Nucleosome positioning and transcription: fission yeast CHD remodellers make their move

Abstract

Regularly positioned nucleosomes are a common feature of 5' ends of most eukaryotic genes. A series of three studies, Shim et al (2012) and Pointner et al (2012) in this issue of The EMBO Journal and Hennig et al (2012) in EMBO Reports, now show that in the fission yeast Schizosaccharomyces pombe this intragenic nucleosome positioning mostly requires two ATP-dependent remodellers of the CHD family, Hrp1 and Hrp3. Moreover, they suggest that Hrp1- and Hrp3-dependent nucleosome spacing contributes to the silencing of cryptic antisense transcription.

Figure 1

Model for the positioning of nucleosomes at the 5′ end of genes and the suppression of intragenic cryptic transcription in the fission yeast S. pombe. In S. pombe, as in many eukaryotes, the chromatin organization at the 5′ end of most genes is well defined. It consists of a nucleosome-free region (NFR) at the promoter bordered by positioned nucleosomes (grey circles). This nucleosome positioning decreases as the distance from the promoter increases. Two CHD-type ATP-dependent remodellers, Hrp1 and Hrp3 (blue ovals), play a major role in positioning nucleosomes downstream transcription start sites (TSSs). A lack of both remodellers also leads to an increase in cryptic antisense transcription (dashed arrows), suggesting that Hrp1- and Hrp3-dependent nucleosomal positioning may silence intragenic cryptic promoters. Such silencing may act in parallel with Clr6 histone deacetylase (HDAC) complex II, a Rdp3-type HDAC complex, and Set2, the lysine 36 histone methyltransferase (KMT) (green ovals), which also participates in the suppression of such cryptic transcription.