NicE-seq: high resolution open chromatin profiling

Ponnaluri, V. K. Chaithanya; Zhang, Guoqiang; Estève, Pierre‐Olivier; Spracklin, George; Sian, Stephanie; Xu, Shuang-yong; Benoukraf, Touati; Pradhan, Sriharsa

doi:10.1186/s13059-017-1247-6

Cited by 45 publications

(36 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Looking at open chromatin regions (using DNaseI, ATAC-seq or NicE-seq techniques) between silenced and expressed transgenes could shed additional light on the mechanism leading to gene expression or repression (Chandler and Vaucheret, 2001;Ponnaluri et al, 2017;Wang et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Impact of differential DNA methylation on transgene expression in cotton (Gossypium hirsutum L.) events generated by targeted sequence insertion

Verkest¹,

Bourout²,

Debaveye³

et al. 2019

Plant Biotechnology Journal

View full text Add to dashboard Cite

Summary Targeted Genome Optimization ( TGO ) using site‐specific nucleases to introduce a DNA double‐strand break ( DSB ) at a specific target locus has broadened the options available to breeders for generation and combination of multiple traits. The use of targeted DNA cleavage in combination with homologous recombination ( HR )‐mediated repair, enabled the precise targeted insertion of additional trait genes (2m epsps, hppd, axmi115 ) at a pre‐existing transgenic locus in cotton. Here we describe the expression and epigenome analyses of cotton Targeted Sequence Insertion ( TSI ) events over generations. In a subset of events, we observed variability in the level of transgene ( hppd , axmi115 ) expression between independent but genetically identical TSI events. Transgene expression could also be differential within single events and variable over generations. This expression variability and silencing occurred independently of the transgene sequence and could be attributed to DNA methylation that was further linked to different DNA methylation mechanisms. The trigger(s) of transgene DNA methylation remains elusive but we hypothesize that targeted DSB induction and repair could be a potential trigger for DNA methylation.

show abstract

Section: Discussionmentioning

confidence: 99%

Impact of differential DNA methylation on transgene expression in cotton (Gossypium hirsutum L.) events generated by targeted sequence insertion

Verkest¹,

Bourout²,

Debaveye³

et al. 2019

Plant Biotechnology Journal

View full text Add to dashboard Cite

show abstract

“…To establish a causal link between chromatin state and p53 binding, we treated MCF7 cells with decitabine, a methylase inhibitor that has been shown to broadly alter chromatin structure [25]. We then treated these cells with IR and preformed p53 ChIP-seq and ATAC-seq.…”

Section: Perturbation Of Cell State Alters P53 Dna Bindingmentioning

confidence: 99%

Identification of universal and cell-type specific p53 DNA binding

Hafner

Kublo

Tsabar

et al. 2020

BMC Mol and Cell Biol

View full text Add to dashboard Cite

Background: The tumor suppressor p53 is a major regulator of the DNA damage response and has been suggested to selectively bind and activate cell-type specific gene expression programs. However recent studies and meta-analyses of genomic data propose largely uniform, and condition independent p53 binding and thus question the selective and cell-type dependent function of p53. Results: To systematically assess the cell-type specificity of p53, we measured its association with DNA in 12 p53 wild-type cancer cell lines, from a range of epithelial linages, in response to ionizing radiation. We found that the majority of bound sites were occupied across all cell lines, however we also identified a subset of binding sites that were specific to one or a few cell lines. Unlike the shared p53-bound genome, which was not dependent on chromatin accessibility, the association of p53 with these atypical binding sites was well explained by chromatin accessibility and could be modulated by forcing cell state changes such as the epithelial-to-mesenchymal transition. Conclusions: Our study reconciles previous conflicting views in the p53 field, by demonstrating that although the majority of p53 DNA binding is conserved across cell types, there is a small set of cell line specific binding sites that depend on cell state.

show abstract

“…To establish a causal link between chromatin state and p53 binding, we treated MCF7 cells with decitabine, a methylase inhibitor that has been shown to broadly alter chromatin structure (33). We then treated these cells with IR and preformed p53 ChIP-seq and ATAC-seq on the samples.…”

Section: Perturbation Of Cell State Alters P53 Dna Bindingmentioning

confidence: 99%

Identification of universal and cell type specific p53 DNA binding

Hafner

Kublo

Lahav

et al. 2017

Preprint

View full text Add to dashboard Cite

The tumor suppressor p53 is a major regulator of the DNA damage response and has been suggested to selectively bind and activate cell type specific gene expression programs, however recent studies and meta-analyses of genomic data propose largely uniform, and condition independent, p53 binding. To systematically assess the cell type specificity of p53, we measured its association with DNA in 12 p53 wildtype cell lines, from a range of epithelial linages, in response to ionizing radiation. We found that the majority of bound sites were occupied across all cell lines, however we also identified a subset of binding sites that were specific to one or a few cell lines. Unlike the shared p53-bound genome, which was not dependent on chromatin accessibility, the association of p53 with these atypical binding sites was well explained by chromatin accessibility and could be modulated by forcing cell state changes such as the epithelial-to-mesenchymal transition. These results position p53 as having both universal and cell type specific regulatory programs that have different regulators and dependence on chromatin state.

show abstract

NicE-seq: high resolution open chromatin profiling

Cited by 45 publications

References 45 publications

Impact of differential DNA methylation on transgene expression in cotton (Gossypium hirsutum L.) events generated by targeted sequence insertion

Impact of differential DNA methylation on transgene expression in cotton (Gossypium hirsutum L.) events generated by targeted sequence insertion

Identification of universal and cell-type specific p53 DNA binding

Identification of universal and cell type specific p53 DNA binding

Contact Info

Product

Resources

About