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LFY is pioneer transcription factor [MNase-seq]

ABSTRACT: LFY is pioneer transcription factor [MNase-seq]

PROVIDER: PRJNA594411 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13215550_1.fastq.gz	Fastqsanger.gz
	SRR13215550_2.fastq.gz	Fastqsanger.gz
	SRR13215551_1.fastq.gz	Fastqsanger.gz
	SRR13215551_2.fastq.gz	Fastqsanger.gz
	SRR13215552_1.fastq.gz	Fastqsanger.gz

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LFY is pioneer transcription factor [MNase-seq]

Project description:This study identified LEAFY (LFY) as a pioneer transcription factor. We made use of 35S:LFY-GR, an inducible version of the LFY protein fused to the rat glucocorticoid hormone binding domain. In root explants, steroid activated LFY-GR triggers synchronous and abundant flower induction (PMID: 15225291). We combined LFY ChIP-seq, MNase-seq before and after LFY binding and time-course RNA-seq in 35S:LFY-GR root explants to characterize the role of LFY as a pioneer transcription factor.

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LFY is pioneer transcription factor

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LFY is pioneer transcription factor [RNA-seq]

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LFY is pioneer transcription factor [ChIP-seq]

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Nucleosome binding by the pioneer transcription factor OCT4

Project description:The nucleosome is a fundamental unit of chromatin in eukaryotes, and generally prevents the binding of transcription factors to genomic DNA. Pioneer transcription factors overcome the nucleosome barrier, and bind their target DNA sequences in chromatin. OCT4 is a representative pioneer transcription factor that plays a role in stem cell pluripotency. In the present study, we biochemically analyzed the nucleosome binding by OCT4. Crosslinking mass spectrometry showed that OCT4 binds the nucleosome.

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Pioneer transcription factor FoxA maintains an open nucleosome configuration for tissue-specific gene activation [MNase-Seq]

Project description:Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal status of such open chromatin, e.g., at active enhancers, is not clear. Here we develop a combination of low and high levels of MNase digestion along with core histone ChIP-seq to assess the presence of nucleosomes at enhancers and promoters in mouse liver. We find that liver-specific enhancers retain preferentially MNase-accessible nucleosomes, with factors bound, substantially more than ubiquitous enhancers. Furthermore, the pioneer factor FoxA2 is required to keep enhancer nucleosomes accessible in chromatin at active liver genes. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.

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CLK:BMAL1 is a pioneer-like transcription factor [MNase-Seq]

Project description:The mammalian circadian clock relies on the master genes CLOCK (CLK) and BMAL1 and drives rhythmic gene expression to regulate biological functions under circadian control. We recently uncovered a surprising disconnect between the rhythmic binding of CLK:BMAL1 on DNA and the transcription of its target genes, suggesting that they are regulated by as yet uncharacterized mechanisms. Here we show that rhythmic CLK:BMAL1 DNA binding promotes rhythmic chromatin opening. The underlying mechanisms include CLK:BMAL1 binding to nucleosomes and rhythmic chromatin modifications, including the incorporation of the histone variant H2A.Z. This rhythmic chromatin remodeling mediates the rhythmic binding of other transcription factors adjacent to CLK:BMAL1, suggesting that the activity and the tissue-specific expression of these other transcription factors contribute to the genome-wide CLK:BMAL1 heterogeneous transcriptional output. These data therefore indicate that the clock regulation of transcription relies on the rhythmic regulation of chromatin accessibility and suggest that the concept of pioneer function extends to acute gene regulation, well beyond the current confines of developmental/cell specification. Mouse liver nucleosome profile assayed by MNase-Seq over 6 time points of the 24h light:dark cycle (4 wild-type and 4 Bmal1-/- mice per time point). Illumina libraries containing a mononucleosome insert were sequenced using Ilumina HiSeq2000.

2014-01-06 | E-GEOD-47142 | biostudies-arrayexpress

Pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation [ChIP-seq]

Project description:Nuclear DNA is wrapped around core histones to form nucleosomes, which constrains how transcription factors bind to gene regulatory sequences. Pioneer transcription factors have the special ability to bind target DNA on nucleosomes and initiate gene regulatory events, often leading to a local opening of chromatin. Yet the nucleosomal configuration of such open chromatin and the basis for chromatin opening is unclear. Here we combine low and high levels of MNase digestion along with core histone ChIP-seq to assess the presence of nucleosomes at enhancers and promoters in mouse liver. We find that the pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and helping other transcription factors bind. MNase-accessible nucleosomes, bound by transcription factors, are retained substantially more at liver-specific enhancers than promoters and tissue-ubiquitous enhancers. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.

2016-04-08 | GSE77670 | GEO

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