Figure 4

A hypothetical model for antisense transcription from var loci. Sense and antisense RNA at several var loci appear to be coordinately regulated. This may result from the altered chromatin state of the encoding genomic DNA, which is differentially modified between silent and active var loci [3]. Silencing factors such as the SIR complex (indicated by blue spheres) bind to inactive var genes, maintaining the chromatin in a condensed state. In the absence of SIR, the active var assumes a relaxed chromatin conformation that makes the surrounding locus competent for transcription. While a stable transcription complex with appropriate assembly of elongation factors generates abundant sense mRNA of full length, transcription from the opposite strand initiates and quickly terminates to produce fragments of antisense. Simultaneous transcription of the same bases from opposite directions is unviable, but in a population, both transcription events may occur at the same time. A chromatin barrier located in the intron [11] may maintain the first exon in a silencing conformation while allowing relaxation of the second exon, leading to partial 3' transcripts from a subset of otherwise silenced var genes.