Transcription starts from the constitutive PL, PR and PRE promoters producing the ‘Immediate Early -IE' transcripts: the N (aNtiterminator) and, cro (Control of Repressor’s operator) genes. The N protein is an antiterminator, and functions to extend the reading frames passing 2 IE genes: N & cro. N binds to the two Nut (N utilisation) sites, one in the N gene in the PL reading frame, and one in the cro gene in the PR reading frame cro binds to OR3 preventing access to the PRM promoter preventing expression of the cI gene.

The cII and cIII genes are needed to establish lysogeny The delayed early gene products cII and cIII are necessary for RNA polymerase to initiate transcription at the promoter PRE. cII acts direct at the promoter and, cIII protects cII from degradation. Transcription from PRE leads to synthesis of repressor and also blocks the transcription of cro.

Lysogeny is maintained solely by cI (clear1). cI represses transcription from PL and PR while upregulating and controlling its own expression from PRM. Cl is a transcription inhibitor, binds OR1, OR2 and OR3 (affinity OR1 > OR2 = OR3). At low concentrations blocks the pR promoter (preventing cro production). It is, therefore, the only protein expressed by lysogenic phage.