The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank; Li, Yun; Hu, Ming; Hardison, Ross C.; Wang, Ting; Yue, Feng

doi:10.1186/s13059-018-1519-9

Cited by 439 publications

(490 citation statements)

References 60 publications

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“…Chromatin conformation capture assays provide the best evidence for interactions between regulatory elements and target genes. While these assays are cost-prohibitive to run on all samples, data has been generated from an increasing number of diverse cell-types and tissues through individual labs and within the ENCODE consortium that are being compiled and visualized in browsers [96]. In addition, software such as TargetFinder [97] can predict gene targets in specific samples using accessible chromatin data.…”

Section: Opinion: Studies Of Gene×environment×epigenome In Geneticallmentioning

confidence: 99%

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants

Lewis

Crawford

Furey

et al. 2017

Current Opinion in Toxicology

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It is well established that genetic variability has a major impact on susceptibility to common diseases, responses to drugs and toxicants, and influences disease-related outcomes. The appreciation that epigenetic marks also vary across the population is growing with more data becoming available from studies in humans and model organisms. In addition, the links between genetic variability, toxicity outcomes and epigenetics are being actively explored. Recent studies demonstrate that gene-by-environment interactions involve both chromatin states and transcriptional regulation, and that epigenetics provides important mechanistic clues to connect expression-related quantitative trait loci (QTL) and disease outcomes. However, studies of Gene×Environment×Epigenetics further extend the complexity of the experimental designs and create a challenge for selecting the most informative epigenetic readouts that can be feasibly performed to interrogate multiple individuals, exposures, tissue types and toxicity phenotypes. We propose that among the many possible epigenetic experimental methodologies, assessment of chromatin accessibility coupled with total RNA levels provides a cost-effective and comprehensive option to sufficiently characterize the complexity of epigenetic and regulatory activity in the context of understanding the inter-individual variability in responses to toxicants.

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Section: Opinion: Studies Of Gene×environment×epigenome In Geneticallmentioning

confidence: 99%

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants

Lewis

Crawford

Furey

et al. 2017

Current Opinion in Toxicology

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“…We confirmed that the hs1150 element is deeply conserved at DNA sequence levels across species. 24 We found that the hs1150 enhancer and OTX2 are in the same TAD ( Figure 1B), suggesting 3D chromatin interactions between hs1150 element and OTX2 transcription unit in the human genome. Cis-acting elements and their regulated genes are usually in topologically associated domains (TADs), and TADs are largely stable across different cell types.…”

Section: Introductionmentioning

confidence: 70%

“…21,22 To assess the regulatory landscape in the OTX2 locus, we examined Hi-C data of H1 human embryonic stem cells 23 using a 3D genome browser. 24 We found that the hs1150 enhancer and OTX2 are in the same TAD ( Figure 1B), suggesting 3D chromatin interactions between hs1150 element and OTX2 transcription unit in the human genome. Collectively, deep conservation across species, reporter expression in transient transgenic mouse embryos at E11.5, and 3D chromatin landscapes of the human genome suggest that the hs1150 element is related to the regulation of OTX2 expression.…”

Section: Introductionmentioning

confidence: 70%

A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina

Bhansali

Cvekl

Liu

2019

Developmental Dynamics

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Background: Homeodomain transcription factor Otx2 is essential for embryonic development of multiple head tissues, including retinal pigment epithelium (RPE) and neuroretina. Temporospatial regulation of Otx2 expression is critical for its functions. Molecular dissection of the cis-acting enhancers will help elucidate how Otx2 expression is regulated. Results:We comprehensively characterized distal enhancer hs1150 that was previously identified in a high throughput study. We established multiple transgenic mouse lines in which human hs1150, corresponding mouse hs1150, and two highly conserved sub-fragments in the mouse hs1150 were individually fused to a minimal hsp68 promoter to drive reporter expression. We found that hs1150 enhancer directed reporter expression in the RPE, neuroretina, and brain in a developmentally regulated manner. Human hs1150-directed reporter expression largely recapitulated Otx2 expression in the RPE, in the early neuroretina, and to a lesser degree in the early brain. Mouse hs1150, although shorter than human hs1150, exhibited similar enhancer activity, indicating functional conservation of hs1150 enhancer across species. Both of the highly conserved subfragments in mouse hs1150 enhancer directed reporter expression in the early neuroretina, indicating that the hs1150 enhancer has two functional components. Conclusions: Our findings provide insight into the molecular mechanisms underlying the regulation of Otx2 retinal expression. K E Y W O R D Sdistal enhancer, neuroretina, Otx2 expression, retinal pigment epithelium, transgenic mice

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“…Both of these resources feed into the VISION project, which provides raw and normalized data sets selected to cover specific groups of features in mouse and human hematopoiesis, segmentations by integrative modeling (see below), and catalogs of cCREs, among other resources, on the website http://usevision.org. This website includes a link to a genome browser with epigenetic and expression data sets during hematopoiesis as well as the 3D Genome Browser developed by the Yue lab . In addition to the effort to compile and analyze existing data, new data are being generated both within the VISION project and in other laboratories that expand the coverage of epigenetic features across cell types and bring in data sets on new transcription factors or co‐factors.…”

Section: Compile and Determine Epigenetic Features And Transcript Levmentioning

confidence: 99%

“…This website includes a link to a genome browser with epigenetic and expression data sets during hematopoiesis as well as the 3D Genome Browser developed by the Yue lab. 30 In addition to the effort to compile and analyze existing data, new data are being generated both within the VISION project and in other laboratories that expand the coverage of epigenetic features across cell types and bring in data sets on new transcription factors or co-factors.…”

Section: Compile and Determine Epigenetic Features And Transcript Lmentioning

confidence: 99%

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

et al. 2019

Self Cite

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Members of the GATA family of transcription factors play key roles in the differentiation of specific cell lineages by regulating the expression of target genes. Three GATA factors play distinct roles in hematopoietic differentiation.combinations of features (epigenetic states) simultaneously in two dimensions-along chromosomes and across cell types. The result is a segmentation that effectively paints the regulatory landscape in readily interpretable views, revealing constitutively active or silent loci as well as the loci specifically induced or repressed in each stage and lineage. Nuclease accessible DNA segments in active chromatin states were designated candidate cis-regulatory elements in each cell type, providing one of the most comprehensive registries of candidate hematopoietic regulatory elements to date. Applications of VISION resources are illustrated for the regulation of genes encoding GATA1, GATA2, GATA3, and Ikaros. VISION resources are freely available from our website http://usevision.org.

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The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Cited by 439 publications

References 60 publications

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants

A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

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