Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3’-end formation

Genome-wide mapping of nucleosomes generated by micrococcal nuclease (MNase) suggests that yeast promoter and terminator regions are very depleted of nucleosomes, predominantly because their DNA sequences intrinsically disfavor nucleosome formation. However, MNase has strong DNA sequence specificity that favors cleavage at promoters and terminators and accounts for some of the correlation between occupancy patterns of nucleosomes assembled in vivo and in vitro. Using an improved method for measuring nucleosome occupancy in vivo that does not involve MNase, we confirm that promoter regions are strongly depleted of nucleosomes, but find that terminator regions are much less depleted than expected. Unlike at promoter regions, nucleosome occupancy at terminators is strongly correlated with the orientation of and distance to adjacent genes. In addition, nucleosome occupancy at terminators is strongly affected by growth conditions, indicating that it is not primarily determined by intrinsic histone–DNA interactions. Rapid removal of RNA polymerase II (pol II) causes increased nucleosome occupancy at terminators, strongly suggesting a transcription-based mechanism of nucleosome depletion. However, the distinct behavior of terminator regions and their corresponding coding regions suggests that nucleosome depletion at terminators is not simply associated with passage of pol II, but rather involves a distinct mechanism linked to 3’-end formation.

[1]  J Seth Strattan,et al.  Nucleosomes unfold completely at a transcriptionally active promoter. , 2003, Molecular cell.

[2]  W Hörz,et al.  Sequence specific cleavage of DNA by micrococcal nuclease. , 1981, Nucleic acids research.

[3]  Steven M. Johnson,et al.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. , 2008, Genome research.

[4]  Ronald W. Davis,et al.  A high-resolution atlas of nucleosome occupancy in yeast , 2007, Nature Genetics.

[5]  Eran Segal,et al.  Evidence against a genomic code for nucleosome positioning? , 2010 .

[6]  Irene K. Moore,et al.  The DNA-encoded nucleosome organization of a eukaryotic genome , 2009, Nature.

[7]  H. Reinke,et al.  Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. , 2003, Molecular cell.

[8]  N. Krogan,et al.  Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes , 2004, The EMBO journal.

[9]  Cizhong Jiang,et al.  A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome , 2009, Genome Biology.

[10]  Irene K. Moore,et al.  A genomic code for nucleosome positioning , 2006, Nature.

[11]  Lani F. Wu,et al.  Genome-Scale Identification of Nucleosome Positions in S. cerevisiae , 2005, Science.

[12]  J. Lieb,et al.  Evidence for nucleosome depletion at active regulatory regions genome-wide , 2004, Nature Genetics.

[13]  J. Boeke,et al.  Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications , 1998, Yeast.

[14]  Kevin Struhl,et al.  Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. , 2005, Molecular cell.

[15]  Yaniv Lubling,et al.  Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals , 2008, PLoS Comput. Biol..

[16]  Clifford A. Meyer,et al.  Model-based analysis of tiling-arrays for ChIP-chip , 2006, Proceedings of the National Academy of Sciences.

[17]  William Stafford Noble,et al.  Nucleosome positioning signals in genomic DNA. , 2007, Genome research.

[18]  U. K. Laemmli,et al.  The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. , 2008, Molecular cell.

[19]  Kevin Struhl,et al.  Preferential Accessibility of the Yeast his3 Promoter Is Determined by a General Property of the DNA Sequence, Not by Specific Elements , 2000, Molecular and Cellular Biology.

[20]  L. Steinmetz,et al.  Bidirectional promoters generate pervasive transcription in yeast , 2009, Nature.

[21]  Bryan J Venters,et al.  A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. , 2008, Genome research.

[22]  K. Struhl,et al.  Histone Acetylation at Promoters Is Differentially Affected by Specific Activators and Repressors , 2001, Molecular and Cellular Biology.

[23]  Kevin Struhl,et al.  Evidence for Eviction and Rapid Deposition of Histones upon Transcriptional Elongation by RNA Polymerase II , 2004, Molecular and Cellular Biology.

[24]  Timothy B. Stockwell,et al.  Evaluation of next generation sequencing platforms for population targeted sequencing studies , 2009, Genome Biology.

[25]  K. Struhl,et al.  Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo , 2009, Nature Structural &Molecular Biology.

[26]  A. Kristjuhan,et al.  Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo , 2004, The EMBO journal.

[27]  G. Felsenfeld,et al.  DNAase I, DNAase II and staphylococcal nuclease cut at different, yet symmetrically located, sites in the nucleosome core , 1978, Cell.

[28]  Kevin Struhl,et al.  Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments , 2008, Nucleic acids research.

[29]  K. Struhl,et al.  Chromatin Immunoprecipitation for Determining the Association of Proteins with Specific Genomic Sequences In Vivo , 2004, Current protocols in molecular biology.

[30]  Michael R. Green,et al.  Dissecting the Regulatory Circuitry of a Eukaryotic Genome , 1998, Cell.

[31]  Steven J. M. Jones,et al.  Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation , 2007, PLoS biology.

[32]  Eran Segal,et al.  Nucleosome sequence preferences influence in vivo nucleosome organization , 2010, Nature Structural &Molecular Biology.

[33]  Xin Wang,et al.  A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding , 2010, Cell.

[34]  Nir Friedman,et al.  High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. , 2010, Genome research.

[35]  Kevin Struhl,et al.  Evidence against a genomic code for nucleosome positioning Reply to “Nucleosome sequence preferences influence in vivo nucleosome organization” , 2010, Nature Structural &Molecular Biology.