Unknown,Transcriptomics,Genomics,Proteomics

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Assessing SMARCA4 restoration contribution to global changes in p300 occupancy in BIN-67 cells

ABSTRACT: We aim to test how SMARCA4 restoration impacts p300 occupancy distribution. To this aim we generated ChIP-seq samples in BIN-67 with or without A-485 treatment (1 μM, 24h), as a proxy for p300 acetylatransferase inhibition, and BIN-67 with inducible SMARCA4 restoration (1 μg/ml Doxycycline for 24h). We pulled down p300 and H3K27ac as a marker for p300 acetyltransferase activity on the chromatin.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Giulio Aceto

PROVIDER: E-MTAB-15699 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:While the majority of protein-coding genes in the human genome have been identified, the location of the regulatory sequences that control their expression in time and space remains poorly defined. The importance of identifying these elements is underscored by a growing number of studies (such as GWAS) supporting a relationship between variation in non-coding sequences and human disease. M-BM- emonstrated that ChIP-Seq with p300 directly on human or mouse tissues represents a powerful method to identify the location and tissue-specific activity pattern of enhancers in the genome.M-BM- a highly specific chromatin mark for the prediction of in vivo enhancers, it is not without limitations. M-BM- comparison of p300-bound regions with previously generated enhancer sets shows that the majority of enhancers are activated independently of p300. To attempt to identify a larger proportion of enhancers in vivo, we have focused on several additional transcriptional coactivators that are hypothesized to be associated with active tissue-specific enhancers. M-BM- limited availability of ChIP-seq grade antibodies for these coactivators, FLAG-tag knock-in mice were generated and ChIP-seq using a FLAG antibody was performed on various tissues from e11.5 mouse embryos. Indeed, as these mouse lines have become available we have validated their valuable role as marks for transcriptional enhancers in vivo.M-BM- studies are expected to further expand the catalogue of in vivo functional enhancers, which will aid in the decoding of the regulatory genome and provide new insights into the role of gene regulation in human biology and disease. In addition to FLAG data, this accession includes histone acetylation / methylation ChIP-seq data from e11.5 mouse embryonic tissues. Histone ChIP-seq data was used in combination with FLAG data for various computational analyses. Examination of FLAG-labeled transcriptional coactivator binding in mouse embryonic stage 11.5 and embryonic stem cells

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Assessing SMARCA4 restoration contribution to global changes in p300 occupancy in BIN-67 cells

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