Fig. 5

Stranded RNA-Seq data provides improved resolution of imprinting at overlapping antisense genes. Several loci in the genome contain multiple imprinted transcripts, including pairs of overlapping antisense genes with opposite imprinting patterns. Strand-specific RNA-Seq provided considerably improved ability to discern the correct imprinting patterns at these loci when compared to the use of unstranded libraries. a–d KCNQ1 and KCNQ1OT1 lie within the 11p15.5 imprinted region. KCNQ1 on the plus strand is maternally expressed, while KCNQ1OT1 on the negative strand is paternally expressed. In whole blood where only unstranded data was available, no significant parental bias was detected from either transcript, likely due to the combined signal from the two overlapping transcripts giving the appearance of biparental expression. However, the use of stranded RNA-Seq in LCLs clearly shows that the two transcripts are antisense and have opposite imprinting patterns. e Similarly, GNAS and GNAS-AS1 are antisense transcripts located in 20q13.32. In LCLs, the stranded RNA-Seq data shows that while GNAS-AS1 is a paternally expressed imprinted gene, GNAS shows biparental expression