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Genome-wide maps of chromatin accessibility in response to Hh signaling in mouse embryonic forelimb buds

ABSTRACT: Purpose: The response to Hedgehog signaling in the limb is driven by GLI bound enhancers and the majority of Hh targets in the developing limb bud are regulated solely by the activity of GLI-repressor. Currently, we do not have a comprehensive understanding of how GLI bound enhancers respond to Hedgehog signaling. The goal of this study is to identify how GLI bound enhancers are regulated by Hedgehog signaling and specifically by GLI-repressor. Methods: ATAC-seq was done in embryonic day 10.5 posterior limb buds from control and Shh-null embryos to identify GLI enhancers that change chromatin accessibility in response to Hedgehog signaling. Results: We found that Hedgehog signaling regulates the chromatin accessibility of a subset of GLI binding regions. This subset of GLI bound enhancers has reduced accessibility in the absence of Hedgehog signaling and largely overlaps with GLI enhancers that also have reduced H3K27ac in the absence of Hedgehog signaling.

ORGANISM(S): Mus musculus

PROVIDER: GSE107877 | GEO | 2020/01/21

REPOSITORIES: GEO

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Genome wide maps of chromatin modification in response to Hh signaling in mouse embryonic forelimb buds

Project description:Purpose: The response to Hedgehog signaling in the limb is driven by GLI bound enhancers and the majority of Hh targets in the developing limb bud are regulated solely by the activity of GLI-repressor. Currently we do not have a comprehensive understanding of how GLI bound enhancers respond Hedgehog signaling. The goal of this study is to identify how GLI bound enhancers are regulated by Hedgehog signaling and specifically by GLI-repressor. Methods: Histone modification ChIP-sequencing was done in Embryonic day 10.5 limb buds from control and Shh null embryos to identify histone modifications that change in response to Hedgehog signaling. We also did a comparative analysis of histone modificaiton response to Hedgehog stimulation in NIH3T3 cells to assess tissue specificity of GLI bound enhancer response to Hedgehog signaling. Results: We found that Hedgehog signaling specifically regulates the acetylation status of Histone 3 lysine 27 at a subset of GLI binding regions. These regions correlate with both known Hedgehog target genes in the limb bud and with characterized enhancers in the limb. This set of Hedgehog responsive GLI bound enhancers demonstrate enhanced tissue specificity.

2020-01-21 | GSE106948 | GEO

GLI3 binding regions in mouse embryonic forelimb buds

2020-01-21 | GSE133710 | GEO

HDAC1 binding regions in mouse embryonic limbs

2020-01-21 | GSE141998 | GEO

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

Project description:Purpose: The response to Hedgehog signaling in the limb is driven by GLI bound enhancers. While most Hh targets in the developing limb bud appear to be regulated by the activity of GLI-repressor, the role of GLI activator in this regulation is unclear. Here we assess the roles of GLI activator and repressor in regulating H3K27ac to activate their enhancers. Methods: ChIP-seq was performed in Embryonic day 10.5 mouse limb buds from WT, Shh-/- and Shh-/-Gli3-/- embryos Results: We found that most GLI binding regions can be activated in the absence of both GLI activator and repressor, while a small subset require GLI activator for activity. These indicate that most GLI enhancers in the limb are regulated by GLI repression.

2020-01-21 | GSE133712 | GEO

GLI transcriptional repression is inert prior to HH pathway activation

Project description:Purpose: Most Hedgehog responsive gene expression is mediated through GLI de-repression. Additionally GLI -repression is proposed to play roles in limb pre-patterning before HH pathway activation. This study evaluates if GLI repression is established prior to HH pathway activation. Methods: To determine if GLI-repression is established prior to pathway activation, we used genomic approaches to study GLI-mediated repression using the mouse developing limb as a model. We identified pre-HH (E9.25, 21-23S) and post-HH (E10.5, 32-25S) GLI3 binding regions using CUT&RUN for endogenous FLAG-tagged GLI3 proteins. Using a combination of ChIP-seq, CUT&RUN, CUT&Tag, ATAC-seq and RNA-seq, we tested whether loss of Gli3 prior to HH signaling was able to de-repress genes and enhancers, as it does after HH signaling. Results: Prior to HH signaling, GLI3 binds to poised, accessible regions with histone deacetylase (HDAC) proteins, similar to post-HH signaling. Despite GLI3 binding to most regions as it does in the post-HH limb, loss of Gli3 is unable to prematurely active target genes or enhancers. Furthermore, we find that GLI3-dependent chromatin compaction does not occur until roughly 10 hours after HH signaling would have normally been induced. Collectively, these results support that GLI repressor proteins are inert prior to HH pathway activation.

2022-01-21 | GSE178838 | GEO

Genome-Wide Gli3 Binding Sites in the E11.5 Mouse Limb Bud

2008-09-15 | GSE11062 | GEO

A Genome-Scale Analysis of the Cis-Regulatory Circuitry Underlying Hedgehog Mediated Patterning of the Mammalian Limb

Project description:Sonic hedgehog (Shh) signals via Gli transcription factors to direct digit number and identity in the vertebrate limb. We have characterized the Gli-dependent cis-regulatory network through a combination of whole genome ChIP-on-chip and transcriptional profiling of the developing mouse limb. These analyses identified approximately 5,000 high quality Gli3 binding sites, including all known Gli-dependent enhancers. Discrete binding regions exhibit a higher-order clustering, highlighting the complexity of cis-regulatory interactions. Further, Gli3 binds inertly to previously identified neural-specific Gli enhancers, demonstrating the accessibility of their cis-regulatory elements. Intersection of DNA binding data with gene expression profiles predicted 205 putative limb target genes. A subset of putative cis-regulatory regions were analyzed in transgenic embryos, establishing Blimp1 as a direct Gli target and identifying Gli-activator signaling in a direct, long-range regulation of the BMP antagonist Gremlin. In contrast, a long range silencer cassette downstream of Hand2 likely mediates Gli3 repression in the anterior limb. These studies provide the first comprehensive characterization of the transcriptional output of a Shh-patterning process in the mammalian embryo and a framework for elaborating regulatory networks in the developing limb. This SuperSeries is composed of the SubSeries listed below.

2008-09-15 | GSE11077 | GEO

Identification of GLI-associated proteins by mass spectrometry

Project description:The Hedgehog signaling pathway is essential for the maintenance and response of several types of stem cells. To study the transcriptional response of stem cells to HH signaling, we searched for proteins binding to GLI proteins, the transcriptional effectors of the HH pathway in mouse embryonic stem (ES) cells. We purified GLI protein complex from an ES cell line that contained a tamoxifen-inducible 3XFLAG-tagged GLI3 repressor allele by anti-FLAG immunoprecipitation and several novel GLI co-factors were identified in the complex by subsequent mass spectrometry analysis.

2016-02-04 | PXD002494 | Pride

The BAF complex does not mediate GLI repression (WT Cut&RUN)

Project description:Purpose: This study seeks to identify SMARCC1-bound regions in the mouse limb. Methods: To identify SMARCC1 bound regions in the limb, we performed Cut&Run on pooled anterior and posterior wild-type forelimbs at E11.5 (43-44s; 3 replicates each) and on whole forelimb pairs at E9.5 (21-24s; 2 replicates). We identified 28,082 SMARCC1-bound regions in the anterior forelimb at E11.5, 42,530 regions in the E11.5 posterior limb, and 10,792 SMARCC1-bound regions at E9.5 (FDR<0.05). Results: We find that SMARCC1 is bound to most limb enhancer regions at late stages (E11.5). Additionally, We find that SMARCC1 is bound to the majority of HH-responsive GLI enhancers at E11.5 but only a small portion of GLI enhancers at E9.5.

2024-02-03 | GSE224507 | GEO

Phosphoproteomics of induced and inhibited early Hh signaling in human medulloblastoma cells

Project description:Aberrant sonic hedeghog signaling is implicated in the development of various cancer entities such as medulloblastoma. The canonical signaling cascade has been studied for years. Activation of GLI transcription factors was revealed as the driving force upon pathway activation. Phosphorylation by Proteinkinase A, Casein Kinase 1 and Glycogen Synthase Kinase 3 β has been found to influence the degradation of the GLI transcription factors. However, the deeper role of phosphorylation in the signal transduction remains unclear. We, therefore, applied comprehensive HPLC-MS/MS based phosphoproteomics to reveal phosphorylation dynamics underlying the chemical activation and inhibition of sonic hedgehog signaling in human medulloblastoma cells. Human medulloblastoma cells were treated with SAG (Hh pathway induction) and Vismodegib (Hh pathway inhibition) for 5 and 15 minutes. Our phosphoproteomic profiling revealed a central role of phosphorylation in the regulation of ciliary assembly, trafficking and signal transduction after 5 minutes treatment. ERK/MAPK signaling besides protein kinase A signaling and mTOR signaling were differentially regulated. Activation of Polo-like kinase 1 and inhibtion of Caseinkinase 2A1 was characteristic for Vismodegib treatment while SAG treatment induced Aurora kinase A activity. Distinctive phosphorylation of central players of sonic Hh signaling such as Smoothened, SUFU, Gli2 and Gli3 was obtained after 15 minutes treatment.

2021-09-08 | PXD013408 | Pride

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