Genome-wide Nucleosome Occupancy Research Articles

Chromatin is an ancient innovation conserved between Archaea and Eukarya

The eukaryotic nucleosome is the fundamental unit of chromatin, comprising a protein octamer that wraps ∼147 bp of DNA and has essential roles in DNA compaction, replication and gene expression. Nucleosomes and chromatin have historically been considered to be unique to eukaryotes, yet studies of select archaea have identified homologs of histone proteins that assemble into tetrameric nucleosomes. Here we report the first archaeal genome-wide nucleosome occupancy map, as observed in the halophile Haloferax volcanii. Nucleosome occupancy was compared with gene expression by compiling a comprehensive transcriptome of Hfx. volcanii. We found that archaeal transcripts possess hallmarks of eukaryotic chromatin structure: nucleosome-depleted regions at transcriptional start sites and conserved -1 and +1 promoter nucleosomes. Our observations demonstrate that histones and chromatin architecture evolved before the divergence of Archaea and Eukarya, suggesting that the fundamental role of chromatin in the regulation of gene expression is ancient.DOI:http://dx.doi.org/10.7554/eLife.00078.001.

Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy

Nucleosome positioning dictates eukaryotic DNA compaction and access. To predict nucleosome positions in a statistical mechanics model, we exploited the knowledge that nucleosomes favor DNA sequences with specific periodically occurring dinucleotides. Our model is the first to capture both dyad position within a few base pairs, and free binding energy within 2 k(B)T, for all the known nucleosome positioning sequences. By applying Percus's equation to the derived energy landscape, we isolate sequence effects on genome-wide nucleosome occupancy from other factors that may influence nucleosome positioning. For both in vitro and in vivo systems, three parameters suffice to predict nucleosome occupancy with correlation coefficients of respectively 0.74 and 0.66. As predicted, we find the largest deviations in vivo around transcription start sites. This relatively simple algorithm can be used to guide future studies on the influence of DNA sequence on chromatin organization.

An evolutionary perspective on nucleosome positioning

Through a comparison of genome-wide nucleosome occupancy maps from 13 species of fungi, these authors provide insight into the relationship between genome evolution and chromatin structure. Although they found substantial conservation across species in levels of nucleosome depletion at many sites, they also found important differences among species in the roles played by sequence or trans-acting factors in determining nucleosome positioning. This work suggests evolutionary plasticity in regulation of chromatin structure.

Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization

The packaging of eukaryotic genomes into nuclesomes plays critical roles in chromatin organization and gene regulation. Studies in Saccharomyces cerevisiae indicate that nucleosome occupancy is partially encoded by intrinsic antinucleosomal DNA sequences, such as poly(A) sequences, as well as by binding sites for trans-acting factors that can evict nucleosomes, such as Reb1 and the Rsc3/30 complex. Here, we use genome-wide nucleosome occupancy maps in 13 Ascomycota fungi to discover large-scale evolutionary reprogramming of both intrinsic and trans determinants of chromatin structure. We find that poly(G)s act as intrinsic antinucleosomal sequences, comparable to the known function of poly(A)s, but that the abundance of poly(G)s has diverged greatly between species, obscuring their antinucleosomal effect in low-poly(G) species such as S. cerevisiae. We also develop a computational method that uses nucleosome occupancy maps for discovering trans-acting general regulatory factor (GRF) binding sites. Our approach reveals that the specific sequences bound by GRFs have diverged substantially across evolution, corresponding to a number of major evolutionary transitions in the repertoire of GRFs. We experimentally validate a proposed evolutionary transition from Cbf1 as a major GRF in pre-whole-genome duplication (WGD) yeasts to Reb1 in post-WGD yeasts. We further show that the mating type switch-activating protein Sap1 is a GRF in S. pombe, demonstrating the general applicability of our approach. Our results reveal that the underlying mechanisms that determine in vivo chromatin organization have diverged and that comparative genomics can help discover new determinants of chromatin organization.

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast

The packaging of eukaryotic DNA into chromatin has profound consequences for gene regulation, as well as for other DNA transactions such as recombination, replication and repair. Understanding how this packaging is determined is consequently a pressing problem in molecular genetics. DNA sequence, chromatin remodelers and transcription factors affect chromatin structure, but the scope of these influences on genome-wide nucleosome occupancy patterns remains uncertain. Here, we use high resolution tiling arrays to examine the contributions of two general regulatory factors, Abf1 and Rap1, to nucleosome occupancy in Saccharomyces cerevisiae. These factors have each been shown to bind to a few hundred promoters, but we find here that thousands of loci show localized regions of altered nucleosome occupancy within 1 h of loss of Abf1 or Rap1 binding, and that altered chromatin structure can occur via binding sites having a wide range of affinities. These results indicate that DNA-binding transcription factors affect chromatin structure, and probably dynamics, throughout the genome to a much greater extent than previously appreciated.

Revisiting the Contribution of cis-Elements to Expression Divergence between Duplicated Genes: The Role of Chromatin Structure

Although divergence in expression is thought to be a hallmark of functional dispersal between paralogs postduplication, there is currently a limited understanding of the mechanisms underlying the necessary transcriptional alterations as recent studies have suggested that only a very small proportion of expression variation could be explained by transcriptional variation between paralogs. To further this understanding, we examined comprehensively curated regulatory interactions and genomewide nucleosome occupancy in budding yeast to specifically determine the contribution of cis-elements to expression divergence between extant duplicates. We found that divergence in activation by transcription factors plays a more important role in expression divergence of paralogs than previously appreciated; further, analysis of promoter chromatin structure demonstrated that differential nucleosome organization is coupled with divergent expression of paralogs. By incorporating information of cis-elements encoding transcriptional regulation and chromatin structure, we improved the fraction of expression variation that was previously shown to be explained based on known cis-transcriptional effects by approximately 3-fold. Taken together, our analysis highlights the importance of chromatin divergence involved in expression evolution between paralogs.

Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy

Motivation: Understanding the mechanisms that govern nucleosome positioning over genomes in vivo is essential for unraveling the role of chromatin organization in transcriptional regulation. Until now, models for predicting genome-wide nucleosome occupancy have assumed that the DNA associations of neighboring nucleosomes on the genome are independent. We present a new model that relaxes this independence assumption by modeling interactions between adjacent nucleosomes.Results: We show that modeling interactions between adjacent nucleosomes improves genome-wide nucleosome occupancy predictions in an in vitro system that includes only nucleosomes and purified DNA, where the resulting model has a preference for short spacings (linkers) of less than 20 bp in length between neighboring nucleosomes. Since nucleosome occupancy in vitro depends only on properties intrinsic to nucleosomes, these results suggest that the interactions we find are intrinsic to nucleosomes and do not depend on other factors, such as transcription factors and chromatin remodelers. We also show that modeling these intrinsic interactions significantly improves genome-wide predictions of nucleosome occupancy in vivo.Contact: eran.segal@weizmann.ac.ilSupplementary information: Supplementary data are available at Bioinformatics online.