The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes

Abstract

Eukaryotic chromosomes are folded into higher-order conformations to coordinate genome functions. In addition to long-range chromatin loops, recent chromosome conformation capture (3C)-based studies have indicated higher levels of chromatin structures including compartments and topologically associating domains (TADs), which may serve as units of genome organization and functions. However, the molecular machinery underlying these hierarchically three-dimensional (3D) chromatin architectures remains poorly understood. Via high-throughput assays, including in situ Hi-C, DamID, ChIP-seq, and RNA-seq, we investigated roles of the Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU), a nuclear matrix (NM)-associated protein, in 3D genome organization. Upon the depletion of HNRNPU in mouse hepatocytes, the coverage of lamina-associated domains (LADs) in the genome increases from 53.1% to 68.6%, and a global condensation of chromatin was observed. Furthermore, disruption of HNRNPU leads to compartment switching on 7.5% of the genome, decreases TAD boundary strengths at borders between A (active) and B (inactive) compartments, and reduces chromatin loop intensities. Long-range chromatin interactions between and within compartments or TADs are also significantly remodeled upon HNRNPU depletion. Intriguingly, HNRNPU mainly associates with active chromatin, and 80% of HNRNPU peaks coincide with the binding of CTCF or RAD21. Collectively, we demonstrated that HNRNPU functions as a major factor maintaining 3D chromatin architecture, suggesting important roles of NM-associated proteins in genome organization.

Differential contribution of steady‐state RNA and active transcription in chromatin organization

“…Indeed, although the compartmentalization was not markedly altered (Fig ) we observed a reduction in TAD boundary strength upon transcriptional inhibition (Fig ). These results are concordant with a model where the act of transcription and or its product influences the nuclear positioning of the newly transcribed DNA locus via interaction with nuclear matrix proteins .…”

hnRNPU/TrkB Defines a Chromatin Accessibility Checkpoint for Liver Injury and Nonalcoholic Steatohepatitis Pathogenesis

“…hnRNPU is a nuclear matrix protein that maintains three‐dimensional genome architecture in hepatocytes through its association with chromatin . These molecular observations led us to postulate that hnRNPU may serve as a chromatin checkpoint for liver metabolism and disease.…”

“…Hepatocyte‐specific inactivation of hnRNPU exacerbated diet‐induced NASH pathogenesis in mice, including liver injury, inflammation, and fibrosis. hnRNPU is a nuclear matrix protein that regulates three‐dimensional chromatin structure and gene transcription . In the heart, hnRNPU is required for postnatal development and cardiac function .…”

Chromosome territories and the global regulation of the genome

“…Several proteins associated with isolated nuclear matrix have been identified as potential factors involved at chromatin loop S/MAR attachment sites and/or higher order CD. These include topoisomerase II, CTCF, cohesin, matrin 3 (also called as P‐130 nuclear scaffold protein), HnRNP‐U (also called as SAF‐A, for Scaffold/Matrix attachment region factor), SAF‐B, ARBP (Attachment Region Binding Protein), SAT‐B, and nuclear lamins . Recent proteomic approaches have further confirmed the S/MAR binding activities of SAF‐A, matrin 3, and nuclear lamins .…”

“…CTCF and cohesin have been identified as key players in the arrangement of chromatin into higher order domains termed Topologically Associated Domains (TADs), which mediate long range intrachromosomal and interchromosomal interactions within the nucleus . Recently, HnRNP‐U (SAF‐A) has been demonstrated to be integral to maintaining genome organization at TADs and higher levels of chromatin …”