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ORIGINAL RESEARCH PAPER Hughes, A. L. et al.

A functional evolutionary approach to identify

determinants of nucleosome positioning:

a unifying model for establishing the genome-wide

pattern. Mol. Cell 9 Aug 2012 (doi:10.1016/

j.molcel.2012.07.003)

Nucleosome positioning is influencedby DNA sequence preferences and by

various protein complexes, but the rel-

ative contribution of these influenceshas been under debate. This paper

describes a functional evolutionaryapproach to assess the contribution ofDNA sequence and proteins further,and the authors propose a model

for the establishment of nucleosomepositioning in vivo.

Hughes and colleagues generated

seven strains ofSaccharomycescerevisiae that contained yeast artifi-cial chromosomes (YACs) with large

segments of foreign DNA fromthree yeast species (Kluyveromyceslactis, Kluyveromyces waltii and

Debaryomyces hansenii). Bycrosslinking the chromatin withformaldehyde and then digesting

the chromatin using miccrococcalnuclease, mononucelosomal DNA

could be analysed by deep sequenc-ing. The authors were then able tocompare nucleosome-mapping data

between the endogenous genomeand the modified S. cerevisiae strainsto describe the contribution of DNA

sequence (cis) and protein factors(trans) in nucleosome positioning

further. The principle of their func-tional evolutionary approach is asfollows: features that change when

a genomic region is placed in thecontext ofS. cerevisiae are influenced

by protein factors that differ betweenthe two species, whereas featuresthat are maintained when the foreignDNA is present in the S. cerevisiae

must be due either to intrinsic DNAsequence or to conserved trans-actingregulators.

Promoter nucleosome-depletedregions (NDRs) were largely main-tained in the YACs and were usually

located close to their endogenousposition, which is consistent withthe idea that nucleosome depletion

at fungal promoters is largely influ-enced by DNA sequence. However,nucleosome positions were generally

found to change across the YACstrains, and thus the authors suggest

that these differences must be dueto a trans-acting factor (or factors).They propose that nucleosome-

remodelling complexes recognizethe NDRs and position nucleosomesflanking the NDR, and the RNA

polymerase II preinitiation complexfine-tunes the position of the

CHROMATIN

A model fornucleosome positioning

+1 nucleosome. This idea is sup-ported by the observation that the

locations of the +1 nucleosome andRNA start sites shift in concert.

The third step of their model

involves the positioning of down-stream nucleosomes. The authorspropose that this may depend on

transcriptional elongation throughthe recruitment of nucleosome-remodelling activites and histone

chaperones by the elongating RNApolymerase II machinery. This model

is supported by previous work show-ing that yeast mutant strains lackingnucleosome-remodelling complexeshave drastically reduced positioning

of downstream nucleosomes but fairlynormal positioning of the +1 and +2nucleosomes.

In summary, this model suggeststhat determining nucleosome posi-tioning in vivo is a three-step process

that involves DNA sequence, nucleo-some remodellers, transcriptionfactors and transcriptional elongation

machinery. The authors state that thismodel can explain why the generalpattern of nucleosome positioning

is conserved across eukaryotes butshows species-specific differences

regarding chromatin structure.Bryony Jones

R E S E A R C H H I G H L I G H T S

NATURE REVIEWS |GENETICS VOLUME 13 | OCTOBER 2012

Nature Reviews Genetics| AOP, published online 29 August 2012; doi:10.1038/nrg3331

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