Flexibility and constraint in the nucleosome core landscape of <i>Caenorhabditis elegans</i> chromatin

Johnson, Steven; Tan, Frederick J.; McCullough, Heather; Riordan, Daniel P.; Fire, Andrew

doi:10.1101/gr.5560806

Cited by 178 publications

(169 citation statements)

References 56 publications

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“…In particular, AT and TA dinucleotides peaked at nucleosome borders that are adjacent to core promoter regions and to a lesser extent in genic regions. A similar pattern occurred at the linker/nucleosome borders in C. elegans (Johnson et al 2006a). For reasons explained in the Supplemental Figure S8 legend, this is unlikely to be a consequence of MNase preference for cleavage of A/T dinucleotides.…”

Section: Dna Sequences That Organize Nucleosomes Are Concentrated At mentioning

confidence: 65%

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

Mavrich¹,

Ioshikhes²,

Venters³

et al. 2008

Genome Res.

620

849

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Most nucleosomes are well-organized at the 5Ј ends of S. cerevisiae genes where "−1" and "+1" nucleosomes bracket a nucleosome-free promoter region (NFR). How nucleosomal organization is specified by the genome is less clear. Here we establish and inter-relate rules governing genomic nucleosome organization by sequencing DNA from more than one million immunopurified S. cerevisiae nucleosomes (displayed at http://atlas.bx.psu.edu/). Evidence is presented that the organization of nucleosomes throughout genes is largely a consequence of statistical packing principles. The genomic sequence specifies the location of the −1 and +1 nucleosomes. The +1 nucleosome forms a barrier against which nucleosomes are packed, resulting in uniform positioning, which decays at farther distances from the barrier. We present evidence for a novel 3Ј NFR that is present at >95% of all genes. 3Ј NFRs may be important for transcription termination and anti-sense initiation. We present a high-resolution genome-wide map of TFIIB locations that implicates 3Ј NFRs in gene looping.

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Section: Dna Sequences That Organize Nucleosomes Are Concentrated At mentioning

confidence: 65%

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

Mavrich¹,

Ioshikhes²,

Venters³

et al. 2008

Genome Res.

620

849

View full text Add to dashboard Cite

show abstract

“…This chromatin structure can also be studied using a high-throughput sequencing approach (Johnson et al, 2006). The histone proteins themselves, particularly the N-terminal tails, are also subject to a large number of posttranslational modifications, such as methylation and acetylation of specific amino acid residues (Kouzarides, 2007).…”

Section: Epigeneticsmentioning

confidence: 99%

Applications of next generation sequencing in molecular ecology of non-model organisms

2010

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As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.

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“…We further investigated the rules of nucleosome positioning by scanning promoter regions for correlations to nucleosome positioning sequences previously identified for a relatively small number of yeast or human nucleosomes 24 , in which AA/TT (yeast 25 and worms 26 ) or CC/GG (human) 27 dinucleotides occur in a biased and/or periodic arrangement across nucleosomal DNA. Unlike in yeast, the AA/TT positioning pattern failed to identify nucleosome locations (Fig.…”

Section: Drosophila Use a Cc/gg Patterning Rather Than Aa/tt For Demamentioning

confidence: 99%

Nucleosome organization in the Drosophila genome

Mavrich

Jiang

Ioshikhes

et al. 2008

Nature

662

690

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Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly D. melanogaster, and compare it to that from the yeast S. cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical −1, NFR (nucleosome-free region), +1 arrangement. However, Drosophila does not incorporate H2A.Z into the −1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome appears to be fundamentally different between lower and higher eukaryotes.Knowledge of the precise location of nucleosomes in a genome is essential in order to understand the context in which chromosomal processes such as transcription and DNA replication operate. A common theme to emerge from recent genome-wide maps of nucleosome locations is a general deficiency of nucleosomes in promoter regions and an enrichment of certain histone modifications towards the 5′ end of genes [1][2][3][4][5][6][7] . A high resolution genomic map of nucleosome locations in the budding yeast S. cerevisiae has further revealed Correspondence and request for material should be addressed to B.F.P. (bfp2@psu.edu). * These authors contributed equally to this work.Author Information Sequence data deposition is through NCBI Trace Archives TI SRA000283, Sequencing Center = "CCGB", and microarray deposition through ArrayExpress, Accession numbers E-MEXP-1515 and -1519. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interest.Author Contributions T.M. prepared and purified the nucleosomes including Pol II-bound nucleosomes; C.J. analyzed the nucleosome mapping data and its relationship to other genomic features; I.P.I. performed computational analyses related to nucleosome positioning sequences; X.L. conducted ChIP-chip on Pol II; B.J.V. conducted ChIP-chip on nucleosome-Pol II interactions; S.J.Z. provided bioinformatics support; L.T. constructed libraries and sequenced nucleosomal DNA; J.Q. mapped sequencing reads to the yeast genome; RG provided H2A.Z antibodies; SCS directed the DNA sequencing phase; DSG directed embryo preparations and helped interpret the data; I.A. developed computational approaches to derive nucleosome maps from the read locations and developed the associated browser; B.F.P. directed the project, interpreted the data, and wrote the paper. S6). Those 112,750 nucleosomes detected three or more times were further analyzed, although patterns were identical when all nucleosomes were analyzed. The internal median error of the data was 4 bp (Fig. S7). H2A.Z nucleosomes were predominantly distributed at 175 bp intervals from the TSS (compared to 165 ...

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Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin

Cited by 178 publications

References 56 publications

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

Applications of next generation sequencing in molecular ecology of non-model organisms

Nucleosome organization in the Drosophila genome

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