Major Determinants of Nucleosome Organization

RAZVAN V CHEREJI; JOSEFINA OCAMPO; TARA L BURKE; DAVID J CLARK

West Palm Beach

Conferencia; Transcription Chromatin and epigenetics; 2015

FASEB

In the past decade, genome-wide nucleosome mapping experiments suggested a conserved nucleosome organization near gene promoters, consisting of regular nucleosome arrays on the gene bodies and a nucleosome-depleted region (NDR) immediately upstream of the transcription start site (TSS). This organization is common among different species, e.g. yeast, fly, mouse, human. We study the major determinants of nucleosome organization in vivo, and the common principles that can explain the similarities in nucleosome distribution among different organisms. Using in vitro nucleosome reconstitution experiments, we show that in yeast, the DNA sequence alone is not able to generate neither the proper NDRs, nor the nucleosome phasing that is observed in vivo. Transcription [1] and chromatin remodeling factors [2] play key roles in establishing the steady state distribution of the nucleosomes. We analyze the roles of four remodelers (Isw1, Isw2, Chd1 and RSC) in chromatin organization, by mapping the nucleosome positions in yeast strains lacking one, two, three or all four remodelers. We find that in vivo, Isw2 and RSC are responsible for creating proper NDRs and positioning the neighboring nucleosomes at the correct locations, while Isw1 and Chd1 act on gene bodies to generate regular arrays of nucleosomes.Although nucleosome organization at the majority of yeast genes conforms to the overall average distribution across the genome, many other genes have a nucleosome distribution that differs from the average pattern. The position of the NDR relative to the TSS varies from gene to gene, and nucleosome arrays at individual genes can also have different spacing between nucleosomes. To understand the principles of chromatin organization that are universally true for different species, we conduct a comprehensive study, juxtaposing data obtained from different techniques: MNase-seq, DNase-seq, ChIP-seq, RNA-seq. We observe that genes with accessible promoters contain nucleosome arrays that are phased relative to the TSS and are transcriptionally active. Lastly, we use biophysical models [2-7] to explain the common patterns observed in nucleosome organization among different species. We construct a minimal model which can explain the nucleosome phasing at the 5' ends of the genes by competition between histones and other DNA-binding proteins, in a transcription-dependent way. We also propose a model for ATP-dependent nucleosome positioning by the chromatin remodeling enzymes [2].[1] HA Cole, J Ocampo, JR Iben, RV Chereji & Clark DJ, NAR (2014)[2] D Ganguli*, RV Chereji*, J Iben, HA Cole, DJ Clark, Genome Res. (2014) [3] RV Chereji, D Tolkunov, G Locke, AV Morozov, Phys. Rev. E (2011)[4] RV Chereji and AV Morozov, J. Stat. Phys. (2011)[5] RV Chereji and AV Morozov, PNAS (2014)