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Epigenomic analysis of H. miamia development identifies regions of accessible chromatin. (A) Schematic phylogenetic tree of selected metazoan lineages demonstrating the placement of Xenacoelomorpha (pink outline) as the likely sister group to all other bilaterians or sister to the Ambulacraria (dotted line). Public domain silhouettes courtesy of PhyloPic. (B) Schematic of chromatin profiling workflow illustrating how data were generated and how regions of the genome are compared to each other. (C) Schematic of the different developmental stages that were sampled – gastrula, dimple, post-dimple, pigmented prehatchling and hatched juvenile – highlighting the earliest expression of differentiated cell markers, as well as other previously published RNA-seq that was analyzed in this study (Kimura et al., 2021, 2022). (D) Principal component analysis of triplicate ATAC-seq libraries that were generated in this study. (E) Bar plots showing the proportions of peaks contained within promoters, exons, introns and intergenic regions across the different developmental timepoints.
Published: 23 May 2025
Fig. 1. Epigenomic analysis of H. miamia development identifies regions of accessible chromatin. (A) Schematic phylogenetic tree of selected metazoan lineages demonstrating the placement of Xenacoelomorpha (pink outline) as the likely sister group to all other bilaterians or sister to the Ambu... More about this image found in Epigenomic analysis of H. miamia development identifies regions of access...
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Differential accessibility across the H. miamia genome reflects major developmental transitions. (A) Heatmap of all chromatin peaks that show significant changes during H. miamia development. (B) Fuzzy c-means clustering of regions of accessible chromatin with each cluster plotted individually. GO functional annotation enrichment for different peaksets; x-axis denotes the percentage of GO term enrichment; bars are colored according to P-value.
Published: 23 May 2025
Fig. 2. Differential accessibility across the H. miamia genome reflects major developmental transitions. (A) Heatmap of all chromatin peaks that show significant changes during H. miamia development. (B) Fuzzy c-means clustering of regions of accessible chromatin with each cluster plotted in... More about this image found in Differential accessibility across the H. miamia genome reflects major dev...
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Genome-wide analyses implicate key transcription factor motifs in developmental lineage decision-making. (A) t-Distributed stochastic neighbor embedding (t-SNE) plot showing groupings of samples, including biological replicates, based on chromatin accessibility of the consensus peakset. Replicate samples are colored by time point. (B) chromVAR chromatin variability scores for a curated list of 78 H. miamia transcription factor-binding motifs across all time points of development. The top five most variable motifs (RUNT, CTCF, TP63, ISL2 and NFIC) are in red; the most variable regeneration motif (EGR) is labeled in cyan. (C) Accessibility of the RUNT-binding motif overlaid on the same t-SNE plot as A, with the scale indicating more accessible chromatin (red) at genome-wide sites at gastrula and dimple stages, and less accessible chromatin in pigmented prehatchling and hatched juvenile stages (purple). The scale varies for each ChromVar plot. (D) Accessibility of NFIC-binding motifs. (E) Accessibility of ASCL1-binding motifs. (F) Accessibility of EGR-binding motifs. (G) Heatmap of the top 20 most variable motifs at various developmental stages. Motifs with homeodomain in lilac, neural motifs in orange and epidermal motifs in yellow. Four major patterns were colored: high to low (purple), low at dimple and hatched juvenile stages (magenta), low to high to low (orange), and low to high (green). Asterisks indicate motifs with a 1:1 correspondence to a single H. miamia TF encoding gene. (H) TOBIAS normalized binding score for each corresponding motif.
Published: 23 May 2025
Fig. 3. Genome-wide analyses implicate key transcription factor motifs in developmental lineage decision-making. (A) t-Distributed stochastic neighbor embedding (t-SNE) plot showing groupings of samples, including biological replicates, based on chromatin accessibility of the consensus peakset. ... More about this image found in Genome-wide analyses implicate key transcription factor motifs in developme...
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RUNT is among the most variably accessible motifs across H. miamia development, suggesting Runt as a major regulator of early development. (A) URD tree with major tissue lineages labeled (Kimura et al., 2022). (B) URD tree with expression of runt. The color of the branch represents the average expression of a cell in pseudotime. (C) runt expression over URD pseudotime, with pseudotime on the x-axis, progressing from earlier pseudotime on the left to later pseudotime on the right, and gene expression on the y-axis. (D) Fraction of bound RUNT sites. (E) GO term enrichment for genes with RUNT binding. (F) Accessibility of the dlx gene locus with candidate RUNT-binding sites (top). URD tree with expression of dlx (bottom). Epidermal lineage is outlined. (G) Accessibility of the soxC gene locus with candidate RUNT-binding sites (top). URD tree with expression of soxC (bottom). Neural lineage is outlined. (H) Accessibility of the foxA gene locus with candidate RUNT-binding sites (top). URD tree with expression of foxA (bottom). Gut and endodermal lineages are outlined. (I) Accessibility of the zic-1 gene locus with candidate RUNT-binding sites (top). URD tree with expression of zic-1 (bottom). Muscle lineage is outlined. Tick marks represent predicted binding sites and gray boxes represent gene models.
Published: 23 May 2025
Fig. 4. RUNT is among the most variably accessible motifs across H. miamia development, suggesting Runt as a major regulator of early development . (A) URD tree with major tissue lineages labeled ( Kimura et al., 2022 ). (B) URD tree with expression of runt . The color of the branch represents... More about this image found in RUNT is among the most variably accessible motifs across H. miamia develo...
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Motif enrichment and predicted binding provide hypotheses for regulatory relationships of known epidermal differentiation genes. (A) Accessibility of the p63/p73 gene locus with candidate RUNT-binding sites. (B) URD tree showing p63/p73 expression, with the epidermal lineage outlined on the left and the pharyngeal epidermis outlined on the right. (C) Pseudotime p63/p73 expression. (D) Accessibility of the nfi gene locus with candidate TP63-binding sites. (E) URD tree with expression of nfi. Epidermal lineage outlined on the left and the pharyngeal epidermis outlined on the right. (F) Pseudotime nfi expression. (G) In situ hybridization of p63/p73 at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages. (H) URD tree with the co-expression of nfi in red and epiA in green. (I) Accessibility of the epiA gene locus with candidate NFIC-binding sites. (J) In situ hybridization of nfi at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages. (K) URD tree with the co-expression of nfi in red and cah6 in green. (L) Accessibility of the cah6 gene locus with candidate NFIC-binding sites. (M) In situ hybridization of epiA at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages. (N) Linked ATAC-seq peak-accessibility and corresponding RNA expression of previously described epidermal markers. EP, early pooled; PH, prehatchling; PPH, pigmented prehatchling. Tick marks represent predicted binding sites and gray boxes represent gene models. Scale bars in G,J,M: 100 µm
Published: 23 May 2025
Fig. 5. Motif enrichment and predicted binding provide hypotheses for regulatory relationships of known epidermal differentiation genes. (A) Accessibility of the p63 / p73 gene locus with candidate RUNT-binding sites. (B) URD tree showing p63 / p73 expression, with the epidermal lineage outl... More about this image found in Motif enrichment and predicted binding provide hypotheses for regulatory re...
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Predicted transcription factor binding uncovers a regulatory network with Pitx, Fox and Zic transcription factors in H. miamia muscle development. (A) URD tree with muscle lineages outlined. (B) tropomyosin gene expression (magenta), and tropomyosin antibody staining (green) in developing H. miamia embryonic stages. Peripheral, parenchymal, pharyngeal and body wall muscles are labeled. (C) Expression of zic-1 and zic-2 in URD muscle branches. Dashed outline indicates the putative muscle progenitor population. (Right) Chromatin accessibility of zic-1 loci with candidate ZIC4-, PITX1- and FOX-binding sites. (D) In situ hybridization of zic-1 at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages, and co-expression of zic-1 with tropomyosin. (E) Expression of pitx and pitx-like in URD muscle branches. Dashed outline indicates the putative muscle progenitor population. (Right) Chromatin accessibility of pitx loci with candidate ZIC4-, PITX1- and FOX-binding sites. (F) In situ hybridization of pitx at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages, and co-expression of pitx with tropomyosin. (G) Expression of foxL2 and foxC in URD muscle branches. Dashed outline indicates putative muscle progenitor population. (Right) Chromatin accessibility of foxL2 loci with candidate ZIC4-, PITX1- and FOX-binding sites. (H) In situ hybridization of foxL2 at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages, and co-expression of foxL2 with tropomyosin. (I) Expression of follistatin in URD muscle branches. (Right) Chromatin accessibility of follistatin locus with candidate ZIC4-, PITX1- and FOX-binding sites. (J) In situ gene expression of follistatin at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages, and co-expression of follistatin with pitx and p73 at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages and co-expression of follistatin with pitx. (K) Expression of bmp in URD muscle branches. (Right) Chromatin accessibility of the bmp locus with candidate ZIC4-, PITX1- and FOX-binding sites. (L) In situ gene expression of bmp at post-dimple (left), prehatchling (center) and pigmented prehatchling (right) stages, and co-expression of bmp with follistatin. (M) ATACseq peak-accessibility and corresponding RNA expression of transcription factors and differentiated markers of muscle. EP, early pooled; PH, prehatchling; PPH, pigmented prehatchling. Black arrowheads denote URD branches with enriched expression. White arrowheads indicate co-expression. Scale bars: 100 µm.
Published: 23 May 2025
Fig. 6. Predicted transcription factor binding uncovers a regulatory network with Pitx, Fox and Zic transcription factors in H. miamia muscle development. (A) URD tree with muscle lineages outlined. (B) tropomyosin gene expression (magenta), and tropomyosin antibody staining (green) in devel... More about this image found in Predicted transcription factor binding uncovers a regulatory network with P...
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FD and FDP are expressed in floral organs. (A) In situ hybridization of (i) FD and (ii) FDP mRNAs in inflorescences of plants grown for 20 long days (LDs) (i) and in 2-week-old plants grown under short days and then transferred to LDs for 9 days (ii). (B) Confocal images of (i) VENUS:FD and (ii) VENUS:FDP in longitudinal views of inflorescences in 18-day-old plants. (C) Confocal images of VENUS:FD floral buds at the end of stage 3 (i), stage 6 (ii) and stage 9 (iii), and VENUS:FDP at stage 3 (iv), stage 5 (v) and stage 9 (vi). pe, petals. (D) Colocalization of VENUS:FDP and mCHERRY:FD in floral buds at stage 3 (i), stage 4 (ii), stage 6 (iii) and stage 7 (iv) of floral development, as visualized by confocal microscopy. Violet signal corresponds to mCHERRY:FD and green signal corresponds to VENUS:FDP. Whiter signal is merged expression of both fluorescent proteins. Red arrowheads indicate colocalization of expression. Scale bars: 100 µm in A-C (i,ii,iv,v); 20 µm in C (iii,vi); 50 µm in D.
Published: 22 May 2025
Fig. 1. FD and FDP are expressed in floral organs. (A) In situ hybridization of (i) FD and (ii) FDP mRNAs in inflorescences of plants grown for 20 long days (LDs) (i) and in 2-week-old plants grown under short days and then transferred to LDs for 9 days (ii). (B) Confocal images of (i)... More about this image found in FD and FDP are expressed in floral organs. (A) In situ hybridization ...
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The fd fdp double mutant shows floral organ defects under long-day conditions. (A) Representative flowers of the genotypes illustrated. The red arrowheads indicate petals and the orange arrowhead indicates sepals. (B) The numbers of sepals, petals and stamens in flowers of the illustrated genotypes. n corresponds to the total number of flowers analyzed. (C) SEM images of inflorescences (top) and floral buds (bottom) at stage 4 to 5 of floral development of the genotypes illustrated. Col-0, fdp-2 and fdp-CRP2 inflorescences were imaged at day 20, fd-3 inflorescences at day 30, and fdp-2 fd-3 and fdp-CRP2 fd-3 inflorescences at day 34. Red arrowheads indicate sepals with abnormal shapes or growth. Scale bars: 5 mm in A (i-iii); 1 mm in A (iv-vi); 100 µm in C (top); 20 µm in C (bottom).
Published: 22 May 2025
Fig. 2. The fd fdp double mutant shows floral organ defects under long-day conditions. (A) Representative flowers of the genotypes illustrated. The red arrowheads indicate petals and the orange arrowhead indicates sepals. (B) The numbers of sepals, petals and stamens in flowers of the illustra... More about this image found in The fd fdp double mutant shows floral organ defects under long-day condit...
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The ft tsf double mutant shows floral defects under long-day conditions. (A) Floral phenotypes of an inflorescence/flower 30-day-old Col-0 (i,ii) and 45-day-old ft-10 tsf-1 (iii,iv) plants, showing petal loss (red arrowheads). Carpels in ft-10 (stage 15 and 16 siliques) resemble Col-0, while ft-10 tsf-1 carpels have size and number defects (v,vi). (B) Frequency of sepals, petals and stamens in the genotypes shown. n indicates the total number of flowers analyzed. (C) SEM images: (i-iv) inflorescences; (v-viii) stage 4 floral buds; (ix-xii) stage 6 floral buds. Col-0 and tsf-1 at day 25, ft-10 at day 39 and ft-10 tsf-1 at day 46. (D) SEM images of stage 13 flowers from Col-0 and tsf-1 (i-iv) and stage 12 from ft-10 and ft-10 tsf-1 (v-viii). Orange arrowheads indicate unbranched trichomes (i,iii); white arrowheads indicate branched trichomes (vi and viii in ft-10 and ft-10 tsf-1); blue arrowhead indicates a stellate trichome (vii in ft-10 tsf-1); yellow arrowhead indicates stipules on the pedicel (viii in ft-10 tsf-1). Pedicel width is indicated by black lines (ii, iv, vi and viii). Scale bars: 2 mm in A (i,iv); 1 mm in A (ii,iii); 1.25 mm in A (v,vi); 100 µm in C (i-iv) and D (ii,iv,vi,viii); 10 µm in C (v,vii,viii,xi); 20 µm in C (vi,ix,x,xii); 200 µm in D (i,iii,v,vii).
Published: 22 May 2025
Fig. 3. The ft tsf double mutant shows floral defects under long-day conditions. (A) Floral phenotypes of an inflorescence/flower 30-day-old Col-0 (i,ii) and 45-day-old ft-10 tsf-1 (iii,iv) plants, showing petal loss (red arrowheads). Carpels in ft-10 (stage 15 and 16 siliques) resemble Co... More about this image found in The ft tsf double mutant shows floral defects under long-day conditions. ...
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Floral defects in ft-10 tsf-1 under short-day conditions. (A) Flowering time under short-day conditions (SDs) of the Col-0 and ft-10 tsf-1 plants shown as rosette (left) and cauline leaf numbers (right). Asterisks indicate significant differences (unpaired Student's t-test: ****P<0.0001). Box represents the median value and the middle two quartiles of the data, and whiskers represent the remaining two quartiles. (B) Floral phenotypes: top views of inflorescences (i-iv) taken after the first flower had opened in all genotypes. Single flowers (v-viii) for each genotype. (C) Frequency of sepals, petals and stamens for the depicted genotypes. (D) SEM images of stage 13 flowers. Higher magnification views (v-viii) show stipules in ft-10 (vii) and in ft-10 tsf-1 (viii) (orange arrowheads). In Col-0 (i,v) and tsf-1 (ii,vi), most of the trichomes are unbranched (pink arrowheads) (Perazza et al., 1999), but in ft-10 (iii,vii) and in ft-10 tsf-1 (iv,viii), trichomes are bifurcated (white arrowheads). Scale bars: 2 mm in B (i-iv); 1 mm in B (v-viii); 200 µm in D (i-iv), 100 µm in D (v-viii).
Published: 22 May 2025
Fig. 4. Floral defects in ft-10 tsf-1 under short-day conditions. (A) Flowering time under short-day conditions (SDs) of the Col-0 and ft-10 tsf-1 plants shown as rosette (left) and cauline leaf numbers (right). Asterisks indicate significant differences (unpaired Student's t -test: **** P ... More about this image found in Floral defects in ft-10 tsf-1 under short-day conditions. (A) Flowering ...
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ft tsf and fd fdp double mutants show defects in floral meristem size and shape. (A) 3D confocal images of stage 4 floral buds: Col-0 (i), fd-3 fdp-CRP2 (ii) and ft-10 tsf-1 (iii). (B) Quantified floral meristem width (n: Col-0=17; ft-10 tsf-1=16; fd-3 fdp-CRP2=24) with significant differences indicated by different letters (one-way ANOVA with Tukey's test; P≤0.05). (C) Longitudinal confocal images of stage 4 floral buds of Col-0 (i), ft-10 tsf-1 (ii) and fd-3 fdp-CRP2 (iii). White lines depict the width of the lateral axis (iv-vi), red lines depict the width of the medial axis (i-iii) and green lines indicate the height. (D) Quantified floral meristem height. Numbers of flowers measured and statistical analysis was carried out as in B. Scale bars: 50 µm in A; 10 µm in C.
Published: 22 May 2025
Fig. 5. ft tsf and fd fdp double mutants show defects in floral meristem size and shape. (A) 3D confocal images of stage 4 floral buds: Col-0 (i), fd-3 fdp-CRP2 (ii) and ft-10 tsf-1 (iii). (B) Quantified floral meristem width ( n : Col-0=17; ft-10 tsf-1 =16; fd-3 fdp-CRP2 =24) with sig... More about this image found in ft tsf and fd fdp double mutants show defects in floral meristem size an...
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Presence of FT:GFP in floral meristems and complementation of floral organ defects. (A) Confocal images of a SUC2::FT:GFP ft-7 25-day-old plant (i,ii) and a pFT::FT:GFP ft-7 30-day-old plant at various stages (iii-v), showing FT:GFP signal (white arrowheads) in the vasculature (i,ii) and floral meristems (iii-v). (B) Frequency of sepals, petals and stamens for the genotypes shown. n indicates the total number of flowers analyzed. Scale bars: 100 µm.
Published: 22 May 2025
Fig. 6. Presence of FT:GFP in floral meristems and complementation of floral organ defects. (A) Confocal images of a SUC2::FT:GFP ft-7 25-day-old plant (i,ii) and a pFT::FT:GFP ft-7 30-day-old plant at various stages (iii-v), showing FT:GFP signal (white arrowheads) in the vasculature (i,ii)... More about this image found in Presence of FT:GFP in floral meristems and complementation of floral organ ...
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FT TSF and FD FDP positively activate SEP genes and AG, and repress WUS in developing flowers. (A) In situ hybridization of AG mRNA in inflorescences of the depicted genotypes. Flower buds shown were at the indicated stages. Plants were grown for 24 LDs for Col-0, for 28 LDs for fd-3, for 33 LDs for fd-3 fdp-CRP2, for 35 LDs for ft-10 and for 45 LDs for ft-10 tsf-1. (B) In situ hybridizations of WUS mRNA in inflorescences of the depicted genotypes. Flower buds shown were at the indicated stages. Plants were grown for 24 LDs for Col-0, for 28 LDs for fd-3, for 31 LDs for fd-3 fdp-CRP2, for 35 LDs for ft-10 and for 40 LDs for ft-10 tsf-1. (C) RNAscope in situ hybridizations of SEP3 and FD mRNAs in inflorescences of Col-0. SCRI Renaissance 2200 stains cell walls in white. SEP3 and FD mRNAs appear in the depicted colors. Flower buds shown are at stage 3 and stage 4. Plants were grown for 18 LDs. (D) In situ hybridizations of SEP2 and SEP3 mRNAs in inflorescences of the depicted genotypes. Flower buds shown were at the indicated stages. Plants were grown for 19 or 23 LDs for Col-0, for 27 or 31 LDs for fd-3 fdp-CRP2, and for 37 or 45 LDs for ft-10 tsf-1. Images show flower buds at stages 2 and 3. Scale bars: 50 µm in A,B,D; 20 µm in C.
Published: 22 May 2025
Fig. 7. FT TSF and FD FDP positively activate SEP genes and AG , and repress WUS in developing flowers. (A) In situ hybridization of AG mRNA in inflorescences of the depicted genotypes. Flower buds shown were at the indicated stages. Plants were grown for 24 LDs for Col-0, for 28 LDs for ... More about this image found in FT TSF and FD FDP positively activate SEP genes and AG , and repress WUS ...
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Comparison of FD ChIPseq gene targets with the targets of other floral organ identity MADS-box transcription factors. (A) Binding profiles of FD and MADS box transcription factors to SEP1, SEP2 and SEP3, and other genes involved in flower development. The panels display, from the top, AP1, PI, AP3, FD, FDP and control (INPUT-gray) peaks at the loci shown, visualized with the IGB browser. (B) Venn diagrams comparing the common target genes in ChIP-seq datasets for FD and AP1, PI, AP3 and SEP3. For the comparison between two datasets (FD versus MADS-box transcription factors), the P-values of the overlaps were calculated using a one-sided Fisher's exact test. (C) The GO terms enriched among the 74 genes bound by FD and AP1, AP3, PI and SEP3. The image on the left shows an overview of all GO terms (labels have been removed for a clearer depiction of the different clusters); on the right is a more detailed view for the GO term ‘Regulation of biological process’. (D) qRT-PCR analysis of the mRNA abundance of SOC1, ARF6 and AS1 in inflorescences of Col-0, tsf-1, ft-10 and ft-10 tsf-1 double mutants (top), and Col-0, fd-3, fdp-CRP2 and fd-3 fdp-CRP2 (bottom). Common letters among genotypes indicate no significant differences in mRNA levels (one-way ANOVA followed by Tukey's multiple comparisons test). Different letters indicate statistically significant differences at P≤0.05. (E) Model depicting the regulation of floral meristem size and determinacy by the FT and FD FDP proteins, as described in the text. FD FDPs are also expressed in other floral organs, and their effects on floral organs likely also involve the activation of SEP gene transcription, but the precise regulatory mechanisms remain unknown.
Published: 22 May 2025
Fig. 8. Comparison of FD ChIPseq gene targets with the targets of other floral organ identity MADS-box transcription factors. (A) Binding profiles of FD and MADS box transcription factors to SEP1 , SEP2 and SEP3 , and other genes involved in flower development. The panels display, from the t... More about this image found in Comparison of FD ChIPseq gene targets with the targets of other floral orga...