A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

doi:10.1186/GB-2009-10-10-R109

Home
/
Papers
/
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

Journal Article•DOI•

A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome

Cizhong Jiang¹, Cizhong Jiang², B. Franklin Pugh¹•Institutions (2)

Tongji University¹, Pennsylvania State University²

08 Oct 2009-Genome Biology (BioMed Central)-Vol. 10, Iss: 10, pp 1-11

TL;DR: Six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms are compiled, and new insights are reported.

read less

Abstract: Nucleosomes have position-specific functions in controlling gene expression. A complete systematic genome-wide reference map of absolute and relative nucleosome positions is needed to minimize potential confusion when referring to the function of individual nucleosomes (or nucleosome-free regions) across datasets. We compiled six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms, and report new insights. Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/.

...read moreread less

Content maybe subject to copyright Report

Citations

PDF

Open Access

More filters

Journal Article•DOI•

A hierarchical combination of factors shapes the genome-wide topography of yeast meiotic recombination initiation.

[...]

Jing Pan¹, Mariko Sasaki¹, Mariko Sasaki², Ryan Kniewel¹, Ryan Kniewel², Hajime Murakami¹, Hannah G. Blitzblau³, Sam E. Tischfield², Sam E. Tischfield¹, Xuan Zhu¹, Xuan Zhu², Matthew J. Neale⁴, Matthew J. Neale¹, Maria Jasin¹, Nicholas D. Socci¹, Andreas Hochwagen³, Scott Keeney¹ - Show less +13 more•Institutions (4)

Memorial Sloan Kettering Cancer Center¹, Cornell University², Massachusetts Institute of Technology³, University of Sussex⁴

04 Mar 2011-Cell

TL;DR: This analysis offers mechanistic insight into DSB formation and early processing steps, supporting the view that the recombination terrain is molded by combinatorial and hierarchical interaction of factors that work on widely different size scales.

...read moreread less

501 citations

Cites result from "A compiled and systematic reference..."

...Moreover, patterns agreed well with prior studies in vegetatively growing haploids of different strains (Jiang and Pugh, 2009), attesting to the conserved structure of yeast chromatin (Radman-Livaja and Rando, 2010; Tsankov et al....
[...]
...Moreover, patterns agreed well with prior studies in vegetatively growing haploids of different strains (Jiang and Pugh, 2009), attesting to the conserved structure of yeast chromatin (Radman-Livaja and Rando, 2010; Tsankov et al., 2010)....
[...]

Journal Article•DOI•

Stepwise histone replacement by SWR1 requires dual activation with histone H2A.Z and canonical nucleosome.

[...]

Ed Luk¹, Anand Ranjan¹, Peter C. FitzGerald¹, Gaku Mizuguchi¹, Yingzi Huang¹, Debbie Wei¹, Carl Wu¹ - Show less +3 more•Institutions (1)

National Institutes of Health¹

24 Nov 2010-Cell

TL;DR: It is shown that promoter-proximal nucleosomes are highly heterogeneous for H2A.Z in Saccharomyces cerevisiae, with substantial representation of nucleosome containing one, two, or zero H2a.Z molecules.

...read moreread less

402 citations

Cites background from "A compiled and systematic reference..."

...With its NFR-proximal edge covering the transcription start site (TSS), the +1 nucleosome acts as a barrier that occludes the TSS and helps position downstream nucleosomes in the coding region (Jiang and Pugh, 2009b)....
[...]
...…chromatin architecture, characterized by two well-positioned nucleosomes (+1 and 1) flanking an 80–230 base pair region that is relatively depleted for histones and is commonly referred to as the ‘‘nucleosome-free region’’ (NFR) (Cairns, 2009; Jiang and Pugh, 2009b; Weiner et al., 2010)....
[...]
...(B) Normalized average nucleosome distribution in and around the +1 nucleosome center of 466 genes (Jiang and Pugh, 2009a)....
[...]

Journal Article•DOI•

Understanding nucleosome dynamics and their links to gene expression and DNA replication.

[...]

William K. M. Lai¹, B. Franklin Pugh¹•Institutions (1)

Pennsylvania State University¹

01 Sep 2017-Nature Reviews Molecular Cell Biology

TL;DR: Nucleosome dynamics are governed by a complex interplay of histone composition, histone post-translational modifications, nucleosome occupancy and positioning within chromatin, which are influenced by numerous regulatory factors, including general Regulatory factors, chromatin remodellers, chaperones and polymerases.

...read moreread less

Abstract: Advances in genomics technology have provided the means to probe myriad chromatin interactions at unprecedented spatial and temporal resolution. This has led to a profound understanding of nucleosome organization within the genome, revealing that nucleosomes are highly dynamic. Nucleosome dynamics are governed by a complex interplay of histone composition, histone post-translational modifications, nucleosome occupancy and positioning within chromatin, which are influenced by numerous regulatory factors, including general regulatory factors, chromatin remodellers, chaperones and polymerases. It is now known that these dynamics regulate diverse cellular processes ranging from gene transcription to DNA replication and repair.

...read moreread less

361 citations

Journal Article•DOI•

DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing.

[...]

Kaifu Chen, Yuanxin Xi, Xuewen Pan¹, Zhaoyu Li², Klaus H. Kaestner², Jessica K. Tyler, Sharon Y.R. Dent³, Xiangwei He, Wei Li - Show less +5 more•Institutions (3)

Baylor College of Medicine¹, University of Pennsylvania², University of Texas MD Anderson Cancer Center³

01 Feb 2013-Genome Research

TL;DR: A comprehensive bioinformatics pipeline, DANPOS, explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution is reported, demonstrating that bias correction in preliminary data processing and optimal statistical testing significantly enhances the functional interpretation of dynamic nucleOSomes.

...read moreread less

Abstract: Recent developments in next-generation sequencing have enabled whole-genome profiling of nucleosome organizations. Although several algorithms for inferring nucleosome position from a single experimental condition have been available, it remains a challenge to accurately define dynamic nucleosomes associated with environmental changes. Here, we report a comprehensive bioinformatics pipeline, DANPOS, explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. Using both simulated and real nucleosome data, we demonstrated that bias correction in preliminary data processing and optimal statistical testing significantly enhances the functional interpretation of dynamic nucleosomes. The single-nucleotide resolution analysis of DANPOS allows us to detect all three categories of nucleosome dynamics, such as position shift, fuzziness change, and occupancy change, using a uniform statistical framework. Pathway analysis indicates that each category is involved in distinct biological functions. We also analyzed the influence of sequencing depth and suggest that even 200-fold coverage is probably not enough to identify all the dynamic nucleosomes. Finally, based on nucleosome data from the human hematopoietic stem cells (HSCs) and mouse embryonic stem cells (ESCs), we demonstrated that DANPOS is also robust in defining functional dynamic nucleosomes, not only in promoters, but also in distal regulatory regions in the mammalian genome.

...read moreread less

325 citations

Journal Article•DOI•

Genome-wide nucleosome specificity and directionality of chromatin remodelers.

[...]

Kuangyu Yen¹, Vinesh Vinayachandran¹, Kiran Batta¹, R. Thomas Koerber¹, B. Franklin Pugh¹ - Show less +1 more•Institutions (1)

Pennsylvania State University¹

22 Jun 2012-Cell

TL;DR: The genome-wide binding of remodeler complexes SWI/SNF, RSC,ISW1a, ISW1b, ISw2, and INO80 to individual nucleosomes in Saccharomyces is determined and their functional contributions to nucleosome positioning through deletion analysis are determined.

...read moreread less

321 citations

Cites background or methods from "A compiled and systematic reference..."

...Genome-wide mapping of nucleosome positions reveals that they are organized into uniformly spaced arrays at the 50 and, to a lesser extent, 30 ends of genes (Jiang and Pugh, 2009b)....
[...]
...Nucleosome Shift Analysis Nucleosomes whose positions were called as previously described (Jiang and Pugh, 2009a) and differed between mutants and wild-type having a t test p value lower than 0.05 were regarded as a valid nucleosome shift, as previously described (Tirosh et al., 2010), althoughwe…...
[...]

1
2
3
4
…
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50

Collapse

References

PDF

Open Access

More filters

Journal Article•DOI•

Crystal structure of the nucleosome core particle at 2.8 Å resolution

[...]

Karolin Luger¹, Armin W. Mäder¹, Robin K. Richmond¹, David F. Sargent¹, Timothy J. Richmond¹ - Show less +1 more•Institutions (1)

ETH Zurich¹

18 Sep 1997-Nature

TL;DR: The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it.

...read moreread less

Abstract: The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the DNA superhelix to contact neighbouring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry.

...read moreread less

7,841 citations

"A compiled and systematic reference..." refers background in this paper

...Rationale Eukaryotic chromatin exists as a repeating unit of nucleosome particles [1,2], where approximately 147 bp of DNA coils around a histone octamer [3,4]....
[...]

Journal Article•DOI•

Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome

[...]

Roger D. Kornberg¹, Yahli Lorch¹•Institutions (1)

Stanford University¹

06 Aug 1999-Cell

TL;DR: The chromatin field needs much more information about structure beyond the nucleosome, and there is insufficient evidence that acetylation actually causes chromatin unfolding, and functional analysis in cell-free systems must be extended beyond theucleosome to the chromosomal context.

...read moreread less

1,779 citations

"A compiled and systematic reference..." refers background in this paper

...Rationale Eukaryotic chromatin exists as a repeating unit of nucleosome particles [1,2], where approximately 147 bp of DNA coils around a histone octamer [3,4]....
[...]

Journal Article•DOI•

Dynamic Regulation of Nucleosome Positioning in the Human Genome

[...]

Dustin E. Schones¹, Kairong Cui¹, Suresh Cuddapah¹, Tae-Young Roh¹, Artem Barski¹, Zhibin Wang¹, Gang Wei¹, Keji Zhao¹ - Show less +4 more•Institutions (1)

National Institutes of Health¹

07 Mar 2008-Cell

TL;DR: It is found that nucleosome phasing relative to the transcription start sites is directly correlated to RNA polymerase II (Pol II) binding and the first nucleosomes downstream of a start site exhibits differential positioning in active and silent genes.

...read moreread less

1,354 citations

"A compiled and systematic reference..." refers background or methods in this paper

...their preferential methylation on lysine 4 of histone H3 (H3K4me3) [16]....
[...]
...The genome-wide maps of nucleosome positions have shown that nucleosomes are highly phased near the 5' end of genes, and reside at a canonical distance from transcription start sites (TSSs) [8-16]....
[...]
...Genome-wide maps of nucleosome positions have also been produced in other species, such as in Drosophila using Roche/454 pyrosequencing [14], in Caenorhabditis elegans using the Applied Biosystems SOLiD sequencer [15], and in humans using the Illumina/Solexa 1G sequencer [16]....
[...]
...For example, the nucleosome closest to the 3' end of a gene has been labeled as a -1 nucleosome [9], and the rare nucleosome that appears in the NFR region has been defined as the -1 nucleosome in humans [16]....
[...]

Journal Article•DOI•

The structure of DNA in the nucleosome core

[...]

Timothy J. Richmond¹, Curt A. Davey¹•Institutions (1)

ETH Zurich¹

08 May 2003-Nature

TL;DR: Comparison of the 147-base-pair structure with two 146- base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.

...read moreread less

Abstract: The 1.9-A-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein-DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.

...read moreread less

1,250 citations

"A compiled and systematic reference..." refers background in this paper

...Rationale Eukaryotic chromatin exists as a repeating unit of nucleosome particles [1,2], where approximately 147 bp of DNA coils around a histone octamer [3,4]....
[...]

Journal Article•DOI•

The DNA-encoded nucleosome organization of a eukaryotic genome

[...]

Noam Kaplan¹, Irene K. Moore², Yvonne N. Fondufe-Mittendorf², Andrea J. Gossett³, Desiree Tillo⁴, Yair Field, Emily M LeProust⁵, Timothy P. Hughes⁴, Jason D. Lieb³, Jonathan Widom², Eran Segal¹ - Show less +7 more•Institutions (5)

Weizmann Institute of Science¹, Northwestern University², University of North Carolina at Chapel Hill³, University of Toronto⁴, Agilent Technologies⁵

19 Mar 2009-Nature

TL;DR: The results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization ofucleosomes in vivo.

...read moreread less

Abstract: The nucleosomes are the basic repeating units of eukaryotic chromatin, and nucleosome organization is critically important for gene regulation. Kaplan et al. tested the importance of the intrinsic DNA sequence preferences of nucleosomes by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map is remarkably similar to in vivo nucleosome maps, indicating that the organization of nucleosomes in vivo is largely governed by the underlying genomic DNA sequence. This study tests the importance of the intrinsic DNA sequence preferences of nucleosomes by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map is similar to in vivo nucleosome maps, indicating that the organization of nucleosomes in vivo is largely governed by the underlying genomic DNA sequence. Nucleosome organization is critical for gene regulation1. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers2, competition with site-specific DNA-binding proteins3, and the DNA sequence preferences of the nucleosomes themselves4,5,6,7,8. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo7,9,10,11, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for ∼40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.

...read moreread less

1,205 citations

"A compiled and systematic reference..." refers background in this paper

...However, most genes have 5' NFRs, and such nucleosome exclusion is typically hard-coded into the DNA [23,25]....
[...]
...Indeed, several studies have implicated locally bound proteins and/or poly dA:dT tracts as important for maintaining NFRs [7,11,12,17,19,20,22-24]....
[...]