. Sci., 16, 21442, 10.3390/ijms160921442 Kondo, 2001, The medaka rs-3 locus required for scale development encodes ectodysplasin-A receptor, Curr. Biol., 11, 1202, 10.1016/S0960-9822(01)00324-4 Li, 2017, The receptor genes PfBMPR1B and PfBAMBI are involved in regulating shell biomineralization in the pearl oyster Pinctada fucata, Sci. Rep., 7, 9219, 10.1038/s41598-017-10011-y Li, 2018, Byssus structure and protein composition in the highly invasive fouling mussel Limnoperna fortunei, Front. Physiol., 9, 418, 10.3389/fphys.2018.00418 Li, 2019, Chemical oxidants affect byssus adhesion in the highly invasive fouling mussel Limnoperna fortunei, Sci. Total Environ., 646, 1367, 10.1016/j.scitotenv.2018.07.434 Lian, 2012, MicroRNA control of bone formation and homeostasis, Nat. Rev. Endocrinol., 8, 212, 10.1038/nrendo.2011.234 Liu, 2016, The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts, Nat. Commun., 7, 11757, 10.1038/ncomms11757 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method, Methods, 25, 402, 10.1006/meth.2001.1262 Lv, 2017, A genomic survey of SCPP family genes in fishes provides novel insights into the evolution of fish scales, Int. J. Mol. Sci., 18, 2432, 10.3390/ijms18112432 Makeyev, 2008, Multilevel regulation of gene expression by microRNAs, Science, 319, 1789, 10.1126/science.1152326 Makeyev, 2007, The microRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing, Mol. Cell, 27, 435, 10.1016/j.molcel.2007.07.015 Mann, 2015, Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and Turkey eggshell proteomes, Proteome Sci., 13, 22, 10.1186/s12953-015-0078-1 Marycz, 2016, Sphingosine-1-phosphate enhance osteogenic activity of multipotent stromal cells cultured in biodegradable 3D alginate hydrogels, J. Biomater. Tissue Eng., 6, 85, 10.1166/jbt.2016.1423 Mass, 2014, Immunolocalization of skeletal matrix proteins in tissue and mineral of the coral Stylophora pistillata, Proc. Natl. Acad. Sci. U. S. A., 111, 12728, 10.1073/pnas.1408621111 McCarthy, 2008, MicroRNA-206: the skeletal muscle-specific myomiR, Biochim. Biophys. Acta, Gene Regul. Mech., 1779, 682, 10.1016/j.bbagrm.2008.03.001 Miyashita, 2008, Gene cloning and biochemical characterization of the BMP-2 of Pinctada fucata, Biosci. Biotechnol. Biochem., 72, 37, 10.1271/bbb.70302 Mu, 2015, Dynamic expression of miR-206-3p during mouse skin development is independent of keratinocyte differentiation, Mol. Med. Rep., 12, 8113, 10.3892/mmr.2015.4456 Nakagawa, 2018, CREBH regulates systemic glucose and lipid metabolism, Int. J. Mol. Sci., 19, 1396, 10.3390/ijms19051396 Nohno, 1995, Involvement of the sonic hedgehog gene in chick feather formation, Biochem. Biophys. Res. Commun., 206, 33, 10.1006/bbrc.1995.1005 Pasqualetti, 2012, The zebrafish scale as model to study the bone mineralization process, J. Mol. Histol., 43, 589, 10.1007/s10735-012-9425-z Passadouro, 2016, Managing pancreatic adenocarcinoma: a special focus in microRNA gene therapy, Int. J. Mol. Sci., 17, 718, 10.3390/ijms17050718 Rasmussen, 2018, Fish scales dictate the pattern of adult skin innervation and vascularization, Dev. Cell, 46, 344, 10.1016/j.devcel.2018.06.019 Schneider, 2001, Mutations leading to X-linked hypohidrotic ectodermal dysplasia affect three major functional domains in the tumor necrosis factor family member ectodysplasin-A, J. Biol. Chem., 276, 18819, 10.1074/jbc.M101280200 Schönbörner, 1979, The mineralization processes in teleost fish scales, Cell Tissue Res., 202, 203, 10.1007/BF00232235 Stepicheva, 2015, MicroRNA-31 modulates skeletal patterning in the sea urchin embryos, Development, 142, 3769, 10.1242/dev.127969 Sun, 2015, Fish-scale bio-inspired multifunctional ZnO nanostructures, NPG ASIA Mater., 7, 10.1038/am.2015.133 Tong, 2017, Comprehensive transcriptomic analysis of Tibetan Schizothoracinae fish Gymnocypris przewalskii reveals how it adapts to a high altitude aquatic life, BMC Evol. Biol., 17, 74, 10.1186/s12862-017-0925-z Tong, 2017, The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: a case study in Schizothoracinae fish on the Tibetan Plateau, PLoS One, 12, 10.1371/journal.pone.0174534 Uchida, 2016, Two ceramide metabolites, sphingosine-1-phosphate and ceramide-1-phosphate signal to stimulate innate immunity trough independent-mechanisms, J. Dermatol. Sci., 84, 10.1016/j.jdermsci.2016.08.214 Wang, 2003, Unusual physiology of scale-less carp, Gymnocypris przewalskii, in Lake Qinghai: a high altitude alkaline saline lake, Comp. Biochem. Physiol. A Mol. Integr. Physiol., 134, 409, 10.1016/S1095-6433(02)00317-3 Wang, 2010, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26, 136, 10.1093/bioinformatics/btp612 Wang, 2015, BMP and RA signaling cooperate to regulate Apolipoprotein C1 expression during embryonic development, Gene, 554, 196, 10.1016/j.gene.2014.10.047 Wang, 2018, Comparative microRNA-seq analysis depicts candidate miRNAs involved in skin color differentiation in red tilapia, Int. J. Mol. Sci., 19, 1209, 10.3390/ijms19041209 Weiner, 2011, Crystallization pathways in biomineralization, Annu. Rev. Mater. Res., 41, 21, 10.1146/annurev-matsci-062910-095803 Wu, 2016, TGF-β and BMP signaling in osteoblast, skeletal development, and bone formation, homeostasis and disease, Bone Res., 4, 16009, 10.1038/boneres.2016.9 Zhang, 2017, Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: a case study in Tibetan Schizothoracine fish, PLoS One, 12 Zheng, 2016, Computational prediction of candidate miRNAs and their potential functions in biomineralization in pearl oyster Pinctada martensii, Saudi J. Biol. Sci., 23, 372, 10.1016/j.sjbs.2015.04.001 Zhu, 2012, Structure and mechanical performance of a “modern” fish scale, Adv. Eng. Mater., 14, 185, 10.1002/adem.201180057