Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

ChIP-seq analysis of histone modifications and RNA polymerase II at 4 stages of directed cardiac differentiation of mouse embryonic stem cells

ABSTRACT: We interrogated the genome-wide occupancy of histone modifications and RNA polymerase II at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of histone modifications during differentiation that are coordinated with stage-specific gene expression including a novel preactivation chromatin pattern found at genes associated with cardiac function. In addition, this study identified distal enhancer elements and enriched transcription factor motifs within enhancer regions for each stage of differentiation, which were used to predict novel transcription regulatory networks. ChIP-seq analysis of histone modifications and RNA polymerase II at 4 stages of directed cardiac differentiation of mouse embryonic stem cells. Each stage in biological duplicate or triplicate

ORGANISM(S): Mus musculus

SUBMITTER: Laurie Boyer

PROVIDER: E-GEOD-47949 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Wamstad Joseph A JA Alexander Jeffrey M JM Truty Rebecca M RM Shrikumar Avanti A Li Fugen F Eilertson Kirsten E KE Ding Huiming H Wylie John N JN Pico Alexander R AR Capra John A JA Erwin Genevieve G Kattman Steven J SJ Keller Gordon M GM Srivastava Deepak D Levine Stuart S SS Pollard Katherine S KS Holloway Alisha K AK Boyer Laurie A LA Bruneau Benoit G BG

Cell 20120912 1

Heart development is exquisitely sensitive to the precise temporal regulation of thousands of genes that govern developmental decisions during differentiation. However, we currently lack a detailed understanding of how chromatin and gene expression patterns are coordinated during developmental transitions in the cardiac lineage. Here, we interrogated the transcriptome and several histone modifications across the genome during defined stages of cardiac differentiation. We find distinct chromatin ...[more]

PMID: 22981692

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Project description:Missense mutations in the TP53 gene are frequent genetic alterations in human tumor tissue and cell lines. In contrast to wild-type p53, the mutant p53 (mutp53) protein has lost the transcriptional activity towards pro-apoptotic and growth arrest genes, but retained the property to interact with DNA in a structure-specific fashion. Expression of mutp53 is advantageous for tumor cells, however the molecular mechanism of mutp53 action is still not known. We used the glioblastoma-derived U-251 MG human cell line to analyze DNA binding of mutant p53 (R273H mutation) on a Nimblegen custom 135k tiling array and to correlate mutp53 binding regions with the epigenetic state and occupation by other transcription factors (ETS1 and SP1). We found that mutp53-binding regions are G/C-rich and are located around transcriptional start sites (TSS) of many protein-coding genes, which in most cases are active, but are not always regulated upon transient mutp53 depletion. We propose a model which does not only rely on interactions of mutp53 with diverse transcriptional regulators at active promoters, but primarily is based on a DNA binding activity of mutp53. We designed a Nimblegen custom 135k tiling array that covers a large set of putative and known p53 (wild-type and mutant) target genes in the human genome. For analysis of the epigenetic state of genes covered by the tiling array in control and mutant p53-depleted U251 cells we focused on changes in active histone marks, H3K4me3 and H3K9Ac, and RNA polymerase II recruitment and processivity. H3K4me3 and H3K9Ac marks are enriched in active promoter regions and the phosphorylation of serine 5 (S5-P) and serine 2 (S2-P) in the CTD of RNA polymerase II have been described to define initiated and elongating complexes, respectively. We performed the ChIP-chip experiments for H3K4me3, H3K9Ac, RNA polymerase II (S5-P) and RNA polymerase II (S2-P) from U251 cells transfected with p53-specific siRNA or control siRNA (2 biological replicates each). To analyze binding of mutant p53 to the genes covered by the tiling array we performed mutant p53 ChIP-chip experiments in 4 biological replicates of. In addition, we analyzed the distribution of SP1 and ETS1 binding sites in 3 biological replicates.

Dataset Information

ChIP-seq analysis of histone modifications and RNA polymerase II at 4 stages of directed cardiac differentiation of mouse embryonic stem cells

Publications

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Similar Datasets

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