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High-throughput sequencing methods have created exciting opportunities to explore the regulatory landscape of the entire genome. Here we introduce methods to characterize the genomic locations of bound proteins, open chromatin, and sites of DNA-DNA contact in Xenopus embryos. These methods include chromatin immunoprecipitation followed by sequencing (ChIP-seq), a combination of DNase I digestion and sequencing (DNase-seq), the assay for transposase-accessible chromatin and sequencing (ATAC-seq), and the use of proximity-based DNA ligation followed by sequencing (Hi-C).
Akkers,
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
2009, Pubmed,
Xenbase
Akkers,
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
2009,
Pubmed
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Xenbase
Boyle,
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.
2011,
Pubmed
Briggs,
The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution.
2018,
Pubmed
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Xenbase
Bright,
Assay for Transposase-Accessible Chromatin-Sequencing Using Xenopus Embryos.
2019,
Pubmed
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Xenbase
Buenrostro,
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
2013,
Pubmed
Chen,
A rapid and robust method for single cell chromatin accessibility profiling.
2018,
Pubmed
Chiu,
Genome-wide view of TGFβ/Foxh1 regulation of the early mesendoderm program.
2014,
Pubmed
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Xenbase
Cho,
DNase-seq to Study Chromatin Accessibility in Early Xenopus tropicalis Embryos.
2019,
Pubmed
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Xenbase
Cusanovich,
The cis-regulatory dynamics of embryonic development at single-cell resolution.
2018,
Pubmed
Elurbe,
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis.
2017,
Pubmed
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Xenbase
Gentsch,
Mapping Chromatin Features of Xenopus Embryos.
2019,
Pubmed
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Xenbase
Gentsch,
In vivo T-box transcription factor profiling reveals joint regulation of embryonic neuromesodermal bipotency.
2013,
Pubmed
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Xenbase
Gilchrist,
Transcriptomics and Proteomics Methods for Xenopus Embryos and Tissues.
2020,
Pubmed
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Xenbase
Hellsten,
The genome of the Western clawed frog Xenopus tropicalis.
2010,
Pubmed
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Xenbase
Hontelez,
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2015,
Pubmed
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Xenbase
Hontelez,
ChIP-Sequencing in Xenopus Embryos.
2019,
Pubmed
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Xenbase
Jäger,
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci.
2015,
Pubmed
Kalhor,
Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.
2011,
Pubmed
Kaya-Okur,
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2019,
Pubmed
Mitros,
A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.
2019,
Pubmed
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Xenbase
Nakamura,
Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules.
2016,
Pubmed
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Xenbase
Neph,
An expansive human regulatory lexicon encoded in transcription factor footprints.
2012,
Pubmed
Nicoletti,
Computational methods for analyzing genome-wide chromosome conformation capture data.
2018,
Pubmed
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Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation.
2019,
Pubmed
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Xenbase
Quigley,
Generating a Three-Dimensional Genome from Xenopus with Hi-C.
2019,
Pubmed
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Xenbase
Quigley,
Rfx2 Stabilizes Foxj1 Binding at Chromatin Loops to Enable Multiciliated Cell Gene Expression.
2017,
Pubmed
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Xenbase
Rozenblatt-Rosen,
The Human Cell Atlas: from vision to reality.
2017,
Pubmed
Savova,
Transcriptomic insights into genetic diversity of protein-coding genes in X. laevis.
2017,
Pubmed
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Xenbase
Session,
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2016,
Pubmed
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Xenbase
Song,
DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.
2010,
Pubmed
Thélie,
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus.
2015,
Pubmed
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Xenbase
van Heeringen,
Nucleotide composition-linked divergence of vertebrate core promoter architecture.
2011,
Pubmed
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Xenbase
Yasuoka,
Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.
2014,
Pubmed
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Xenbase
Yoon,
HEB and E2A function as SMAD/FOXH1 cofactors.
2011,
Pubmed
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Xenbase
