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Genome-wide maps of Tbx2-binding sites in mouse melanoma cells

ABSTRACT: Genome-wide maps of Tbx2-binding sites in mouse melanoma cells

PROVIDER: PRJNA733222 | ENA |

REPOSITORIES: ENA

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Genome-wide maps of Tbx2-binding sites in mouse melanoma cells

Project description:We report the high-throughput profiling of Tbx2 binding sites in mouse melanoma B16 cells. We generated B16 clones that have endogenous Tbx2 tagged with 3xHA, and used HA antibody for immunoprecipitation. This study provides a high-quality genome-wide Tbx2 binding profile and helps further understand Tbx2 role in melanoma progression

2022-01-07 | GSE175703 | GEO

Genome-wide chromatin occupancy of transcription factor TBX2 in luminal breast cancer cells

Project description:Here we demonstrate a previously unknown mechanism of TBX2-mediated gene repression in breast tumours, whereby TBX2 physically interacts with CoREST-associated proteins LSD1, HDAC1 and the ZNF217 oncogene. Through Chromatin Immunoprecipitation sequencing (ChIP-seq) we find that while over 80% of TBX2 binding sites are concentrated at promoters, these regions show remarkably no enrichment for the T-box element; rather TBX2-bound regions are biased toward a small number of non-T-box motifs, with the most abundant being Specificity Protein 1 (Sp1), EGR1 and Nuclear Transcription Factor Y (NF-Y). Furthermore, we uncover that Sp1 is crucial for recruitment of TBX2 to the NDRG1 promoter and subsequent repression of this gene. We also observe that ZNF217 cooccupies approximately 30% of TBX2-bound sites, a number of which contain RCOR1 and exhibit upregulation of the associated transcripts following disruption of TBX2/CoREST function. Overall these data highlight a novel potential therapeutic opportunity whereby poor-prognosis, TBX2 overexpressing breast tumours may be pharmacologically exploited by targeting the CoREST-dependent gene repression network, to recover normal growth control.

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ETV1 binding sites in GIST and Melanoma cells

Project description:ETV1 is an oncogene in GIST and melanoma and a downstream transcriptional effector of MAP kinase signaling. Here, mapped the ETV1 binding sites in GIST and melanoma cell lines using ChIP-seq.

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Genome-wide maps of FOXO1 binding sites in human endothelial cells

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ChIP-seq of neuroblastoma IMR-32, CLB-GA, NGP, IMR-5/75, GI-M-EN, CHP-212, and IMR-5 cell lines to identify TBX2, MYCN, H3K27ac, H3K4me1 and H3K4me3 binding sites

Project description:ChIP-seq to define bindings sites for TBX2, MYCN, H3K27ac, H3K4me1, H3K4me3 and Input in the cell lines IMR-32, CLB-GA, NGP, IMR-5/75, GI-M-EN, CHP-212, and IMR-5.

2018-10-16 | E-MTAB-6570 | biostudies-arrayexpress

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Genome-wide maps of apurinic sites (AP-sites) and 8-oxoG derived secondary AP-sites

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Genome-wide maps of RAP1 binding sites.

Project description:By performing chromatin immunoprecipitation coupled with ultra-high-throughput sequencing (ChIP-seq), we find that RAP1 binds to telomeres as well as to extra-telomeric sites through the (TTAGGG)2 consensus motif. Extra-telomeric RAP1 binding sites are particularly abundant at subtelomeric regions, and this is in agreement with preferential deregulation of subtelomeric genes in Rap1-deficient cells. Significantly, more than 70% of extratelomeric RAP1 binding sites are located in the vicinity of known genes and about 40% of the genes deregulated in Rap1-null cells contain binding sites for RAP1, suggesting a role of RAP1 in transcriptional control.

2010-07-10 | GSE20867 | GEO

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