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. 2018 Oct 26;7:e37344. doi: 10.7554/eLife.37344

Figure 4. Shared dynamics of promoter accessibility in development and ageing.

Clusters of promoters with shared relative accessibility patterns across (A) development or (B) ageing. Relative promoter accessibility is log2 of the depth-normalized ATAC-seq coverage at a given time point divided by the mean ATAC-seq coverage across the time series (see Materials and methods). The percentage of associated genes that have enriched expression in the indicated tissues was determined from single-cell L2 larval RNA-seq data (Cao et al., 2017); see Materials and methods). Right hand panels show examples of GO terms enriched in genes associated with development or ageing clusters.

Figure 4—source data 1. Element accessibility dynamics and promoter accessibility clusters in development and ageing.
● chrom_ce10, start_ce10, end_ce10 location of the accessible site (bed-style coordinates, ce10). ● devel_is_dynamic True or False based on whether the site shows differential accessibility between any two developmental stages. ● ageing_is_dynamic True or False based on whether the site shows differential accessibility between any two ageing time points. ● devel_prom_cluster_label assigned developmental accessibility promoter cluster. ● ageing_prom_cluster_label assigned ageing accessibility promoter cluster. ● HOTness based on the number of transcription factors overlapping the accessible site, either HOT (19 or more factors), cold (between 1 and 18 factors) or none (zero factors). ● factor_count number of transcription factors with binding sites overlapping the accessible site. ● factor_names comma-separated list of the names of transcription factors with binding sites overlapping the accessible site.
elife-37344-fig4-data1.txt (4.5MB, txt)
DOI: 10.7554/eLife.37344.021

Figure 4.

Figure 4—figure supplement 1. Characteristics of developmental promoter clusters (continued in Figure 4—figure supplement 2).

Figure 4—figure supplement 1.

Characteristics of promoter clusters with shared accessibility patterns across development. Relative promoter ATAC-seq coverage is shown across the time series as a graph (each line representing a promoter) and a heatmap (each row representing a promoter). Values are scaled from −2 (dark blue) to 0 (white) to +2 (dark red). Heatmap showing relative expression of the associated genes across the time series, using the same color scale. Tissue expression box plots show TPMs of clustered genes in individual tissues (data from Cao et al., 2017). Percentage of genes with tissue-enriched expression shows the percentage of genes within the cluster with enriched expression in the indicated tissues. Enriched GO terms show the top five enriched GO terms obtained for each cluster from the corresponding list of genes using gProfiler. MF = Molecular Function, CC = Cellular Component, BP = Biological Process.
Figure 4—figure supplement 2. Characteristics of developmental promoter clusters (continued from Figure 4—figure supplement 1).

Figure 4—figure supplement 2.

Characteristics of promoter clusters with shared accessibility patterns across development. Relative promoter ATAC-seq coverage is shown across the time series as a graph (each line representing a promoter) and a heatmap (each row representing a promoter). Values are scaled from −2 (dark blue) to 0 (white) to +2 (dark red). Heatmap showing relative expression of the associated genes across the time series, using the same color scale. Tissue expression box plots show TPMs of clustered genes in individual tissues (data from Cao et al., 2017). Percentage of genes with tissue-enriched expression shows the percentage of genes within the cluster with enriched expression in the indicated tissues. Enriched GO terms show the top five enriched GO terms obtained for each cluster from the corresponding list of genes using gProfiler. MF = Molecular Function, CC = Cellular Component, BP = Biological Process.
Figure 4—figure supplement 3. Characteristics of ageing promoter clusters.

Figure 4—figure supplement 3.

Characteristics of promoter clusters with shared accessibility patterns across ageing. Relative promoter ATAC-seq coverage is shown across the time series as a graph (each line representing a promoter) and a heatmap (each row representing a promoter). Values are scaled from −2 (dark blue) to 0 (white) to +2 (dark red). Heatmap showing relative expression of the associated genes across the time series, using the same color scale. Tissue expression box plots show TPMs of clustered genes in individual tissues (data from Cao et al., 2017). Percentage of genes with tissue-enriched expression shows the percentage of genes within the cluster with enriched expression in the indicated tissues. Enriched GO terms show the top five enriched GO terms obtained for each cluster from the corresponding list of genes using gProfiler. MF = Molecular Function, CC = Cellular Component, BP = Biological Process. Note that Cluster Mix5 does not have any enriched GO terms.