Journal: bioRxiv

Article Title: Differential expression and homotypic enrichment of a classic Cadherin directs tissue-level contractile asymmetry during neural tube closure

doi: 10.1101/425165

Figure Lengend Snippet: (A) Sequence-based phylogeny for GAP domains from metazoan Rho GTPase activating proteins. Position of Ciona robusta Gap21/23 is marked with a pink square. (B) List of Ciona robusta Rho GAPs tested in this study. (C) Gap21/23 gene expression pattern from eight-cell to gastrula stage. Scale bars = 25 μm.

Article Snippet: We amplified a fragment corresponding to the conserved AHPH domain of Ciona robusta Anillin from Cogenics clone VES88_P24.

Techniques: Sequencing, Expressing

Journal: The EMBO Journal

Article Title: Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors

doi: 10.1038/s44318-025-00613-y

Figure Lengend Snippet: ( A – C ) Developmental dynamics of Gata4/5/6 gene expression. a. Representative confocal images showing double FISH detection of Gata4/5/6 and Depdc1b expression. Segmented cells, nuclei and transcripts shown on the right. Magenta: nuclei (GFP::PCNA); blue: Gata4/5/6 nascent RNA; green: Depdc1b mRNA. Scale bar = 5 µm; arrowhead: TVC; open arrowhead: ATM. ( B , C ) Semi-quantification of Gata4/5/6 ( B ) and Depdc1b ( C ) gene expression spanning TVC migration but prior to TVC division. ( D ) Cell cycle phases as determined by the GFP::PCNA reporter. ( E ) Confocal images of double FISH revealing Gata4/5/6 and Depdc1b mRNAs in Tyr CRISPR control and Gata4/5/6 CRISPR embryos. Scale bar = 10 µm Arrowhead: TVC; Open arrowhead: ATM. ( F – F’ , G – G’ ). Semi-quantification of Gata4/5/6 ( F – F’ ) and Depdc1b ( G – G’ ) expression in indicated conditions. ( H ) Accessibility of the Depdc1b locus during cardiopharyngeal development showing distal and proximal regulatory accessible regions upstream of the Depdc1b start site. Data from Racioppi et al, . ( I ) Systematic deletion of distal and proximal regulatory regions upstream of a 2xGFP reporter. The diagram shows control and deletion constructs. The dot plot on the right shows the level of GFP expression detected in either the mesenchyme or the TVCs upon disruption of regulatory regions, separately or in combination. Jitter is added to the graph for ease of visualizing expression changes. ( J ) Hypergeometric tests of GFP expression based on regulatory region perturbation. Color scale indicates log 10 odds ratio, and size indicates log 10 P value. ( K ) Micrographs of GFP expression as driven by constructs containing both proximal and distal regulatory regions or lacking one or both regulatory regions. ( L ) Regions of the Depdc1b regulatory region showing conservation of the Flank region, and putative GATA and FOX-binding sites, between Ciona robusta and Ciona savignyi . ( M ) Constructs containing the Flank, GATA, and FOX binding sites driving 2xGFP expression and subsequent analysis of binding site requirements for the tissue specific expression of GFP. The dot plot on the right shows proportions of GFP+ detected in either the Mesenchyme or the TVCs upon disruption of regulatory regions, separately or in combination. Jitter was added to the graph for ease of visualizing expression changes. ( N ) Hypergeometric tests of GFP expression based on regulatory region perturbation. Color scale indicates log 10 odds ratio, and size indicates log 10 P value. ( O ) Micrographs of GFP expression as driven by constructs containing both proximal and distal regulatory regions or lacking one or both regulatory regions. For both ( K , O ), arrows – First Heart Precursors (FHPs), open arrowheads – Second Heart Precursors (SHPs), solid arrowheads Atrial Siphon Muscle Founder cells (ASMF). .

Article Snippet: Adult Ciona robusta were purchased from M-Rep, USA or collected from coastal waters in Rongcheng, China, maintained in artificial seawater with constant lighting, and used for experiments within one week of arrival.

Techniques: Gene Expression, Expressing, Migration, CRISPR, Control, Construct, Disruption, Binding Assay

Journal: The EMBO Journal

Article Title: Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors

doi: 10.1038/s44318-025-00613-y

Figure Lengend Snippet: ( A ) (Top) The cardiopharyngeal lineage in Ciona robusta . The lineage of a B7.5 blastomere is shown to give rise to two founder cells, each producing a TVC and an ATM. (Bottom) Correspondence of FABA stages, post-fertilization developmental time points (18 °C), and color codes of scRNA-seq barcodes. TVC trunk ventral cell, ATM anterior tail muscle, STVC second trunk ventral cell, FHP first heart precursor, ASMF atrial siphon muscle founder cells, SHP second heart precursor. ( B ) (Top) Schematic diagram of asymmetrically oriented division of TVCs. (Bottom) Confocal images of before (left, 12 hpf) and after (right, 15 hpf) TVC division. Cyan: nuclei (NLS::LacZ); Magenta: cell membranes (hCD4::mCherry). The dashed line represents the embryo midline. M medial, L lateral. Scale bar = 5 µm. ( C ) Schematic of TVC cell cycle stages and genetic perturbations of mitotic entry. ( D – I’ ) Cell division patterns ( E , G , I ) and Tbx1/10 expression ( E’ , G’ , I’ ) following cell cycle perturbations. Control TVC division ( D , E , 3´HA), inhibition of TVC mitotic entry ( F , G , Wee1::3´HA), and induction of TVC mitotic entry ( H , I , Cdc25::3´HA) conditions are examined from 8 to 15 hpf. Perforated bars in ( G , G’ ) indicate timepoints not analyzed. Magenta: nuclei (GFP::PCNA); blue: cell membranes (hCD4::mCherry); green arrowhead: Tbx1/10 mRNA, Scale bar = 5 µm. ( J ) Schematic of variability of PCNA puncta patterns in the TVC nuclei associated with progression through the cell cycle. ( K ) Confocal images of PCNA puncta distribution in individual TVC nuclei at different stages of the cell cycle. Green: GFP::PCNA. Scale bar = 2.5 µm. ( L – N ) Determination of the S phase of TVC using PCNA. GFP::PCNA expressed in the B7.5-lineage under the Mesp enhancer at 8–12 hpf. Representative confocal images showing the G1, S, and G2 stages of TVC at 8, 10, and 12 hpf ( L ). Green: GFP::PCNA. Scale bar = 5 mm. Developmental distribution of four PCNA localization patterns ( M ). Quantification of GFP::PCNA punctæ per nucleus across developmental stages. Error bars show standard error of the mean (SEM). Data represent two biological replicates ( N ). No blinding was included in the analysis. .

Article Snippet: Adult Ciona robusta were purchased from M-Rep, USA or collected from coastal waters in Rongcheng, China, maintained in artificial seawater with constant lighting, and used for experiments within one week of arrival.

Techniques: Expressing, Control, Inhibition