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. 2022 Feb 25;11:e72834. doi: 10.7554/eLife.72834

Figure 1. Characterization of the transcriptional regulatory landscape surrounding the S. purpuratus kirrelL (Sp-kirrelL) locus.

Figure 1.

(A) Diagram of the Sp-kirrelL locus showing neighboring genes, regions of chromatin differentially accessible in primary mesenchyme cells (PMCs) at the mesenchyme blastula stage (ATAC-seq DE peaks and DNase-seq DE peaks) (Shashikant et al., 2018b), Sp-Alx1-binding sites at the mesenchyme blastula stage (Sp-Alx1 ChIP-seq peaks) (Khor et al., 2019), and enhancer RNA (eRNA) peaks (union of all peaks from the nine developmental stages examined by Khor et al., 2021). (B) Signal obtained from each assay in the vicinity of the Sp-kirrelL locus. The bottom part of the panel shows the expression of eRNAs at the nine developmental stages analyzed by Khor et al., 2021. (C) Phylogenetic footprinting of genomic sequences near S. purpuratus and L. variegatus kirrelL (±10 kb of an exon) using GenePalette. Black lines indicate identical sequences of 15 bp or longer in the same orientation while red lines indicate identical sequences of 15 bp or longer in the opposite orientation. Nine putative cis-regulatory elements (CREs; labeled elements A–I) were identified based on sequence conservation and chromatin signatures.