ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the <i>Drosophila</i> blastoderm

Bozek, Marta; Cortini, Roberto; Storti, Andrea Ennio; Unnerstall, Ulrich; Gaul, Ulrike; Gompel, Nicolas

doi:10.1101/gr.242362.118

Cited by 62 publications

(89 citation statements)

References 58 publications

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“…Alongside reports confirming the correlation between accessibility and activity of enhancers, an increasing number of publications questions this simple one‐to‐one relationship. [ 8,14,15 ] While active enhancers are indeed characterized by open chromatin, they can be also accessible in other cell types or at other developmental timepoints, as demonstrated by the following studies. Arnold et al.…”

Section: An Imperfect Correlation Between Enhancer Accessibility and mentioning

confidence: 90%

“…Even if in two different samples an enhancer is identified as open by a peak caller, it might still display significantly different levels of accessibility. [ 15 ]…”

Section: Binary Distinction Between Open and Closed Chromatin Concealmentioning

confidence: 99%

“…As regulation by TFs requires exposure of their binding sites, repressed enhancers are expected to display some degree of accessibility. [ 15,36 ] Moreover, repressed enhancers can be also simultaneously occupied by activating TFs, as illustrated by enhancers involved in axis patterning during D. melanogaster embryogenesis. [ 21,37 ] These elements are targeted both by activators and repressors, and it is the stoichiometry and affinity of TF binding that determines the net effect on transcription of the target gene.…”

Section: Inactive Enhancers Encompass Multiple Regulatory States Withmentioning

confidence: 99%

“…[ 35,40 ] However, such comparisons might be misleading since they are based on the mean signal across multiple elements. We know from examination of individual enhancers in D. melanogaster embryos [ 15 ] that the range of accessibility signal between individual elements in the same regulatory state can differ even by one order of magnitude. It is more informative then to examine accessibility changes as the same set of enhancers transitions between different states.…”

Section: Inactive Enhancers Encompass Multiple Regulatory States Withmentioning

confidence: 99%

“…[ 46 ] Using ATAC‐seq, a handful of recent publications focusing on the early embryogenesis in D. melanogaster have explored in great detail how enhancer accessibility varies both along the temporal and spatial axes of development. [ 15,45,47,48 ] Additionally, by considering quantitative accessibility differences, they provided valuable insights into chromatin organization of different enhancer states.…”

Section: Resolving Enhancer Accessibility In Space and Timementioning

confidence: 99%

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Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity

Bozek

Gompel

2020

BioEssays

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Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differences between active enhancers and their different inactive counterparts: the closed silenced state and the accessible primed and repressed states. While the open structure as such is not a specific indicator of enhancer activity, active enhancers display a higher degree of accessibility than the primed and repressed states. Molecular mechanisms that may account for these quantitative differences are discussed. A model that relates molecular events at an enhancer to changes in its activity and accessibility in a developing tissue is also proposed.

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Section: An Imperfect Correlation Between Enhancer Accessibility and mentioning

confidence: 90%

“…Even if in two different samples an enhancer is identified as open by a peak caller, it might still display significantly different levels of accessibility. [ 15 ]…”

Section: Binary Distinction Between Open and Closed Chromatin Concealmentioning

confidence: 99%

Section: Inactive Enhancers Encompass Multiple Regulatory States Withmentioning

confidence: 99%

Section: Inactive Enhancers Encompass Multiple Regulatory States Withmentioning

confidence: 99%

Section: Resolving Enhancer Accessibility In Space and Timementioning

confidence: 99%

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Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity

Bozek

Gompel

2020

BioEssays

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Global changes in chromatin accessibility and transcription in growth hormone-secreting pituitary adenoma

Wang

Zhang

et al. 2022

Endocrine

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Purpose Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of growth hormone and insulin-like growth factor 1, causing increased morbidity and mortality. Previous studies have investigated the transcription of GHPA. However, the gene regulatory landscape has not been fully characterized. The objective of our study was to unravel the changes in chromatin accessibility and transcription in GHPA. Methods Six patients diagnosed with GHPA in the Department of Neurosurgery at Huashan Hospital were enrolled in our study. Primary pituitary adenoma tissues and adjacent normal pituitary specimens with no morphologic abnormalities from these six patients were obtained at surgery. RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were applied to investigate the underlying relationship between gene expression and chromatin accessibility changes in GHPA. Results Totally, 1528 differential expression genes (DEGs) were identified by transcriptomics analyses, including 725 up-regulated and 803 down-regulated. Further, we obtained 64 significantly DEGs including 10 DEGs were elevated and 54 DEGs were negligibly expressed in tumors tissues. The up-regulated DEGs were mainly involved in terms related to synapse formation, nervous system development and secretory pathway. In parallel, 3916 increased and 2895 decreased chromatin-accessible regions were mapped by ATAC-seq. Additionally, the chromatin accessible changes were frequently located adjacent to transcription factor CTCF and Rfx2 binding site. Conclusions Our results are the first to demonstrate the landscape of chromatin accessibility in GHPA, which may contribute to illustrate the underlying transcriptional regulation mechanism of this disease.

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Data enhancement in the age of spatial biology

Liao,

Martin,

Kim

et al. 2024

Advances in Cancer Research

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ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm

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Cited by 62 publications

References 58 publications

Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity

Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity

Global changes in chromatin accessibility and transcription in growth hormone-secreting pituitary adenoma

Data enhancement in the age of spatial biology

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