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Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression

ABSTRACT: Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression

PROVIDER: PRJNA919171 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22997801_1.fastq.gz	Fastqsanger.gz
	SRR22997801_2.fastq.gz	Fastqsanger.gz
	SRR22997506_1.fastq.gz	Fastqsanger.gz
	SRR22997506_2.fastq.gz	Fastqsanger.gz
	SRR22997507_1.fastq.gz	Fastqsanger.gz

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Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [WGS]

Project description:The transcription factor MYC plays essential roles in pluripotent stem cells, including the promotion of somatic cell reprogramming to pluripotency and the regulation of cell competition and embryonic diapause; however, how Myc expression is regulated in this context remains unknown. The Myc gene lies within a ~3-megabase gene desert that contains multiple cisregulatory elements. We used large-scale genomic deletions/inversions, BAC transgenesis and nested deletion of regulatory regions to characterize the cis-regulation of Myc transcription in the early mouse embryo and Embryonic Stem Cells (ESCs). We identified an Early Embryonic Expression (EEE) topologically-associated region that homes enhancers dedicated to Myc transcriptional regulation in stem cells of the early embryo, including the pluripotent cells of the inner cell mass, pre-implantation and post-implantation epiblast and other early embryonic stem cell populations. Within this region, we identified elements exclusively dedicated to Myc regulation in pluripotent cells, with distinct enhancers that sequentially regulate Myc ranscription during naive and formative pluripotency. Deletion of these pluripotency-specific enhancers dampens the competitive ability of ESCs. These results identify a topologically defined enhancer cluster dedicated to early embryonic expression and uncover a modular mechanism for the regulation of Myc expression in different states of pluripotency.

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Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [4C-seq]

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Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [WGS]

Project description:Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [WGS]

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Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [4C-seq]

Project description:Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression [4C-seq]

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Modular regulation of Myc transcription by a topologically defined enhancer cluster dedicated to pluripotency and early embryonic expression

Project description:This SuperSeries is composed of the SubSeries listed below.

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Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

Project description:C2H2 zinc fingers (C2H2-ZFs) are the most prevalent type of vertebrate DNA-binding domain, and typically appear in tandem arrays (ZFAs), with sequential C2H2-ZFs each contacting 3 (or more) sequential bases. C2H2-ZFs can be assembled in a modular fashion, providing one explanation for their remarkable evolutionary success. Given a set of modules with defined 3-base specificities, modular assembly also presents a way to construct artificial proteins with specific DNA-binding preferences. However, a recent survey of a large number of three-finger ZFAs engineered by modular assembly reported high failure rates (~70%), casting doubt on the generality of modular assembly. Here, we used protein-binding microarrays to analyze 28 ZFAs that failed in the aforementioned study. Most (17) preferred specific sequences, which in all but one case resembled the intended target sequence. Like natural ZFAs, the engineered ZFAs typically yielded degenerate motifs, binding dozens to hundreds of related individual sequences. Thus, the failure of these proteins in previous assays is not due to lack of sequence-specific DNA-binding activity. Our findings underscore the relevance of individual C2H2-ZF sequence specificities within tandem arrays, and support the general ability of modular assembly to produce ZFAs with sequence-specific DNA-binding activity. Protein binding microarray (PBM) experiments were performed for a set of 20 artificial zinc finger arrays (ZFAs). Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to two double-stranded 44K Agilent microarrays, each containing a different DeBruijn sequence design, in order to determine their sequence preferences. The method is described in Berger et al., Nature Biotechnology 2006.

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Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

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