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The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [HiChIP]

ABSTRACT: The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [HiChIP]

PROVIDER: PRJNA673867 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12965869_1.fastq.gz	Fastqsanger.gz
	SRR12965869_2.fastq.gz	Fastqsanger.gz
	SRR12965870_1.fastq.gz	Fastqsanger.gz
	SRR12965870_2.fastq.gz	Fastqsanger.gz
	SRR12965871_1.fastq.gz	Fastqsanger.gz

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The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo

Project description:The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo

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The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [HiChIP]

Project description:Transcriptional and phenotypic robustness during development is believed to require complex regulatory landscapes whereby multiple enhancers redundantly control the expression of major cell identity genes. In contrast, we previously described a limited and genetically distinct set of distal regulatory elements, known as poised enhancers (PEs), that control the induction of genes involved in early brain development in a hierarchical and non-redundant manner. Before becoming activated in neural progenitors, PEs are already bookmarked in pluripotent cells with unique chromatin and topological features that could contribute to their privileged regulatory properties. However, since PEs were originally identified and subsequently characterized using embryonic stem cells (ESC) as in an in vitro differentiation system, it is currently unknown whether PEs are functionally conserved in vivo. Here, we generate and mine various types of genomic data to conclusively show that the epigenetic and 3D structural features of PEs are conserved among pluripotent cells both in vitro and in vivo. Furthermore, by genetically disrupting evolutionary conserved PEs in mouse and chicken embryos, we demonstrate that these regulatory elements play essential and non-redundant roles during the induction of major anterior neural genes in vivo.

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Project description:The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [ATAC-seq]

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The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [ChIP-seq]

Project description:The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo [ChIP-seq]

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The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo.

Project description:Poised enhancers (PEs) represent a genetically distinct set of distal regulatory elements that control the expression of major developmental genes. Before becoming activated in differentiating cells, PEs are already bookmarked in pluripotent cells with unique chromatin and topological features that could contribute to their privileged regulatory properties. However, since PEs were originally characterized in embryonic stem cells (ESC), it is currently unknown whether PEs are functionally conserved in vivo. Here, we show that the chromatin and 3D structural features of PEs are conserved among mouse pluripotent cells both in vitro and in vivo. We also uncovered that the interactions between PEs and their target genes are globally controlled by the combined action of Polycomb, Trithorax and architectural proteins. Moreover, distal regulatory sequences located close to developmental genes and displaying the typical genetic (i.e. CpG islands) and chromatin (i.e. high accessibility and H3K27me3 levels) features of PEs are commonly found across vertebrates. These putative PEs show high sequence conservation within specific vertebrate clades, with only a few being evolutionary conserved across all vertebrates. Lastly, by genetically disrupting PEs in mouse and chicken embryos, we demonstrate that these regulatory elements play essential roles during the induction of major developmental genes in vivo.

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The chromatin and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo

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