Nucleosome positioning in yeasts: methods, maps, and mechanisms

Abstract

Eukaryotic nuclear DNA is packaged into nucleosomes. During the past decade, genome-wide nucleosome mapping across species revealed the high degree of order in nucleosome positioning. There is a conserved stereotypical nucleosome organization around transcription start sites (TSSs) with a nucleosome-depleted region (NDR) upstream of the TSS and a TSS-aligned regular array of evenly spaced nucleosomes downstream over the gene body. As nucleosomes largely impede access to DNA and thereby provide an important level of genome regulation, it is of general interest to understand the mechanisms generating nucleosome positioning and especially the stereotypical NDR-array pattern. We focus here on the most advanced models, unicellular yeasts, and review the progress in mapping nucleosomes and which nucleosome positioning mechanisms are discussed. There are four mechanistic aspects: How are NDRs generated? How are individual nucleosomes positioned, especially those flanking the NDRs? How are nucleosomes evenly spaced leading to regular arrays? How are regular arrays aligned at TSSs? The main candidates for nucleosome positioning determinants are intrinsic DNA binding preferences of the histone octamer, specific DNA binding factors, nucleosome remodeling enzymes, transcription, and statistical positioning. We summarize the state of the art in an integrative model where nucleosomes are positioned by a combination of all these candidate determinants. We highlight the predominance of active mechanisms involving nucleosome remodeling enzymes which may be recruited by DNA binding factors and the transcription machinery. While this mechanistic framework emerged clearly during recent years, the involved factors and their mechanisms are still poorly understood and require future efforts combining in vivo and in vitro approaches.

Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome

“…5), mononucleotides, trinucleotides, and A + T profile (Quintales et al 2015a) is very different among the four species. Maps of nucleosomal occupancy generated using different methods like MNase digestion or chemical cleavage of DNA at the dyad position are very similar (Brogaard et al 2012;Moyle-Heyrman et al 2013;Lieleg et al 2015;Quintales et al 2015a, b). This implies that matrices derived from well-positioned nucleosomes from different experiments will probably be very similar to those described in this work.…”

Plasmodium falciparum Nucleosomes Exhibit Reduced Stability and Lost Sequence Dependent Nucleosome Positioning

“…In principle, sequences that are already pre-curved, requiring low energy levels to wind around a histone octamer should preferentially bind and position nucleosomes. Models were devised to predict nucleosome positioning in vitro and in vivo from DNA sequence [9], albeit the predictive power is currently being questioned [67]. …”

Dissecting relative contributions ofcis- andtrans-determinants to nucleosome distribution by comparingTetrahymenamacronuclear and micronuclear chromatin

“…The +1 nucleosome in Tetrahymena is placed much further away from TSS than in yeast, in positions similar to metazoa. In yeast, gene promoters are often wrapped up in the +1 nucleosome (22). In metazoa, transcription initiation and promoter proximal pausing are regulated separately, with the latter affected by the +1 nucleosome (41,59).…”

“…All these shape the nucleosome distribution in the gene body bounded by transcription start sites (TSS) and transcription end sites (TES), manifest in stereotypical arrays of well-positioned nucleosomes (referred to as +1, +2, etc., ordered 5′ to 3′) (18–21). The relative contributions of cis - and trans -determinants to nucleosome occupancy and nucleosome positioning are actively studied in various systems (2,22,23). Absence of stereotypical nucleosome arrays in yeast nucleosomes reconstituted without cell extracts and ATP favors trans -determinants as the predominant factor (10,11,24).…”