Chromatin structures and transcription of rDNA in yeastSaccharomyces cerevisiae

Abstract

The chromatin structure of yeast ribosomal DNA was analyzed in vivo by crosslinking intact cells with psoralen. We found that in exponentially growing cultures the regions coding for the 35S rRNA precursor fall into two distinct classes. One class was highly accessible to psoralen and associated with nascent RNAs, characteristic for transcriptionally active rRNA genes devoid of nucleosomes, whereas the other class showed a crosslinking pattern indistinguishable from that of bulk chromatin and was interpreted to represent the inactive rRNA gene copies. By crosslinking the same strain growing in complex or minimal medium, we have shown that yeast cells can modulate the proportion of active (non-nucleosomal) and inactive (nucleosomal) rRNA gene copies in response to variations in environmental conditions which suggests that yeast can regulate rRNA synthesis by varying the number of active gene copies, in contrast to the vertebrate cells studied so far. Whereas intergenic spacers flanking inactive rRNA gene copies are packaged in a regular nucleosomal array, spacers flanking active genes show an unusual crosslinking pattern suggesting a complex interaction of regulatory factors and histones with DNA.

Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules

“…Whereas early analyses based on psoralen accessibilities in rDNA led to the conclusion that actively transcribed rRNA genes are devoid of nucleosomes (Dammann et al 1993), more recent data suggest that active rDNA has nucleosomal structure (Jones et al 2007). We reasoned that ChEC could give more insights into the association of histone molecules with Pol I-transcribed loci.…”

“…The characteristic cross-linking pattern of the f-band visualized by electron microscopy suggested that the DNA had been assembled into nucleosomes in the living cell (Dammann et al 1993). Furthermore, it was demonstrated that nascent rRNA is selectively associated with the heavily psoralen-cross-linked s-band (Conconi et al 1989;Dammann et al 1993), leading to the conclusion that this (presumably) nucleosome-free fraction of rDNA is actively transcribed in vivo.…”

“…Furthermore, it was demonstrated that nascent rRNA is selectively associated with the heavily psoralen-cross-linked s-band (Conconi et al 1989;Dammann et al 1993), leading to the conclusion that this (presumably) nucleosome-free fraction of rDNA is actively transcribed in vivo.…”

Response to acetaldehyde stress in the yeast Saccharomyces cerevisiae involves a strain‐dependent regulation of several ALD genes and is mediatedby the general stress response pathway

“…A 3.7 kb XbaI fragment of rDNA from plasmid pSZ26 (Dammann et al, 1993) was used as loading control. Hybridization and quantification were carried out as described elsewhere (Aranda et al, 2002).…”

Transcriptional homogenization of rDNA repeats in the episome-based nucleolus induces genome-wide changes in the chromosomal distribution of condensin

“…Indeed, active transcription poses a problem for condensin's ability to facilitate segregation of sister chromatids within the nucleolus (Tomson et al, 2006;Wang et al, 2006). However, only half of the rDNA copies are transcriptionally active (Dammann et al, 1993;Dammann et al, 1995;French et al, 2003), and therefore condensin likely utilizes the existence of repeats silent for PolI transcription to mediate segregation of the nucleolus. This theory of compartmentalization between transcription and segregation function in rDNA has been substantiated in the recent study (Wang et al, 2006).…”