ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/000/SRR5274800/SRR5274800_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/009/SRR5274799/SRR5274799_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/007/SRR5274797/SRR5274797_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/007/SRR5274797/SRR5274797_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/008/SRR5274798/SRR5274798_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/009/SRR5274799/SRR5274799_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/008/SRR5274798/SRR5274798_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR527/000/SRR5274800/SRR5274800_1.fastq.gzprimaryOK200GenomicsInstitutes of Biomedical Sciences, Fudan Universityhttps://www.ebi.ac.uk/ena/browser/view/PRJNA376129Mus musculusxref:PubMed:29273625Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. Additionally, upon HNRNPU depletion, chromatin interactions between A-type (active) and B-type (inactive) compartments increase significantly but those among same types of compartments decrease significantly, which associate with global gene expression changes. While TADs remain largely invariant, both inter- and intra-TAD interactions increase significantly in A-type compartments but decrease in B-type compartments. Mechanically, HNRNPU complexes with structural proteins CTCF and RAD21 depletion of HNRNPU specifically weakens the bindings of RAD21 to the chromatin, which is highly correlated with the weakness of chromatin loops. Overall design: RNAseq data in Ctrl and HNRNPU KD AML12 cells.ENANucleoskeleton, RCG20317, Nucleoskeletons, Protein Hnrnpu, Genomes, Scaffold, Nuclear Matrices, Whole Transcriptome Shotgun Sequencing, Nuclear Scaffold, Matrix, Nuclear, RNA-seq., whole genome, nucleoskeleton, regulator, Matrices, isoform CRA_b, Scaffolds, Nuclear ScaffoldsMus musculus, Laboratory Mice., House, Mus, Laboratory, Swiss, Mus domesticus, mouse, Mus musculus domesticus, Swiss Mouse, mouse <Mus musculus>, Mouse, House Mice, Swiss Mice, house mouse, Mice, Laboratory Mouse, House Mouse, mice C57BL/6xCBA/CaJ hybrid, domesticus, Mus muscarisfalseMus musculusThe nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [RNA-Seq]2025-09-242017-12-04PRJNA376129GSE951111009029273625