Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

Gehrig, Jochen; Reischl, Markus; Kalmár, Éva; Ferg, Marco; Hadzhiev, Yavor; Zaucker, Andreas; Song, Chengyi; Schindler, Simone; Liebel, Urban; Müller, Ferenc

doi:10.1038/nmeth.1396

Cited by 114 publications

(97 citation statements)

References 40 publications

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“…We cloned five alternative promoters and five novel promoter regions in reporter construct (Supplemental Table 8). Nine out of 10 predicted core promoters activated neural-specific reporter expression in transient transgenic zebrafish, when linked to the heterologous neural specific islet1 zCREST2 enhancer (Uemura et al 2005;Gehrig et al 2009), while control fragments from random loci remained silent in this assay ( Fig. 2C; Supplemental Fig.…”

Section: Identification and Developmental Dynamics Of Alternative Promentioning

confidence: 95%

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

et al. 2013

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Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.

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Section: Identification and Developmental Dynamics Of Alternative Promentioning

confidence: 95%

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

et al. 2013

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“…ZebrafishMiner offers the possibility to interactively replace domains either by manual marking or by using larvae with fluorescently labelled tissues. All algorithms are suited for high-throughput screening and have already proven to be suitable [3]. Adaptation to modified test conditions like brightness, morphological changes etc.…”

Section: Resultsmentioning

confidence: 99%

“…In [3], we proposed a robust framework for zebrafish analysis being fault-tolerant and self-adaptive. Its aim was to assign signals in a fluorescent channel to eight predefined domains in zebrafish (corresponding to the tissues notochord, spinal cord, heart, skin, eye, brain, midbrain-hindbrain, yolk).…”

Section: Motivationmentioning

confidence: 99%

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ZebrafishMiner: an open source software for interactive evaluation of domain-specific fluorescence in zebrafish

Reischl

Bartschat

Liebel³

et al. 2017

Current Directions in Biomedical Engineering

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High-throughput microscopy makes it possible to observe the morphology of zebrafish on large scale to quantify genetic, toxic or drug effects. The image acquisition is done by automated microscopy, images are evaluated automatically by image processing pipelines, tailored specifically to the requirements of the scientific question. The transfer of such algorithms to other projects, however, is complex due to missing guidelines and lack of mathematical or programming knowledge. In this work, we implement an image processing pipeline for automatic fluorescence quantification in user-defined domains of zebrafish embryos and larvae of different age. The pipeline is capable of detecting embryos and larvae in image stacks and quantifying domain activity. To make this protocol available to the community, we developed an open source software package called "ZebrafishMiner" which guides the user through all steps of the processing pipeline and makes the algorithms available and easy to handle. We implemented all routines in an MATLAB-based graphical user interface (GUI) that gives the user control over all image processing parameters. The software is shipped with a manual of 30 pages and three tutorial datasets, which guide the user through the manual step by step. It can be downloaded at https://sourceforge.net/projects/scixminer/.

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“…The usefulness of quantitative image analysis based on pattern recognition was described for budding yeast (Saccharomyces cerevisiae; Negishi et al, 2009;Wolinski et al, 2009), immortal human cell lines (Pelkmans et al, 2005;Moffat et al, 2006;Collinet et al, 2010), and zebrafish (Danio rerio) embryos (Gehrig et al, 2009). These methods are suitable for imaging single cells or whole organisms at subcellular or cellular resolution.…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Confocal Imaging of Intact Live Tissue Enables Quantification of Membrane Trafficking in Arabidopsis

et al. 2010

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Membrane compartmentalization and trafficking within and between cells is considered an essential cellular property of higher eukaryotes. We established a high-throughput imaging method suitable for the quantitative detection of membrane compartments at subcellular resolution in intact epidermal tissue. Whole Arabidopsis (Arabidopsis thaliana) cotyledon leaves were subjected to quantitative confocal laser microscopy using automated image acquisition, computational pattern recognition, and quantification of membrane compartments. This revealed that our method is sensitive and reliable to detect distinct endomembrane compartments. We applied quantitative confocal laser microscopy to a transgenic line expressing GFP2xFYVE as a marker for endosomal compartments during biotic or abiotic stresses, and detected markedly quantitative adaptations in response to changing environments. Using a transgenic line expressing the plasma membrane-resident syntaxin GFP-PEN1, we quantified the pathogen-inducible extracellular accumulation of this fusion protein at fungal entry sites. Our protocol provides a platform to study the quantitative and dynamic changes of endomembrane trafficking, and potential adaptations of this machinery to physiological stress.

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Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos

Cited by 114 publications

References 40 publications

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

ZebrafishMiner: an open source software for interactive evaluation of domain-specific fluorescence in zebrafish

High-Throughput Confocal Imaging of Intact Live Tissue Enables Quantification of Membrane Trafficking in Arabidopsis

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