||In mammals, more than 60% of the genome is use for transcription for mRNAs and noncoding RNAs (ncRNAs). A fraction of ncRNAs have been believed to downregulate the corresponding mRNA expression level in a pre- or post- transcriptional manner by forming RNA-RNA duplex structures.To examine the directional properties of transcription at the whole genome level, we performed directional RNA-seq analysis of mouse brain and heart samples. Our analysis revealed that there is only a small fraction of the genome where both the top and bottom strands are utilized for transcription.A significant fraction of transcription start sites (TSSs) of protein-coding genes contain borders that separate antisense- and sense-biased transcription, suggesting that head-to-head transcription at the TSS is more prevalent than previously thought.The expression of the resultant promoter-associated ncRNAs (pancRNAs) tends to occur together with that of the corresponding mRNA in a coordinated manner. A fraction of genes with tissue-specific pancRNAs show a positive correlation between their pancRNA and mRNA expression, which is in accord with the proposed role for pancRNA in facultative gene activation, whereas genes with constitutive expression lack an association with pancRNA. More than 90% of head-to-head type promoters contain CpG islands. Moreover, CCG and CGG repeats are significantly enriched in the upstream regions and downstream regions, respectively, of TSSs located in head-to-head type promoters. Here, we propose that head-to-head transcription from GC-rich sequences regulates gene expression.