Khor JM et al. (2021), Global patterns of enhancer activity during sea...

ECB-ART-49052

Genome Res 2021 Sep 01;319:1680-1692. doi: 10.1101/gr.275684.121.

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Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling.

Khor JM , Guerrero-Santoro J , Douglas W , Ettensohn CA .

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We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were located near gene bodies, and temporal patterns of eRNA expression tended to parallel those of nearby genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays was associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are available at Echinobase, the public database of information related to echinoderm genomics.

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	Figure 1. Examples of eRNA peaks near Sp-jun. (A) Three of the four eRNA peaks shown (top track; gray bars) overlap with chromatin regions that are hyperaccessible at 24 hpf but not at the 128-cell stage, as determined by ATAC-seq and DNase-seq (Shashikant et al. 2018). (B) Temporal CAGE-seq coverage tracks illustrate the bidirectional expression of eRNAs and the very low abundance of eRNA reads relative to coding genes (scale: zero to three read counts). Sea urchin jun is expressed at high levels maternally, followed by a second peak of expression at gastrula stage. Spatially, jun is distributed homogenously in unfertilized egg and during early cleavages and is restricted to the PMCs at later stages (Russo et al. 2014).
	Figure 2. Annotation and analysis of eRNA peaks. (A) Frequency histogram illustrating peak-to-gene distances, with each bar representing 5000 bp. (B) Pie chart showing the location of eRNA peaks relative to nearest annotated gene. (C) Venn diagram showing the distribution of eRNA peaks that overlap with regions of chromatin shown to be hyperacessible at 128-cell stage and 24 hpf by ATAC-seq and at 28 hpf by DNase-seq (Shashikant et al. 2018). (D) Total number of eRNAs (greater than zero TPM expression) at each time point. (E) Number of newly-appearing eRNAs at each time point.
	Figure 3. Heatmap based on k-means clustering (K = 20) of eRNA temporal expression profiles. The number of eRNAs in each cluster is shown in parentheses.
	Figure 4. Expression pattern correlation analysis of eRNAs and nearby genes (cluster analysis summarized in Supplemental Fig. S6). (A) Fold enrichment of clustered eRNAs within 20 kb of genes in âparentalâ or other clusters (compared with total eRNAs in this analysis) is represented by the circles, and the color of the circles correspond to the significance of the enrichment, expressed as âlog10(FDR). Only cluster pairs that show greater than 1.5-fold enrichment and FDR < 0.05 are shown. (B) Analysis of eRNA peaks that are exclusively accessible at the 128-cell stage (128-cell eRNAs) or 24 hpf (24 hpf eRNAs) to overlap with eRNA peaks from different temporal expression clusters. (C) Analysis of eRNA peaks that are exclusively accessible at the 128-cell stage or 24 hpf to be within 20 kb of clustered genes. Fold enrichment is represented by the size of the circles, and the colors correspond to the significance of the enrichment, expressed as âlog10(P-value). Only enrichments that show greater than 1.5-fold enrichment and P < 0.05 are shown.
	Figure 5. Experimental validation of eRNA peaks using GFP reporter constructs. (A) Embryos (â¼48 hpf) injected with reporter constructs containing eRNA peaks near genes differentially expressed by PMCs. (B) Embryos (â¼72 hpf) injected with reporter constructs containing eRNA peaks near genes differentially expressed by pigment cells. Scale bar, 50 Âµm.

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Adams, Procuring animals and culturing of eggs and embryos. 2019, Pubmed, Echinobase