Distribution of EBP50 binding motifs.
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE33775 | GEO | 2012/11/16
SECONDARY ACCESSION(S): PRJNA148593
REPOSITORIES: GEO
Similar Datasets
Project description:The aim of this study is to identify EBP50 binding sequence. Chip-on-chip experiment with chromatin immunoprecipated with anti-EBP50 antibody is labeled with Cy5 and mock IP (Input DNA) is labeled with Cy3.
2012-11-16 | E-GEOD-33775 | biostudies-arrayexpress
Project description:RNA binding proteins are key regulators of gene expression, yet only a small fraction of these proteins has been functionally characterized. Here, we report the first large-scale analysis of the RNA motifs recognised by RNA binding proteins, encompassing 205 distinct proteins from 24 diverse eukaryotes. The sequence specificities of RBPs display deep evolutionary conservation, such that the recognition preferences for a large fraction of metazoan RNA binding proteins can be inferred from the sequences of their binding domains. The motifs we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA binding proteins in both normal physiology and in human disease. These data provide an unprecedented global view of RBPs and their targets and constitute an invaluable resource for defining post-transcriptional regulatory mechanisms in eukaryotes. Here, we analyze the RNA-binding preferences of 205 distinct RNA-binding proteins from 24 different eukaryotes, using RNAcompete. In this assay, purified GST-tagged RBPs are incubated with an excess of RNA pool and bound RNA from individual pulldowns are directly labeled, hybridized to a custom Agilent 244K microarray, and analyzed computationally to identify RNA-binding motifs.
2013-05-10 | E-GEOD-41235 | biostudies-arrayexpress
Project description:RNA binding proteins are key regulators of gene expression, yet only a small fraction of these proteins has been functionally characterized. Here, we report the first large-scale analysis of the RNA motifs recognised by RNA binding proteins, encompassing 205 distinct proteins from 24 diverse eukaryotes. The sequence specificities of RBPs display deep evolutionary conservation, such that the recognition preferences for a large fraction of metazoan RNA binding proteins can be inferred from the sequences of their binding domains. The motifs we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA binding proteins in both normal physiology and in human disease. These data provide an unprecedented global view of RBPs and their targets and constitute an invaluable resource for defining post-transcriptional regulatory mechanisms in eukaryotes.
2013-05-10 | GSE41235 | GEO
Project description:The aim of the study was to identify RFX1 and RFX2 binding sites in mouse pancreatic beta cells.
2015-08-22 | GSE72272 | GEO
Project description:High-throughput RNA-IP sequencing was employed to identify the CNBP binding mRNAs and their binding sites in HCT116 cells.
2017-11-16 | GSE106918 | GEO
Project description:The cGAS-STING pathway plays a central role in controlling tumor progression through nucleic acid sensing and type I Interferon production. Here, we identify Poly(rC) Binding Protein 1 (PCBP1) as a tumor suppressor that amplifies cGAS-STING signaling in breast cancer. Using patient datasets and a transgenic mouse model with conditional PCBP1 knockout in mammary epithelial cells, we show that PCBP1 expression correlates with improved survival, reduced tumor burden, increased type I IFN and ISG expression, and elevated cytotoxic T cell infiltration. Mechanistically, PCBP1 binds cytosine-rich single-stranded motifs via its KH domains and increases cGAS affinity to these nucleic acids. Disruption of the conserved GXXG motif impairs PCBP1's nucleic acid binding and cGAS activation. Although cGAS is a double-stranded DNA sensor with no intrinsic sequence specificity, we uncover that the single-stranded nucleic-acid binding protein PCBP1 enhances cGAS sensing by engaging sequence-specific motifs, acting as an important nucleic acid co-sensor that impairs tumorigenesis.
2025-10-15 | GSE307616 | GEO
Project description:The cGAS-STING pathway plays a central role in controlling tumor progression through nucleic acid sensing and type I Interferon production. Here, we identify Poly(rC) Binding Protein 1 (PCBP1) as a tumor suppressor that amplifies cGAS-STING signaling in breast cancer. Using patient datasets and a transgenic mouse model with conditional PCBP1 knockout in mammary epithelial cells, we show that PCBP1 expression correlates with improved survival, reduced tumor burden, increased type I IFN and ISG expression, and elevated cytotoxic T cell infiltration. Mechanistically, PCBP1 binds cytosine-rich single-stranded motifs via its KH domains and increases cGAS affinity to these nucleic acids. Disruption of the conserved GXXG motif impairs PCBP1's nucleic acid binding and cGAS activation. Although cGAS is a double-stranded DNA sensor with no intrinsic sequence specificity, we uncover that the single-stranded nucleic-acid binding protein PCBP1 enhances cGAS sensing by engaging sequence-specific motifs, acting as an important nucleic acid co-sensor that impairs tumorigenesis.
2025-10-15 | GSE307750 | GEO
Project description:The current study provides an opportunity to identify specific MHC I motifs in vitro. The combination of random peptide library, LC-MS/MS and De Novo Sequencing can be an important complement to the identification of MHC I motif. Insight into the length distribution of MHC-I binding peptides helps us better understand the molecular mechanism.
2022-02-25 | PXD020818 | Pride
Project description:Background. Polycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidopsis, loss of PRC2 function leads to pleiotropic effects on growth and development thought to be due to ectopic expression of seed and embryo-specific genes. While there is some understanding of the mechanisms by which specific genes are targeted by PRC2 in animal systems, it is still not clear how PRC2 is recruited to specific regions of plant genomes.Results. We used ChIP-seq to determine the genome-wide distribution of hemagglutinin (HA)-tagged FERTLIZATION INDEPENDENT ENDOSPERM (FIE-HA), the Extra Sex Combs homolog protein present in all Arabidopsis PRC2 complexes. We found that the FIE-HA binding sites co-locate with a subset of the H3K27me3 sites in the genome and the associated genes were more likely to be de-repressed in mutants of PRC2 components. The FIE-HA binding sites are enriched for three sequence motifs including a putative GAGA factor binding site that is also found in Drosophila Polycomb Response Elements (PREs).Conclusions. Our results suggest that PRC2 binding sites in plant genomes share some sequence features with Drosophila PREs. However, RNA was extracted from intermediate phenotype siFIE plants, clf-7 swn-28 and Col using Qiagen Plant RNeasy mini kit. For each sample, three pools of 10-12 plants were used. The siFIE plants were analysed for FIE mRNA by RT-qPCR; the maximum level of FIE mRNA was found to be 10% of wildtype.
2013-09-01 | E-GEOD-48857 | biostudies-arrayexpress
Project description:Background. Polycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidopsis, loss of PRC2 function leads to pleiotropic effects on growth and development thought to be due to ectopic expression of seed and embryo-specific genes. While there is some understanding of the mechanisms by which specific genes are targeted by PRC2 in animal systems, it is still not clear how PRC2 is recruited to specific regions of plant genomes.Results. We used ChIP-seq to determine the genome-wide distribution of hemagglutinin (HA)-tagged FERTLIZATION INDEPENDENT ENDOSPERM (FIE-HA), the Extra Sex Combs homolog protein present in all Arabidopsis PRC2 complexes. We found that the FIE-HA binding sites co-locate with a subset of the H3K27me3 sites in the genome and the associated genes were more likely to be de-repressed in mutants of PRC2 components. The FIE-HA binding sites are enriched for three sequence motifs including a putative GAGA factor binding site that is also found in Drosophila Polycomb Response Elements (PREs).Conclusions. Our results suggest that PRC2 binding sites in plant genomes share some sequence features with Drosophila PREs. However,
2013-09-01 | GSE48857 | GEO