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RNA-seq and ChIP-seq identification of unique and overlapping targets of GLI transcription factors in melanoma cell lines

ABSTRACT: RNA-seq and ChIP-seq identification of unique and overlapping targets of GLI transcription factors in melanoma cell lines

PROVIDER: PRJEB54640 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR9929020_1.fastq.gz	Fastqsanger.gz
	ERR9929020_2.fastq.gz	Fastqsanger.gz
	ERR9929030_1.fastq.gz	Fastqsanger.gz
	ERR9929030_2.fastq.gz	Fastqsanger.gz
	ERR9929040_1.fastq.gz	Fastqsanger.gz

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RNA-seq and ChIP-seq identification of unique and overlapping targets of GLI transcription factors in melanoma cell lines

Project description:Despite significant progress in therapy, melanoma is still the most lethal form of skin cancer, with a rising incidence worldwide. Little is known about the impact of deregulated Hedgehog-GLI (HH-GLI) signalling pathway in the progression of this disease. Based on previous research, we hypothesized that in melanoma activation of HH-GLI signaling pathway is non- canonical due to its crosstalk with MAPK signaling pathway, which is the most deregulated pathway in melanoma. In order to investigate the link between the two pathways and to find novel GLI transcriptional targets that could be considered for potential combination therapy, we performed RNA sequencing on three melanoma cell lines with overexpressed GLI1, GLI2 and GLI3 and combined them with results of ChIP sequencing on endogenous GLI1, GLI2 and GLI3 proteins on the same cell lines. RNA-seq revealed a total of 808 DEGs for GLI1, 941 DEGs for GLI2 and 58 DEGs for GLI3. ChIP-seq identified 527 genes that contained GLI1 binding sites in their promoters, 1103 for GLI2 and 553 for GLI3. After combining these results, 21 targets were selected for validation by qPCR. Fifteen of these targets were validated in the tested cell lines, 6 of which were detected by both RNA-seq and ChIP-seq.

2023-01-01 | E-MTAB-11936 | biostudies-arrayexpress

RNA-seq and ChIP-seq Identification of Unique and Overlapping Targets of GLI Transcription Factors in Melanoma Cell Lines.

Project description:BackgroundDespite significant progress in therapy, melanoma still has a rising incidence worldwide, and novel treatment strategies are needed. Recently, researchers have recognized the involvement of the Hedgehog-GLI (HH-GLI) signaling pathway in melanoma and its consistent crosstalk with the MAPK pathway. In order to further investigate the link between the two pathways and to find new target genes that could be considered for combination therapy, we set out to find transcriptional targets of all three GLI proteins in melanoma.MethodsWe performed RNA sequencing on three melanoma cell lines (CHL-1, A375, and MEL224) with overexpressed GLI1, GLI2, and GLI3 and combined them with the results of ChIP-sequencing on endogenous GLI1, GLI2, and GLI3 proteins. After combining these results, 21 targets were selected for validation by qPCR.ResultsRNA-seq revealed a total of 808 differentially expressed genes (DEGs) for GLI1, 941 DEGs for GLI2, and 58 DEGs for GLI3. ChIP-seq identified 527 genes that contained GLI1 binding sites in their promoters, 1103 for GLI2 and 553 for GLI3. A total of 15 of these targets were validated in the tested cell lines, 6 of which were detected by both RNA-seq and ChIP-seq.ConclusionsOur study provides insight into the unique and overlapping transcriptional output of the GLI proteins in melanoma. We suggest that our findings could provide new potential targets to consider while designing melanoma-targeted therapy.

| S-EPMC9497141 | biostudies-literature

Unique activities of two overlapping PAX6 retinal enhancers

Project description:Unique activities of two overlapping PAX6 retinal enhancers

| PRJNA1004255 | ENA

Identification of Gli-Act targets in the mouse ventral neural tube by ChIP

Project description:In studies investigating Sonic hedgehog (Shh) mediated patterning of the ventral neural tube, a process where Shh acts as a morphogen, we have investigated the transcriptional network underlying neural tube specification. Adopting an ES-cell based Shh neuronal specification assay (embryoid body; EBs) and a FLAG-tagged Gli protein (a transcriptional effector of the Shh pathway), we identified a number of direct targets of Gli action using Chromatin Immunoprecipitation (ChIP). These results will provide a first survey of the genome level response to this critical signaling input in vertebrate patterning Keywords: ChIP-chip, Gli transcription factors, Gli1, neural specification, mouse

2007-04-20 | GSE5683 | GEO

The BAF complex does not mediate GLI repression (ATAC-Seq)

Project description:Purpose: This study seeks to determine whether Smarcc1 mediates GLI repression through chromatin compaction in the limb. Methods: To determine if Smarcc1 mediated GLI repression through chormatin compaction, we used genomic approached to determine changes in chromatin accessibility in control and Smarcc1-conditional mutants. We performed ATAC-seq on individually genotyped anterior forelimbs at E11.5 (40-48s) on control (2 replicates) and PrxCre/+;Smarcc1c/c (3 replicates) embryos. From this experiment we identified ~10,000 differentially accessible regions (FDR<0.05). Results: We find that SMARCC1 is required to maintain chromatin accessibility at thousands of regions within the mouse limb, including most HH-responsive GLI enhancers

2024-02-03 | GSE224506 | 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

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

Proteomics in gastroparesis: Unique and overlapping protein signatures in diabetic and idiopathic gastroparesis

Project description:Proteomics in gastroparesis: Unique and overlapping protein signatures in diabetic and idiopathic gastroparesis

| PRJNA540941 | ENA

Role of GLI-signaling in the postnatal cardiomyocyte development

Project description:Developmentally, we found downregulation of GLI-signaling in adult human CM, adult murine CM, and in late-stage hiPSC-CM. To investigate the role of GLI-signaling in early-stage cardiomyocyte, we inhibited GLI-signaling and undertook bulkRNAseq analysis at two distinct levels of inhibitions.

2024-11-27 | GSE201589 | GEO

RNA-seq analysis of gliotactin (Gli)-knockdown Drosophila melanogaster posterior midguts enterocytes (EC)

Project description:The goal of this study is to analyze changes in gene expression produced in posterior midguts after knocking down Gli in enterocytes (EC) during 9 days. Gli was depleted from ECs using a drug-inducible version of the binary GAL4-UAS system in combination with UAS-GLI-RNAi. Targeted gene expression using the 5966GS-GAL4 driver is observed in adult ECs when flies are fed the progesterone analog RU486 (RU+); addition of ethanol is used as a control (RU-), providing cohorts of isogenic individuals with or without induction of the Gli-RNAi transgene.

2016-12-18 | GSE74168 | GEO

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