Analysis of Ly49 gene transcripts in mature NK cells supports a role for the Prol element in gene activation, not gene expression

The variegated expression of murine Ly49 loci has been associated with the probabilistic behavior of an upstream promoter active in immature cells, the Prol element. However, recent data suggest that Prol may be active in mature natural killer (NK) cells and function as an enhancer element. To assess directly if Prol transcripts are present in mature Ly49-expressing NK cells, RNA-sequencing of the total transcript pool was performed on freshly isolated splenic NK cells sorted for expression of either Ly49G or Ly49l. No Prol transcripts were detected from the Ly49a, Ly49c or Ly49i genes in mature Ly49(+) NK cells that contained high levels of Pro2 transcripts. Low levels of Ly49g Prol transcripts were found in both Ly49G(+) and Ly49G(-) populations, consistent with the presence of a small population of mature NK cells undergoing Ly49g gene activation, as previously demonstrated by culture of splenic NK cells in interleukin-2. Ly49 gene reporter constructs containing Prol failed to show any enhancer activity of Prol on Pro2 in a mature Ly49-expressing cell line. Taken together, the results are consistent with Prol transcription having a role in gene activation in developing NK, and argue against a role for Prol in Ly49 gene transcription by mature NK cells.