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. 2020 Nov 23;55(4):483–499.e7. doi: 10.1016/j.devcel.2020.09.002

Figure 4.

Figure 4

TBX-37/38 Establish a Differentially Accessible State of the lsy-6 Locus

(A) Schematic of the embryo-labeling strategy for ABa and ABp isolation. The indicated time points (90, 200, and 350 min) were used for the experiments in (B) and (C). Representative image of an embryo at the 8 ABa stage carrying the three-reporter combination (Figures S3A–S3C).

(B) (Top) Aggregated GFP-TBX-37/38 ChIP-seq signal over the lsy-6 locus and flanking sequences. (Middle) ATAC-seq signal in ABa- and ABp-derived cells at three different time points showing ABa-specific accessibility of lsy-6, overlapping with the TBX-37/38 binding site (red shading); two biological replicates were analyzed per condition. For reference, downstream locus shows equal accessibility in both lineages (also Figure S3D). Number of ABa/ABp descendants at the different time points are shown. (Bottom) ATAC-seq signal from sorted ASEL and ASER shows accessibility in ASEL upstream of lsy-6, overlapping with a CHE-1 binding site (blue shading). Peaks called by MACS2 are marked with a bar.

(C) Close-up view of the lsy-6 locus and its ATAC-seq signal in ABa, ABp, ASEL, and ASER isolated from wild-type or Δtbs embryos (deletion marked with a red line); two biological replicates were analyzed per condition. Loss of TBX-37/38 binding sites causes loss of accessibility of the CHE-1 binding site in mature ASEs. For Δtbs embryos, ASEL and ASER cannot be distinguished as lsy-6 is not expressed and the cells become symmetric (Figure 2B); the ASE ATAC-seq in this case was done on che-1prom::mCherry-expressing cells, and the same track is shown in duplicate under ASEL and ASER.

(D) Correlation analysis between ATAC-seq data from wild-type or Δtbs embryos shows that datasets are highly similar and differ almost exclusively in their signal over the lsy-6 locus. Plotted are signals in log2 (cpm) for all peaks called by MACS2 in at least one ATAC-seq sample. The p values for the called lsy-6 peaks in ABa (overlapping with TBX-binding sites, red) and ASEL (overlapping with CHE-1 binding site, blue) are shown.