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. 2023 Jun 26;14:3795. doi: 10.1038/s41467-023-39011-5

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — A Schematic illustration of NEAT1 ChIRP assay performed in differentiated HEKn cells (four days of CaCl₂ treatment). B NEAT1 ChIRP enrichment over Transcription Starting Site (TSS) and Transcription Termination Sites (TTS) in differentiated keratinocytes. C Intersection of NEAT1 ChIRP enrichment over TSS against the indicated covalent histone modifications signatures in differentiated keratinocytes (H3K4me3, active genes, GSE98483; H3K27me3, transcriptionally silent genes, GSE175068). D Barplot showing the top gene ontology (GO) terms for Biological Process of the intersection analysis between NEAT1 binding sites over TSSs and the RNA profile of differentiated keratinocytes (GSM1446880). GO terms were ordered by FDR (False Discovery Rate) adjusted p value calculated by ShinyGO version 0.76. E Gene enrichment analysis of the indicated epidermal genes in the entire (ALL), top 50% and top 25% NEAT1 binding sites subgroups. F RNA-seq reads in control (NC) and NEAT1 depleted keratinocytes (LNA-NEAT1) together with NEAT1 ChIRP enrichment and KLF4 genomic occupancy (GSE57702) over the indicated epidermal genes in differentiated keratinocytes. G ChIP-qPCR showing the H3K4me3 epigenetic mark at the indicated epidermal genes loci in differentiated keratinocytes upon NEAT1 depletion (LNA-NEAT1). Average values from n = 2 biological replicates measured using three technical replicates are plotted. H Detection of the interactions between the SWI/SNF epigenetic factor BRG1 or the epidermal transcription factor KLF4 and NEAT1 by RIP assay. After formaldehyde cross-linking, the coimmunoprecipitated RNAs were quantified by qRT-PCR. Average values from n = 2 biological replicates measured using three technical replicates are plotted. I ChIP-qPCR showing SFPQ occupancy at the NEAT1 binding site of the indicated epidermal genes loci. Average values from n = 2 biological replicates measured using three technical replicates are plotted. Source data are provided as a Source Data file.