vU1 snRNAs are packaged into RNP complexes. qRT-PCR analysis of U1 snRNA and vU1 snRNA levels in HeLa (A) and hESC (B) extracts, before and after immunoprecipitation with anti-Sm (Y-12) antibody. The non-Sm-containing 7SK RNA level was used as a negative control. Location of the primers is indicated in A. The level of the U1 snRNA and vU1 snRNAs, enriched in the Sm-immunoprecipitate, is expressed relative to input at 100%. RT (reverse transcription) reactions without “–” or with “+” the addition of Superscript III. Note: Although vU1.15/vU1.16 snRNA was enriched in RNP complexes, molecular cloning, followed by sequencing, indicated that this variant was not properly processed at the 3′ end. The levels of the vU1 snRNAs, enriched in the Sm immunoprecipitates, relative to the U1 snRNA were estimated using a genomic DNA standard to normalize primer efficiency.
