DOI: 10.5061/dryad.ttdz08m2s
title: Data from: Epigenetically distinct synaptic architecture in clonal compartments in the teleostean dorsal pallium

description: The dorsal telencephalon (i.e. the pallium) exhibits high anatomical
 diversity across vertebrate classes. The non-mammalian dorsal pallium
 accommodates various compartmentalized structures among species. The
 developmental, functional and evolutional diversity of the dorsal pallium
 remain unillustrated. Here, we analyzed the structure and epigenetic
 landscapes of cell lineages in the telencephalon of medaka fish (Oryzias
 latipes) which possesses a clearly delineated dorsal pallium (Dd2). We
 found that pallial anatomical regions, including Dd2, are formed by
 mutually exclusive clonal units, and that each pallium compartment
 exhibits a distinct epigenetic landscape. In particular, Dd2 possesses a
 unique open chromatin pattern that preferentially targets synapse-related
 genes. Indeed, Dd2 shows a high density of synapses. Finally, we
 identified several transcription factors as candidate regulators. Taken
 together, we suggest cell lineages are the basic components for the
 functional regionalization in the pallial anatomical compartments, and
 that their changes has been the driving force for evolutionary diversity.
description: Fish
 husbandry Medaka fish are kept at 14h/10h on light at 28 °C.
 The transgenic line　(Tg)
 (HuC:loxp-DsRed-loxp-GFP) and Tg (HSP:Cre/Crystallin-CFP) were generated
 as previously reported <sup>19</sup><sup>.</sup> Both males and females
 were used in the experiments. We used more than 2 months old fish as adult
 fish. Clonal units visualization
 To induce Cre/loxP recombination,
 embryos of the double Tg line, being crossed from female Tg
 (HuC:loxp-DsRed-loxp-GFP) and male Tg (HSP:Cre) line, were mildly heated
 at 38 °C for 15 min. Heat shock was applied using a thermal cycler to
 polymerase chain reaction tubes containing two eggs each. After the mild
 heat shock treatment, the embryos were maintained at 26°C until they
 hatched. Then the fish were kept in the fish tank and raised till the
 adult stage. Whole-brain clearing and
 imaging Adult fish brains were dissected by the usual
 procedure <sup>54</sup>. After  the dissection, the brains were fixed in
 4% paraformaldehyde/phosphate-buffered saline (PBS) overnight. Then the
 brains were washed twice with PBST (0.5% Triton-X100 in PBS) and immersed
 into ScaleA2 solution for about three hours on ice
 <sup>26</sup><sup>.</sup> When the brains were
 confirmed to be transparent, they were transferred into a new Sca/eA2
 solution with DAPI (0.5 ul/2ml) overnight at 4°C. The next day, the brains
 were transferred into the new ScaleA2 solution and washed with PBST. To
 prepare samples for signal detection, the brains were embedded in 0.75%
 agarose gel with Sca/A2-Triton solution and fixed on glass coverslips.
 Fluorescent signal detection was performed using
 a hand-made light sheet microscopy Digital Light-sheet Microscope (DSLM)
 <sup>55</sup> and a commercial one (Zeiss, Lightsheet
 Z.1).
 In order to define the anatomical
 regions, we used DAPI signals as landmarks. For whole-brain imaging, we
 dissected adult medaka brains, fixed with 4% paraformaldehyde/PBS, stained
 with DAPI in ScaleA4 (0.5/2000) for two days and soaked with Sca/eA4 for
 several days.
description: All data can be opened in Fiji.
 In order to do 3d reconstruction, we used
 FluoRender.