ENAapplication/xmlftp.sra.ebi.ac.uk/vol1/fastq/SRR157/009/SRR1571989/SRR1571989.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/SRR157/001/SRR1571991/SRR1571991.fastq.gzftp.sra.ebi.ac.uk/vol1/fastq/SRR157/000/SRR1571990/SRR1571990.fastq.gzprimaryOK2000000GenomicsMultiomicsCenter for Genome Research, Life Sciences, University of Modena and Reggio Emiliahttps://www.ebi.ac.uk/ena/browser/view/PRJNA260624Homo sapiensGenome-wide mapping of transcriptional regulatory elements are essential tools for the understanding of the molecular events orchestrating self-renewal, commitment and differentiation of stem cells. We combined high-throughput identification of nascent, Pol-II-transcribed RNAs by Cap Analysis of Gene Expression (CAGE-Seq) with genome-wide profiling of histones modifications by chromatin immunoprecipitation (ChIP-seq) to map active promoters and enhancers in a model of human neural commitment, represented by embryonic stem cells (ESCs) induced to differentiate into self-renewing neuroepithelial-like stem cells (NESC). We integrated CAGE-seq, ChIP-seq and gene expression profiles to discover shared or cell-specific regulatory elements, transcription start sites and transcripts associated to the transition from pluripotent to neural-restricted stem cell. Our analysis showed that >90% of the promoters are in common between the two cell types, while approximately half of the enhancers are cell-specific and account for most of the epigenetic changes occurring during neural induction, and most likely for the modulation of the promoters to generate cell-specific gene expression programs. Interestingly, the majority of the promoters activated or up-regulated during neural induction have a “bivalent” histone modification signature in ESCs, suggesting that developmentally-regulated promoters are already poised for transcription in ESCs, which are apparently pre-committed to neuroectodermal differentiation. Overall, our study provide a collection of differentially used enhancers, promoters, transcription starts sites, protein-coding and non-coding RNAs in human ESCs and ESC-derived NESCs, and a broad, genome-wide description of promoter and enhancer usage and gene expression programs occurring in the transition from a pluripotent to a neural-restricted cell fate. Genome-wide mapping of H3K4me1 and H3K4me3 in NESCs Overall design: ChIP-seq for H3K4me1 and H3K4me3 in NESCsENAStem Cells, wide, wide/broad, broad, Human Embryonic Stem Cell, Genomes, hESC., Human Embryonic Stem, hESCs, Human Embryonic, Cellshuman being, human., man0.00.00.00.00.00falseHomo sapiensGenome-wide Definition of Promoter and Enhancer Usage During Neural Induction of Human Embryonic Stem Cells [ChIP-seq]2022-05-122015-05-23PRJNA260624GSE61265259786769606