dsRNAs are associated with highly expressed genes and marks of transcriptional elongation. (A) Tukey box plots show the distributions of embryo-stage gene expression (FPKM: fragments per kilobase-million reads) for all genes or EAGs on distal arm or center domains of autosomes or Chromosome X. (*) P < 0.05; (**) P < 0.01; (****) P < 0.0001; Mann–Whitney test. (B) Tukey box plots as in A showing expression in each developmental stage of all genes or EAGs on autosome distal arms. (****) P < 0.0001; Mann–Whitney test. (C) Tukey box plots as in A showing embryo-stage expression of all genes or genes containing a structured intron (Struct.; intron ΔG/nt < −0.5 kcal/mol × nt), separated by chromosomal domain. (*) P < 0.05; (****) P < 0.0001; Mann–Whitney test. (D) Tukey box plot as in A showing embryo-stage expression of all genes, EAGs, or genes containing three or more distinct EER-associated introns and/or UTRs (3+ EER) present on autosome arms. (***) P < 0.001; (****) P < 0.0001; Mann–Whitney test. (E) Heatmap displays the relative ChIP-chip signal for 19 histone modifications over EERs, random regions, structured (ΔG/nt < −0.5 kcal/mol × nt) or unstructured introns, IR loci, and TR loci present on autosome distal arms.
