Figure 1: Large-scale regulatory analysis of the C. elegans genome.

a, Transcription factors (TFs) and regulatory proteins assayed per developmental stage (or treatment) in 241 quality-filtered ChIP-seq experiments. Stages and treatments are early embryo (EE), late embryo (LE), embryo mixed (EM; EE and LE), larval L1 (L1), larval L2 (L2), larval L3 (L3), larval L4 (L4), young adult (YA), mixed larval and young adults (LY), day 4 adult (D4), and starved L1 (S1). Embryonic data sets were combined into a compiled embryonic stage (EX). Analyses in this report focus on embryonic (yellow) and larval (blue) experiments (N = 187). b, Genomic coverage (percent of genomic bases) of regulatory binding (excluding RNA polymerases) in 181 C. elegans (outer circle) and 339 H. sapiens (inner circle) ChIP-seq experiments. Genomic coverage of constitutive HOT (cHOT), HOT, and other regulatory binding (RGB) regions are highlighted in red, yellow and blue, respectively. Constitutive XOT (cXOT) and XOT percentages are shown in parenthesis. cHOT, HOT and RGB region coverage in the human genome are 0.17%, 1.4% and 6.1%, respectively⁷. c, Cut-off-normalized occupancy levels in 126 embryo-specific (yellow) and 91 larval L4-specific (blue) HOT regions. Bars indicate the 25th and 75th percentiles. d, Chromatin state, as determined in ref. 14, of L3 larvae binding regions by occupancy. RGB-, HOT- and XOT-region occupancy levels are indicated along the x axis as blue, yellow and red bars, respectively. Poly. Repress. and Heterochr. indicate Polycomb, repressed and heterochromatin states. e, f, Signal densities near enzymatically derived TSSs²⁹ for BLMP-1 and ALY-2, and RNA Pol II. g, Functional (GO term) enrichment for gene targets of binding³⁰. A subset of biological process terms (level ≥4) are shown for factors enriched (Benjamini–Hochberg-corrected, P < 0.01) in synaptic transmission; early MEP-1 and DPL-1 data sets are included for comparison. h, Example signal tracks near the UNC-104 locus.

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