FIG. 3.
miRNA H6 and H4 loci. (A) Sequence of the genomic locus encoding complementary miRNAs, HSV-1 miR-H1 and -H6. The boxes indicate -3p and -5p strands of miR-H1 (gray shading) and miR-H6 (no shading), with arrows indicating the direction of transcription. Parts of the sequences encoding moR-H6-5p and -3p are shown in italics, with discontinued arrows indicating the direction of transcription. Nucleotide coordinates for the IRL copy of the locus according to HSV-1 strain 17+ genome (NC_001806) are shown on the top of the panel. (B and C) Hairpin structures of HSV-1-encoded precursor of miR-H1 and miR-H6 and HSV-2-encoded precursor of miR-H6 (B); and hairpin structures of HSV-1- and HSV-2-encoded precursors of miR-H4 (C). The most prominently found sequence reads are shown in boldface and encompassed by brackets with arrows. Solid or dotted lines indicate miRNA or moR sequences, respectively. Black and gray arrows point to Dicer and presumed Drosha cleavage sites, respectively. The numbers of detected sequence reads in the productive infection sample are shown below and above the corresponding miRNA or moR strand. (D) Sequence comparison of HSV-1 miR-H1-5p and HSV-2 miR-H6-5p. The seed sequence of each miRNA is shown in boldface, and the identical nucleotides are indicated with the asterisks.