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Profiling of histone modifications in bovine embryonic stem cells

ABSTRACT: Profiling of histone modifications in bovine embryonic stem cells

PROVIDER: PRJNA659993 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12540020_1.fastq.gz	Fastqsanger.gz
	SRR12540020_2.fastq.gz	Fastqsanger.gz
	SRR12540021_1.fastq.gz	Fastqsanger.gz
	SRR12540021_2.fastq.gz	Fastqsanger.gz
	SRR12540022_1.fastq.gz	Fastqsanger.gz

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Profiling of histone modifications in bovine embryonic stem cells

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Project description: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

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H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells

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H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells

Project description:Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. However, it is unknown whether another repressive histone modification, histone 4 lysine 20 trimethylation (H4K20me3), co-localizes with activating histone marks in ES cells. Here, we describe the previously uncharacterized coupling of the repressive H4K20me3 heterochromatin mark with the activating histone modifications H3K4me3 and histone 3 lysine 36 trimethylation (H3K36me3), and transcriptional machinery (RNA polymerase II; RNAPII), in ES cells. These newly described bivalent domains consisting of H3K4me3/H4K20me3 are predominantly located in intergenic regions and near transcriptional start sites of active genes, while H3K36me3/H4K20me3 are located in intergenic regions and within gene body regions of active genes. Global sequential ChIP, also termed reChIP-Seq, confirmed the simultaneous presence of H3K4me3 and H4K20me3 at the same genomic regions in ES cells. Genes containing H3K4me3/H4K20me3 exhibit decreased RNAPII pausing and are poised for deactivation of RNAPII binding during differentiation relative to H3K4me3 marked genes. An evaluation of transcription factor (TF) binding motif enrichment revealed that DNA sequence may play a role in shaping the landscape of these novel bivalent domains. Moreover, H3K4me3/H4K20me3 and H3K36me3/H4K20me3 bound regions are enriched with repetitive LINE and LTR elements.

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