ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR187/058/SRR18733258/SRR18733258.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR187/059/SRR18733259/SRR18733259.fastq.gzprimaryOK200GenomicsNGS facility, DMMBM, Università degli Studi di Napoli Federico IIhttps://www.ebi.ac.uk/ena/browser/view/PRJNA825829Mus musculusxref:PubMed:35918713Hmga2 KO pluripotent stem cells fail to develop into epiblast-like stem cells (EpiLCs). By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in stabilized epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. As nuclear lamina is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of HiC data in wt and Hmga2 KO cells allowed us to observe that inter-TAD interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina. Overall design: Genome binding/occupancy profiling of Hmga2 in EpiLCs by high throughput sequencing.ENAnuclear chromatin, HITS-CLIP, High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, HMGI C Protein, cytoplasmic chromatin, ChIP-Chip, Nuclear Membranes, HMG I C Protein, Chromatin Immuno-precipitation, conformation, Cross Linking and Immunoprecipitation Followed by Deep Sequencing, Stem Cells, ChIP Sequencing, CLIP-Seq, Assay for Transposase-Accessible Chromatin Using Sequencing, Nuclear Envelopes, Pluripotent, ChIP-PET, ChIP-Exo, Stem Cell, PSC cell, Chromatin Immunoprecipitation Sequencing-Chip, Pluripotent Stem Cell, Nuclear, High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, HMG I-C Protein, Chromatins, Membranes, Chromatin Immunoprecipitation Sequencing Chip, Chromatin Immuno precipitation Sequencing, Envelope, ChIP, Chromatin Immunoprecipitation Paired End Tag, Chromatin Immuno Precipitation Paired End Tag, Envelopes, Cross-Linking and Immunoprecipitation Followed by Deep Sequencing, Chromatin Immunoprecipitation, Chromatin Immuno-precipitation Sequencing, ChIP Exonuclease, Membrane, Hmga2 protein, ChIP-Seq, Sequencing, Assay for Transposase Accessible Chromatin Using Sequencing, Chromatin Immunoprecipitation Paired-End Tag, Nuclear Membrane, HMGI-C Protein, ChIA-PET., Chromatin Immuno-Precipitation Paired-End Tag, chromosome scaffold, ATAC-Seq, Chromatin Immunoprecipitation Sequencing-Chips, relational structural quality, ChIP-Exonucleasenuclear chromatin, HITS-CLIP, High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, HMGI C Protein, cytoplasmic chromatin, ChIP-Chip, Nuclear Membranes, HMG I C Protein, Chromatin Immuno-precipitation, conformation, Cross Linking and Immunoprecipitation Followed by Deep Sequencing, Stem Cells, ChIP Sequencing, CLIP-Seq, Assay for Transposase-Accessible Chromatin Using Sequencing, Nuclear Envelopes, Pluripotent, ChIP-PET, ChIP-Exo, Stem Cell, PSC cell, Chromatin Immunoprecipitation Sequencing-Chip, Pluripotent Stem Cell, Nuclear, High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, HMG I-C Protein, Chromatins, Membranes, Chromatin Immunoprecipitation Sequencing Chip, Chromatin Immuno precipitation Sequencing, Envelope, ChIP, Chromatin Immunoprecipitation Paired End Tag, Chromatin Immuno Precipitation Paired End Tag, Envelopes, Cross-Linking and Immunoprecipitation Followed by Deep Sequencing, Chromatin Immunoprecipitation, Chromatin Immuno-precipitation Sequencing, ChIP Exonuclease, Membrane, Hmga2 protein, ChIP-Seq, Sequencing, Assay for Transposase Accessible Chromatin Using Sequencing, Chromatin Immunoprecipitation Paired-End Tag, Nuclear Membrane, HMGI-C Protein, ChIA-PET., Chromatin Immuno-Precipitation Paired-End Tag, chromosome scaffold, ATAC-Seq, Chromatin Immunoprecipitation Sequencing-Chips, relational structural quality, ChIP-ExonucleasefalseHmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [ChIP-seq]Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [ChIP-seq]2025-09-242022-07-10PRJNA825829GSE2006711009035918713