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The SBE7 enhancer is active in Shh expressing brain tissue at E10.5

ABSTRACT: The SBE7 enhancer is active in Shh expressing brain tissue at E10.5

PROVIDER: PRJNA663892 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12653867_1.fastq.gz	Fastqsanger.gz
	SRR12653867_2.fastq.gz	Fastqsanger.gz

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The SBE7 enhancer is active in Shh expressing brain tissue at E10.5

Project description:Using ATAC-seq, we identified an accessible chromatin region within the Shh expressing cell population of eGFP/Cre-Shh mice, which did not correspond to SBE2-4. This open region displayed high levels of vertebrate conservation, and did not map to a known CTCF site. Further analysis revealed the coordinates of this presumptive active enhancer to correspond to the recently identified SBE7 enhancer.

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Shh and ZRS enhancer co-localization is specific to the zone of polarizing activity

Project description:Limb-specific expression of Shh is regulated by the long-range (~one megabasepair distant) ZRS enhancer. In the mouse, murine limb bud restricted spatiotemporal expression of Shh occurs from ~E10 until E11.5 at the distal posterior margin is essential for the correct formation of the autopod. Here, we have analyzed the higher-order chromatin conformation of Shh in expressing and non-expressing tissues, both by fluorescence in situ hybridization (FISH) and by chromosome conformation capture (5C). Conventional and super-resolution light microscopy identified significantly elevated frequences of Shh/ZRS co-localization only in the Shh expressing regions of the limb bud consistent with the formation of an enhancer-promoter loop. However, Shh-ZRS spatial distances were consistently shorter than intervening distances to a neural enhancer in all tissues and developmental stages analyzed – regardless of Shh expression. 5C also identified a topologically associating domain (TAD) over the Shh-ZRS genomic region and enriched interactions between Shh and ZRS, but in the head, body and limb buds of E11.5 embryos, so also not linked to Shh expression. We show that gene-enhancer (Shh/ZRS) co-localization correlates with the spatiotemporal domain of limb bud-specific Shh expression, but that close Shh/ZRS proximity in the nucleus occurs regardless of whether the gene or enhancer is active. We suggest that this constrained chromatin configuration optimises the opportunity for the active enhancer to locate and instigate Shh expression.

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H3K27ac in WT and Shh-/-, and Shh-/- Gli3-/- E10.5 limb buds

Project description:H3K27ac in WT and Shh-/-, and Shh-/- Gli3-/- E10.5 limb buds

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Project description:We wanted to identify differentially expressed genes in wild-type and Shh null E10.5 mouse forelimbs

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Transcriptome of wild type and Shh limb buds at E10.5

Project description:The transcriptome of mouse limb buds of Shh mutant embryos was compared to the transcriptome of limb buds of wild type embryos at embryonic day E10.5

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RNA sequencing of mouse littermate wild-type and Shh null E10.5 forelimbs [Illumina]

Project description:We wanted to identify differentially expressed genes in wild-type and Shh null E10.5 mouse forelimbs Used two wild-type technical replicates and two Shh null technical replicates UT-Genome and Analysis Facility

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Small RNA-seq analysis of E10.5 Tbx18-expressing peri-wolffian duct stroma

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Active enhancer landscape during spermatogenesis.

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H3K27ac in WT and Shh-/-, and Shh-/-;Gli3-/- E10.5 limb buds

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Project description:Expression of Shh in the limb is dependent on a distant enhancer located 850kb away from the gene promoter. We performed chromatin conformation capture (4C-Seq) analysis of the Shh locus in E11.5 mouse limbs so as to better understand the relationship between this regulatory interaction and the structural organisation of the locus. The experiments were performed on wild-type animals as well as on animals carrying an engineered chromosomal inversion (INV(6-C2) (INV6)) . The different viewpoints used (Shh, ZRS, Nom1, Rbm33, Rnf32) enable to characterize the 3D organisation of the locus in the different contexts. The inversion INV6 disrupts the normal topological organisation of the Shh locus in a compact 3D-domain and prevents the physical and regulatory interaction between Shh and its limb enhancer, even though the genomic distance separating the two elements is reduced compared to WT.

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