Nucleosome positioning and gene regulation: advances through genomics

Jiang, Cizhong; Pugh, B. Franklin

doi:10.1038/nrg2522

Cited by 947 publications

(956 citation statements)

References 131 publications

(184 reference statements)

Supporting

Mentioning

895

Contrasting

Unclassified

Order By: Relevance

“…It has been reported that nucleosomes acquire an open chromatin structure following the binding of transcription factors ). To analyze the nucleosome structure, Nucleosome-Seq (Albert et al 2007;Jiang and Pugh 2009;Schones et al 2008) was used in DLD-1 and TIG-3 cells. We generated a total of 130,088,634 36-bp sequence tags from micrococcal nuclease-digested genomic DNA and calculated the occupancy of the nucleosome according to a previously reported procedure (Albert et al 2007) (Supplementary Fig.…”

Section: Epigenetic Regulation In Regions Surrounding Hif-1a Bindingmentioning

confidence: 99%

See 1 more Smart Citation

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Tanimoto

Tsuchihara

Kanai

et al. 2010

HUGO J

View full text Add to dashboard Cite

We identified 531 and 616 putative HIF-1a target sites by ChIP-Seq in the cancerous cell line DLD-1 and the non-cancerous cell line TIG-3, respectively. We also examined the positions and expression levels of transcriptional start sites (TSSs) in these cell lines using our TSS-Seq method. We observed that 121 and 48 genes in DLD-1 and TIG-3 cells, respectively, had HIF-1a binding sites in proximal regions of the previously reported TSSs that were up-regulated at the transcriptional level. In addition, 193 and 123 of the HIF-1a target sites, respectively, were located in proximal regions of previously uncharacterized TSSs, namely, TSSs of putative alternative promoters of protein-coding genes or promoters of putative non-protein-coding transcripts. The hypoxic response of DLD-1 cells was more significant than that of TIG-3 cells with respect to both the number of target sites and the degree of induced changes in transcript expression. The Nucleosome-Seq and ChIP-Seq analyses of histone modifications revealed that the chromatin formed an open structure in regions surrounding the HIF-1a binding sites, but this event occurred prior to the actual binding of HIF1a. Different cellular histories may be encoded by chromatin structures and determine the activation of specific genes in response to hypoxic shock.

show abstract

Section: Epigenetic Regulation In Regions Surrounding Hif-1a Bindingmentioning

confidence: 99%

“…Furthermore, we carried out Illumina GA sequencing analysis using micrococcal nuclease-digested genomic DNA (Nucleosome-Seq) (Albert et al 2007;Jiang and Pugh 2009;Schones et al 2008). We examined the changes in nucleosome structure caused by HIF-1a binding and the subsequent transcriptional activation.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Tanimoto

Tsuchihara

Kanai

et al. 2010

HUGO J

View full text Add to dashboard Cite

show abstract

“…Indeed, several mechanisms that prevent spreading may trivially solve the problem of restoring the parental modification pattern when exact boundaries are important. Examples include nucleosome-depleted regions (see, for example, Jiang and Pugh, 2009;Mavrich et al, 2008;Yadon et al, 2010), bound proteins (e.g., CTCF) or histone variants (e.g., H2A.Z) in the vicinity of positions that border the different chromatin domains, or the marking with a particular histone modification directly after replication due to other signalling factors.…”

Section: Discussionmentioning

confidence: 99%

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

Arnold

Stadler

Prohaska

2013

Journal of Theoretical Biology

View full text Add to dashboard Cite

Eukaryotic histones carry a diverse set of specific chemical modifications that accumulate over the life-time of a cell and have a crucial impact on the cell state in general and the transcriptional program in particular. Replication constitutes a dramatic disruption of the chromatin states that effectively amounts to partial erasure of stored information. To preserve its epigenetic state the cell reconstructs (at least part of) the histone modifications by means of processes that are still very poorly understood. A plausible hypothesis is that the different combinations of reader and writer domains in histone-modifying enzymes implement local rewriting rules that are capable of "recomputing" the desired parental modification patterns on the basis of the partial information contained in that half of the nucleosomes that predate replication.To test whether such a mechanism is theoretically feasible, we have developed a flexible stochastic simulation system (available at http://www.bioinf.uni-leipzig.de/Software/StoChDyn) for studying the dynamics of histone modification states. The implementation is based on Gillespie's approach, i.e., it models the master equation of a detailed chemical model. It is efficient enough to use an evolutionary algorithm to find patterns across multiple cell divisions with high accuracy.We found that it is easy to evolve a system of enzymes that can maintain a particular chromatin state roughly stable, even without explicit boundary elements separating differentially modified chromatin domains. However, the success of this task depends on several previously unanticipated factors, such as the length of the initial state, the specific pattern that should be maintained, the time between replications, and chemical parameters such as enzymatic binding and dissociation rates. All these factors also influence the accumulation of errors in the wake of cell divisions.

show abstract

“…These processes control cell fate through regulating gene and miRNA expression, as well as through parental imprinting, X chromosome inactivation, suppressing of transposons, and regulating developmental processes [4,6]. The epigenome provides the flexibility to address a changing environment above the rather rigid architecture of DNA sequence information and thus greatly affects the development and formation of a phenotype with no alteration in the genotype.…”

Section: What Is Epigenetics?mentioning

confidence: 99%

Epigenetic Landscape of Parkinson's Disease: Emerging Role in Disease Mechanisms and Therapeutic Modalities

2013

View full text Add to dashboard Cite

show abstract

Nucleosome positioning and gene regulation: advances through genomics

Cited by 947 publications

References 131 publications

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

Epigenetic Landscape of Parkinson's Disease: Emerging Role in Disease Mechanisms and Therapeutic Modalities

Contact Info

Product

Resources

About