Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium
- Department of Molecular and Cellular Biology, Faculty of Arts and Sciences, Harvard University, United States
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan
- Graduate School of Natural Science and Technology, Okayama University, Japan
- Department of Basic Biology, Graduate School for Advanced Studies, Japan
- Spatiotemporal Regulations Group, Exploratory Research Center for Life and Living Systems, Japan
- Laboratory for Spatiotemporal Regulations, National Institute for Basic Biology, Japan
- Trans-Scale Biology Center, National Institute for Basic Biology, Japan
- Institute for Quantitative Biosciences (IQB), The University of Tokyo, Japan
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Japan
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Japan
- Kyoto Sangyo University, Faculty of Life Sciences, Kamigamo Motoyama, Japan
Figures
Figure 1 with 4 supplements
Clonal architecture in the adult medaka telencephalon.
(A) A larval medaka fish (1 week day post fertilization) and a dissected adult brain (top left). Pink triangles indicate the position of the telencephalon in the larval and adult brain. The white …
Figure 1—figure supplement 1
Details of redefined atlas of the telencephalon.
Transverse (A) and horizontal (B) optical sections of the reference telencephalon (left) and redefined brain atlas (right). Lines in the schematic drawing of the lateral view of the telencephalon …
Figure 1—figure supplement 2
Expression of cell-type marker genes in the adult medaka telencephalon.
(A) Immunostaining of CaMK2α, Parvalbumin, and GAD65/67 allowed us to define anatomical regions. Numbers in the first row indicate the location of the transverse sections (bottom). Orange triangles …
Figure 1—figure supplement 3
Statistics of clonal units.
(A) Density plot of total number of visualized clusters (VC) per fish (N = 81 fish). (B) Boxplot showing the statistics of localization of VC. Left boxplot shows the number of VC in the left …
Figure 1—figure supplement 4
Radial glial projection in the adult medaka telencephalon.
(A) Projections of the radial glial cells in the adult medaka telencephalon visualized by anti-GFAP immunostaining. In the pallium, cell bodies of GFAP-positive neural stem cells locate on the …
Figure 2
Neuronal projections of clonal units in the telencephalon.
(A) Connectional matrix between clonal units in the telencephalon. The rows indicate the cell body locations and the columns indicate where the projection ends. The number of the projection among 81 …
Figure 3 with 1 supplement
ATAC-seq of clonal units in the adult medaka telencephalon.
(A) Procedure of ATAC-sequencing with extracted clonal units from the adult telencephalon. Cre-loxP recombination was induced at the neurula stage in the transgenic embryos (Tg (HSP-Cre) × Tg …
Figure 3—figure supplement 1
Analysis of ATAC-seq in clonal units.
(A) 130-um-thick brain transverse sections from one adult brain (top). Clonal units used in ATAC-seq are shaded in dark gray in the schematic drawing (bottom). (B) Pictures of extracted GFP-positive …
Figure 4 with 2 supplements
Analyses of Dd2-specific open chromatin region (OCR) clusters reveal specialized synaptic gene transcription.
(A) Gene Ontology (GO) analysis of OCR clusters. GO terms related to axon guidance and neurogenesis (top) and synaptic signaling (bottom) are shown (see also Figure 4—figure supplement 1 for other …
Figure 4—figure supplement 1
Gene Ontology (GO) term enrichment analysis on open chromatin region (OCR) clusters.
Full list of GO terms enriched in OCR cluster-target genes in Figure 3D. In OCR C8, 10, 11, no GO term was enriched. Size and color of circles indicate fold enrichment and false discovery rate …
Figure 4—figure supplement 2
RNA-seq and ATAC-seq analysis on Dd2.
(A) Procedure for RNA-seq analysis. After making 130-um-thick slices, Dd2 (Dd, white lines), the pallium except Dd (D, cyan lines), and subpallium (V, yellow lines) were dissected based on the DsRed …
Figure 5 with 1 supplement
Analyses of Dd2-specific open chromatin region (OCR) clusters reveal specialized synaptic architecture.
(A) Differential expression of synaptic signaling genes in the Dd2 compared to other pallial regions and the subpallium. Expression levels from RNA-seq data are shown for synaptic signaling genes …
Figure 5—figure supplement 1
Characterization of synaptic genes expressed and regulated in Dd2.
Schematic representation of synaptic genes detected as specifically expressed and regulated in Dd2 by ATAC-seq and RNA-seq. We found that different subunits of neurotransmitter receptors and ion …
Figure 6 with 1 supplement
Transcriptional regulation in Dd2.
(A) Enrichment of known transcription factor binding motifs in open chromatin region (OCR) clusters are shown as dot plots. Size and color of circles indicate -log10(p-value) and percent target, …
Figure 6—figure supplement 1
Expression of candidate transcription factors in the adult medaka telencephalon.
(A) Brain regions where RNA signals were detected by in situ hybridization are indicated by names. Expression in Dd2 is shown with the orange line and name. bHLH: beta-helix-loop-helix family; HTH: …
Figure 7
Hypothesized molecular model of specialized synaptic architecture in the dorsal pallium in medaka.
(A) Anatomical regions in the pallium is formed by clonal units mutually exclusively. (B) Clonal ATAC-seq shows unique open-chromatin patterns in some clonal units (left). Transcription is likely …
Videos
Video 1
Reference brain.
DAPI-based reference brain. The slices show the horizontal view from the ventral to the dorsal direction.
Video 2
Pallium.
One of the examples of visualized clonally related units in the pallium (raw movie). GFP-positive cells (green) make a cluster and send a projection to the same site. Red signals indicate DsRed and …
Video 3
Subpallium.
One of the examples of visualized clonally related units in the subpallium (raw movie). GFP-positive cells (green) and DsRed-positive cells (red) were mixed in the subpallial region. Blue signals …
Tables
Table 1
Summary of marker gene expression in the telencephalic regions in medaka.
Several marker gene expressions were assessed with immunostainings (Figure 1—figure supplement 2).
| CaMK2 | Parvalbumin | GAD65/67 | GAD67 | |
|---|---|---|---|---|
| Dla | + | n.a. | n.a. | n.a. |
| Dld | ＋/– | + | + | ＋＋ |
| Dlp | ＋/– | – | - | n.a. |
| Dlv | + | + | + | ＋＋ |
| Dd1 | ＋ | ＋＋ | - | + |
| Dd2a | ＋ | ＋＋ | ＋＋ | + |
| Dd2p | ＋＋(ventral) | ＋ | ＋＋(dorsal) | + |
| Dm1 | – | ー | + | n.a. |
| Dm2a | ＋ | – | + | + |
| Dm2b | ＋＋ | – | + | + |
| Dm3a | ＋＋ | ー | + | + |
| Dm3b | ＋＋ | ー | + | + |
| Dm4 | ＋＋ | ＋＋ | - | n.a. |
| Dp | ＋＋ | ＋ | - | n.a. |
| Dc | ＋ | - | - | n.a. |
| Dcpm | – | - | n.a. | n.a. |
| GL | ＋ | n.a. | ＋＋ | + |
| ICL | – | ＋＋ | n.a. | n.a. |
| Vv | – | ＋＋ | - | - |
| Vd | – | ＋＋ | - | - |
| Vp | ＋＋ | + | - | - |
| Vs | – | + | - | - |
| Vl | – | ＋＋ | - | - |
-
- signals not detected; +: signals detected; ++: signals strongly detected; n.a.: not analyzed.
Table 2
Nomenclature of the adult telencephalon.
For the medaka brain research, two brain atlases of adult medaka have been used (Anken and Bourrat, 1998; Ishikawa et al., 1999). Because performing three-dimensional reconstruction from brain …
| Abbreviation of anatomical region | Name of subregion | Name of anatomical region | Cellular distribution |
|---|---|---|---|
| Dc | The dorso-central telencephalon | In most teleostean species, cells in Dc have larger size of cell body (Cichlid fish Burmeister et al., 2009, sea bass Cerdá-Reverter et al., 2001) and are sparsely distributed. According to the medaka brain atlas of Ishikawa et al., 1999, Dc is defined in the center of the pallium as well. However, in the other brain atlas of medaka fish (Anken and Bourrat, 1998), multiple subregions are separately defined as Dcs. In our atlas, we defined the center region of the pallium that has less dense cell populations as Dc. | |
| Dcpm | The posterior medial nucleus of the dorso-central telencephalon | The aggregates of cells in the posterior medial center of dorsal pallium (Dcpm) were found. | |
| Dm | The medial part of the dorsal pallium | Small cell-body neurons with high density were observed. In the horizontal optic sections, we found several linearly aligned cells on the dorsal surface of the telencephalic hemispheres which correspond to the boundaries of Dm subregions. | |
| Dm1 | Densely packed with small cells. | ||
| Dm2 | Dm2 is packed with cells more densely than Dm1. | ||
| Dm3 | |||
| Dm4 | |||
| Dl | The dorsal lateral pallium | In the previous medaka brain atlas, the anterior region of dorsal lateral pallium is simply named as Dl (Anken and Bourrat, 1998). But here we named this anterior part of dorso-lateral telencephalon the Dla because the nuclear density is less than Dld, Dlv, and Dlp. We also divided Dl into the dorsal and ventral part since the nuclear density is different between the dorsal and ventral parts. | |
| Dla | The anterior part of the dorso-lateral telencephalon | In the horizontal sections, we found that the density of nucleuses are more sparse in Dla than Dld and Dlv. | |
| Dld | The dorsal part of the middle and posterior part of the dorso-lateral telencephalon | The dorsal part of the middle and posterior part of the dorso-lateral telencephalon (Dld) (Anken and Bourrat, 1998) is next to Dla and the cell density is more than that of Dla. | |
| Dlv | The ventral part of the middle and posterior part of the dorso-lateral telencephalon | The boundary between Dld and Dlv is not clear. But the cells are more densely distributed in Dlv than Dld. The ventral part of the middle and posterior part of the dorso-lateral telencephalon (Dlv)(Anken and Bourrat, 1998) is highly packed with cells. | |
| Dlp | The posterior regions of the dorso-lateral telencephalon | Higher DAPI signal density in Dlp than Dld and Dlv were detected. There is no clear boundary among the posterior regions of the dorso-lateral telencephalon (Dlp), the posterior of dorsal telencephalon (Dp), Dld, and Dlv. But we observed that Dlp was highly dense with a small nucleus and the cell distribution pattern was different from neighboring regions. | |
| Dd | The dorso-dorsal telencephalon | In the previous report (Anken and Bourrat, 1998), Dd is subdivided into two regions, Dd1 and Dd2. In the other report (Ishikawa et al., 1999), only Dd is defined which corresponds to Dd2 of Anken and Bourrat, 1998. Since the boundary between Dd1 and Dd2 was visible in DAPI staining, we followed the definition of Ralf H Anken, 1998. | |
| Dd1 | |||
| Dd2 | Dd2 is clearly demarcated in the telencephalon. As observed with the horizontal sections, Dd2 can be subdivided into two regions, Dd2a (anterior part of Dd2) and Dd2p (posterior part of Dd2). Dd2p is surrounded by cells, and the cell density is relatively higher than Dd2a. | ||
| Dp | The posterior part of dorsal telencephalon | The posterior part of dorsal telencephalon (Dp) (Anken and Bourrat, 1998) is remarkably denser with the cell nucleus than other posterior anatomical regions. | |
| Vd | The dorsal medial part of the subpallium | Cells in the dorsal medial part of the subpallium are called Vd. We also observed some cell clusters that are located laterally and inside the pallium. Those cell clusters correspond to the Vc region in some references. But according to the cell density and some gene expression, we define those regions also as Vd. | |
| Vs | The supracommissural part of ventral telencephalon | The supracommissural part of ventral telencephalon (Vs) is located ventral to Vd. But there is no clear boundary between Vs and Vd. | |
| Vv | The ventral part of the subpallium | ||
| ECL | The external layer of the olfactory bulb | In the anterior part of the telencephalon, the external (ECL) and internal (ICL) cellular layer of the olfactory bulb and the glomerular layer of the olfactory bulb (GL) are clearly found. | |
| ICL | The internal layer of the olfactory bulb |
