MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways

Thatcher, Elizabeth J.; Flynt, Alex S.; Li, Nan; Patton, Jonathan R.; Patton, James G.

doi:10.1002/dvdy.21211

Cited by 64 publications

(57 citation statements)

References 66 publications

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“…1). In addition, the miRNA profiles revealed by our sequencing data across all four stages were largely consistent with prior miRNA expression analyses (Chen et al 2005;Thatcher et al 2007).…”

Section: Small Rna Sequencingsupporting

confidence: 82%

“…Previous work has shown that miRNAs play important functional roles during cell specification and differentiation (Giraldez et al 2005;Flynt et al 2007;Mishima et al 2009). In zebrafish, miRNA expression patterns have been extensively examined using direct cloning and microarray analyses (Giraldez et al 2005;Thatcher et al 2007). These studies have shown that most miRNAs are not highly expressed during the first 12 h of zebrafish development, but that the overall pattern becomes increasingly diverse and complex as development proceeds (Chen et al 2005;Thatcher et al 2007).…”

Section: Introductionmentioning

confidence: 99%

“…In zebrafish, miRNA expression patterns have been extensively examined using direct cloning and microarray analyses (Giraldez et al 2005;Thatcher et al 2007). These studies have shown that most miRNAs are not highly expressed during the first 12 h of zebrafish development, but that the overall pattern becomes increasingly diverse and complex as development proceeds (Chen et al 2005;Thatcher et al 2007). Despite the seeming lack of diversity during the earliest stages of development, miRNA function is clearly essential, as maternal-zygotic Dicer mutant fish show severe defects and die by 7 dpf (Giraldez et al 2005).…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome-wide analysis of small RNA expression in early zebrafish development

Wei¹,

Salichos²,

Wittgrove³

et al. 2012

RNA

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During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function for most of these noncoding RNAs remain largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small noncoding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized next-generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 198 known miRNAs within 122 different miRNA families and eight novel miRNAs were determined. Significant sequence variation was observed at the 59 and 39ends of miRNAs, with most extra nucleotides added at the 39 end in a nontemplate directed manner. For the miR-430 family, the addition of adenosine and uracil residues is developmentally regulated and may play a role in miRNA stability during the maternal zygotic transition. Similar modification at the 39 ends of a large number of miRNAs suggests widespread regulation of stability during early development. Beside miRNAs, we also identified a large and unexpectedly diverse set of piRNAs expressed during early development.

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Section: Small Rna Sequencingsupporting

confidence: 82%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Transcriptome-wide analysis of small RNA expression in early zebrafish development

Wei¹,

Salichos²,

Wittgrove³

et al. 2012

RNA

Self Cite

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“…Caudal fins were amputated from adult fish, and RNA was isolated from three regenerative states: adult fins, fins undergoing active regeneration, and fins that appeared to be completely regenerated. Small RNAs from each stage were isolated, fluorescently labeled, and directly hybridized to microarrays to determine the expression patterns of 346 vertebrate miRNAs (20). To obtain sufficient RNA for three independent arrays, fins were amputated from 120 adult fish, which were then returned to the aquarium temperature of 27°C, after which regeneration was allowed to proceed for 2 or 5 weeks at 27°C before reamputation and another round of RNA isolation.…”

mentioning

confidence: 99%

Regulation of zebrafish fin regeneration by microRNAs

Thatcher

Paydar²,

Anderson³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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108

104

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A number of genes have been implicated in regeneration, but the regulation of these genes, particularly pertaining to regeneration in higher vertebrates, remains an interesting and mostly open question. We have studied microRNA (miRNA) regulation of regeneration and found that an intact miRNA pathway is essential for caudal fin regeneration in zebrafish. We also showed that miR-203 directly targets the Wnt signaling transcription factor Lef1 during this process. Repression of Lef1 by miR-203 blocks regeneration, whereas loss of miR-203 results in excess Lef1 levels and fin overgrowth. Expression of Lef1 from mRNAs lacking 3 UTR recognition elements can rescue the effects of excess miR-203, demonstrating that these effects are due to specific regulation of lef1 by miR-203. Our data support a model in which regulation of Lef1 protein levels by miR-203 is a key limiting step during regeneration.M ost vertebrates, including humans, are unable to regenerate the majority of lost or damaged tissues. In contrast, zebrafish are able to regenerate various damaged tissues, including fins, hearts, retinas, and spinal cords (1). For fins, regeneration relies on the formation of blastema cells, stem cell-like cells that either are recruited to the damaged area or originate from the de-differentiation of cells in the area (2, 3). Zebrafish caudal fins undergo isometric growth (i.e., fin grows in proportion to body size) throughout life, and understanding the regulatory mechanisms for controlling such growth remains a key question. The fin is composed of multiple bony rays that grow autonomously and are made up of bony segments, termed lepidotrichia. Each ray is composed of two hemirays, which create a protective shell around nerves, blood vessels, and mesenchymal cells. Fins grow through the addition of bone to the distal tip of the fin. Regeneration proceeds through at least five steps: wound healing, mesenchymal disorganization or reorganization, blastema formation, outgrowth, and termination (1, 4). miRNAs are a recently discovered class of genes that regulate gene expression at the posttranscriptional level and are required for development, stem cell maintenance, and renewal (5-18). Recently, Yin et al. (19) showed that fibroblast growth factor (Fgf) signaling alters the expression of multiple miRNAs during regeneration. One of the miRNA targets of Fgf signaling, miR-133, targets mps1, which encodes a kinase that regulates blastemal proliferation. Interestingly, these authors also found that various other markers of regeneration were indirectly activated on the reduction of miR-133 levels, suggesting that overall regulation of regeneration by miRNAs might be quite complex. Here we show that an intact miRNA pathway indeed is essential for regeneration. Furthermore, we show that in addition to regulation of Fgf signaling during regeneration, Wnt signaling also subject is to miRNA regulation through miR-203 control of Lef1.To examine global miRNA expression patterns in regenerating fins, we first conducted microarrays. Cauda...

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“…However, the exact number of zebrafish miRNAs might be higher, since genome sequencing and annotation has not been fully completed. Thus far, most zebrafish miRNAs exhibit tissue-specific patterns of expression [62].…”

Section: The Role Of Mirnas In Shaping Heart and Vascular Network Inmentioning

confidence: 99%

The admiR-able advances in cardiovascular biology through the zebrafish model system

Gays

Santoro

2012

Cell. Mol. Life Sci.

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MicroRNAs are small non-coding RNAs endogenously expressed by all tissues during development and adulthood. They regulate gene expression by controlling the stability of targeted messenger RNA. In cardiovascular tissues microRNAs play a role by modulating essential genes involved in heart and blood vessel development and homeostasis. The zebrafish (Danio rerio) system is a recognized vertebrate model system useful to study cardiovascular biology; recently, it has been used to investigate microRNA functions during natural and pathological states. In this review, we will illustrate the advantages of the zebrafish model in the study of microRNAs in heart and vascular cells, providing an update on recent discoveries using the zebrafish to identify new microRNAs and their targeted genes in cardiovascular tissues. Lastly, we will provide evidence that the zebrafish is an optimal model system to undercover new microRNA functions in vertebrates and to improve microRNA-based therapeutic approaches.Keywords MicroRNA Á Zebrafish Á Heart Á Blood vessel Á Development MiRNAs: function and mechanismMicroRNAs (e.g., miRs or miRNAs) are evolutionary conserved small non-coding RNAs, usually 21-25 nt long, that regulate gene expression at a post-transcriptional level.

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MiRNA expression analysis during normal zebrafish development and following inhibition of the Hedgehog and Notch signaling pathways

Cited by 64 publications

References 66 publications

Transcriptome-wide analysis of small RNA expression in early zebrafish development

Transcriptome-wide analysis of small RNA expression in early zebrafish development

Regulation of zebrafish fin regeneration by microRNAs

The admiR-able advances in cardiovascular biology through the zebrafish model system

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