Fig 4. RNA-seq analysis of sig-7(RNAi) embryos reveals a global transcription defect.

RNA-seq was performed on RNA purified from sig-7(RNAi) and L4440 control RNAi embryos and the profiles compared. A) Volcano plot of normalized RNA-seq results showing the number of genes exhibiting significantly decreased (1549) and increased (362) RNA abundance in sig-7(RNAi) compared to L4440 (>2-fold differences with q value < 0.05). (B) Genes exhibiting significantly decreased (left) or increased (right panel) transcript accumulation in sig-7(RNAi) compared to L4440 were classified as ubiquitous, germline (germl)-enriched, germline(germl)-specific, soma-specific (broadly defined; soma-all), embryo-expressed (embryo-expr), or X-linked (chrX). Gene class definitions are described in Materials and Methods. The number of genes observed and expected for each class (left y-axis), and the ratio of observed/expected (right y-axis) are shown. The gene classes with zygotic expression are highly overrepresented in those showing reduced expression in sig-7(RNAi) embryos, while genes with germline expression are highly overrepresented in those showing higher expression in sig-7(RNAi) embryos. The significance of the enrichment (green asterisks) or depletion (red asterisks) as determined by the hypergeometric distribution for each gene class is indicated by asterisks (* = p ≤ 0.01, ** = p ≤ 10⁻⁵, *** = p ≤ 10⁻¹⁰).