A microRNA-mRNA expression network during oral siphon regeneration in <i>Ciona</i>

Spina, Elijah J.; Guzman, Elmer; Zhou, Hongjun; Kosik, Kenneth S.; Smith, William C.

doi:10.1242/dev.144097

Cited by 25 publications

(20 citation statements)

References 112 publications

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“…The ability to precisely edit the genomes of a variety of organisms has greatly expanded the usefulness of these systems as models for human development and disease (Cardi, D'Agostino, & Tripodi, ; Chen et al, ; Singh, Braddick, & Dhar, ). Ascidians are gaining prominence as excellent models for examining a wide variety of biological problems including regeneration (Spina, Guzman, Zhou, Kosik, & Smith, ), Alzheimer's studies (Virata & Zeller, ), and climate change research (Lopez et al, ). The ascidian embryo also provides a rapid and useful system for the analysis of complex regulatory elements (Farley et al, ; Kusakabe, ; Satou & Imai, ).…”

Section: Discussionmentioning

confidence: 99%

Efficient genome editing using CRISPR‐Cas‐mediated homology directed repair in the ascidian Ciona robusta

Pickett

Zeller

2018

Genesis

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Eliminating or silencing a gene’s level of activity is one of the classic approaches developmental biologists employ to determine a gene’s function. A recently developed method of gene perturbation called CRISPR-Cas, which was derived from a prokaryotic adaptive immune system, has been adapted for use in eukaryotic cells. This technology has been established in several model organisms as a powerful and efficient tool for knocking out or knocking down the function of a gene of interest. It has been recently shown that CRISPR-Cas functions with fidelity and efficiency in Ciona robusta. Here, we show that in C. robusta CRISPR-Cas mediated genomic knock-ins can be efficiently generated. Electroporating a tissue-specific transgene driving Cas9 and a U6-driven gRNA transgene together with a fluorescent protein-containing homology directed repair (FP-HDR) template results in gene-specific patterns of fluorescence consistent with a targeted genomic insertion. Using the Tyrosinase locus to optimize reagents, we first characterize a new Pol III promoter for expressing gRNAs from the C. savignyi H1 gene, and then adapt technology that flanks gRNAs by ribozymes allowing cell-specific expression from Pol II promoters. Next, we examine homology arm-length efficiencies of FP-HDR templates. Reagents were then developed for targeting Brachyury and Pou4 that resulted in expected patterns of fluorescence, and sequenced PCR amplicons derived from single embryos validated predicted genomic insertions. Finally, using two differentially colored FP-HDR templates, we show that biallelic FP-HDR template insertion can be detected in live embryos of the F0 generation.

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Section: Discussionmentioning

confidence: 99%

Efficient genome editing using CRISPR‐Cas‐mediated homology directed repair in the ascidian Ciona robusta

Pickett

Zeller

2018

Genesis

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“…We used published RNA sequencing (RNA-Seq) data sets for N. vectensis (Schaffer et al. 2016), H. vulgaris , C. intestinalis (Spina et al. 2017), and S. mediterranea (Zeng et al.…”

Section: Methodsmentioning

confidence: 99%

“…2015). Read counts for C. intestinalis were estimated according to our previously published procedure (Spina et al. 2017).…”

Section: Methodsmentioning

confidence: 99%

JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration

Cao

Kumagai

Inoue

et al. 2019

Genome Biology and Evolution

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The capacity for regeneration varies greatly among metazoans, yet little is known about the evolutionary processes leading to such different regeneration abilities. In particular, highly regenerative species such as planarians and cnidarians can regenerate the whole body from an amputated fragment; however, a common molecular basis, if any, among these species remains unclear. Here, we show that genes encoding Jumonji C (JmjC) domain-containing proteins are associated with high regeneration ability. We classified 132 fully sequenced metazoans into two groups with high or low regeneration abilities and identified 118 genes conserved in the high regenerative group that were lost in species in the low regeneration group during evolution. Ninety-six percent of them were JmjC domain-encoding genes. We denoted the candidate genes as high regenerative species-specific JmjC domain-encoding genes ( HRJD s). We observed losses of HRJDs in Helobdella robusta , which lost its high regeneration ability during evolution based on phylogenetic analysis. By RNA sequencing analyses, we observed that HRJD orthologs were differentially expressed during regeneration in two Cnidarians, as well as Platyhelminthes and Urochordata, which are highly regenerative species. Furthermore, >50% of the head and tail parts of amputated planarians ( Dugesia japonica ) died during regeneration after RNA interference of HRJD orthologs. These results indicate that HRJD are strongly associated with a high regeneration ability in metazoans. HRJD paralogs regulate gene expression by histone demethylation; thus, HRJD may be related to epigenetic regulation controlling stem cell renewal and stem cell differentiation during regeneration. We propose that HRJD play a central role in epigenetic regulation during regeneration.

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“…In Ciona robusta, previously known as C. intestinalis type A [28], miR-9 was found to be expressed at gastrula and larval stages [26]. In this species, through a transcriptome-wide study of gene expression of both mRNA and microRNA, it was found that miR-9 is upregulated during oral siphon regeneration and is involved in the differentiation of neural progenitors through regulation of the cytoskeleton and cell cycle [29]. This pro-neural function of miR-9 is conserved between ascidians and vertebrates, in which one of its key functions is to regulate the generation of postmitotic neurons from neural precursor cells [30].…”

Section: Introductionmentioning

confidence: 99%

Exploring miR-9 Involvement in Ciona intestinalis Neural Development Using Peptide Nucleic Acids

Mercurio

Cauteruccio

Manenti

et al. 2020

IJMS

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The microRNAs are small RNAs that regulate gene expression at the post-transcriptional level and can be involved in the onset of neurodegenerative diseases and cancer. They are emerging as possible targets for antisense-based therapy, even though the in vivo stability of miRNA analogues is still questioned. We tested the ability of peptide nucleic acids, a novel class of nucleic acid mimics, to downregulate miR-9 in vivo in an invertebrate model organism, the ascidian Ciona intestinalis, by microinjection of antisense molecules in the eggs. It is known that miR-9 is a well-conserved microRNA in bilaterians and we found that it is expressed in epidermal sensory neurons of the tail in the larva of C. intestinalis. Larvae developed from injected eggs showed a reduced differentiation of tail neurons, confirming the possibility to use peptide nucleic acid PNA to downregulate miRNA in a whole organism. By identifying putative targets of miR-9, we discuss the role of this miRNA in the development of the peripheral nervous system of ascidians.

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A microRNA-mRNA expression network during oral siphon regeneration in Ciona

Cited by 25 publications

References 112 publications

Efficient genome editing using CRISPR‐Cas‐mediated homology directed repair in the ascidian Ciona robusta

Efficient genome editing using CRISPR‐Cas‐mediated homology directed repair in the ascidian Ciona robusta

JmjC Domain-Encoding Genes Are Conserved in Highly Regenerative Metazoans and Are Associated with Planarian Whole-Body Regeneration

Exploring miR-9 Involvement in Ciona intestinalis Neural Development Using Peptide Nucleic Acids

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