ArticleActa pharmaceutica Sinica. B2021
3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing.
Article in Acta pharmaceutica Sinica. B, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 39 citations in OpenAlex.
- Context-Dependent Roles of the Plexin-B Family Across Neurological, Oncological, Immune and Cardiovascular Disorders: Mechanisms and Therapeutic Implications.Life (Basel, Switzerland) · 2026Review
- Decoding organ fibrosis: mechanistic insights and emerging therapeutic strategies.Signal transduction and targeted therapy · 2026Review
- Clinical insight-driven novel drug development: Multidisciplinary integration and transformative opportunities.Acta pharmaceutica Sinica. B · 2026Article
- Integrating Hi-C data and RNA-seq data to reveal the 3D genome in sheep.BMC genomics · 2025Article
- UHPLC-QTOF-MS-based metabolomics joint high-throughput RNA sequencing transcriptomics approach for the analysis of fecal and liver biological samples and application in a case study for the mechanism of Qing-Kai-Ling oral liquid in treating MASLD.Analytical and bioanalytical chemistry · 2025Article
- Hepatic stellate cell-specific Kcnma1 deletion mitigates metabolic dysfunction-associated steatotic liver disease progression via upregulating Amphiregulin secretion.Molecular metabolism · 2025Article
- Integrative analysis of gene expression and chromatin dynamics multi-omics data in mouse models of bleomycin-induced lung fibrosis.Epigenetics & chromatin · 2025Article
- Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet.Journal of animal science and biotechnology · 2024Article
- Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens.Journal of animal science and biotechnology · 2024Article
- Three-dimensional genome structure and function.MedComm · 2023Review
- Multidimensional landscape of non-alcoholic fatty liver disease-related disease spectrum uncovered by big omics data: Profiling evidence and new perspectives.Smart medicine · 2023Review
- The Gut-Organ-Axis Concept: Advances the Application of Gut-on-Chip Technology.International journal of molecular sciences · 2023Review
- 3D genome organization and epigenetic regulation in autoimmune diseases.Frontiers in immunology · 2023Review
- Integrated Bioinformatics Analysis Identifies Robust Biomarkers and Its Correlation With Immune Microenvironment in Nonalcoholic Fatty Liver Disease.Frontiers in genetics · 2022Article
- Transcriptomic Analysis Reveals the Protective Effects of Empagliflozin on Lipid Metabolism in Nonalcoholic Fatty Liver Disease.Frontiers in pharmacology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The three-dimensional (3D) conformation of chromatin is integral to the precise regulation of gene expression. The 3D genome and genomic variations in non-alcoholic fatty liver disease (NAFLD) are largely unknown, despite their key roles in cellular function and physiological processes. High-throughput chromosome conformation capture (Hi-C), Nanopore sequencing, and RNA-sequencing (RNA-seq) assays were performed on the liver of normal and NAFLD mice. A high-resolution 3D chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments, topologically associated domains (TADs), and chromatin loops by Hi-C, and whole genome sequencing identifying structural variations (SVs) and copy number variations (CNVs) by Nanopore sequencing. We identified variations in thousands of regions across the genome with respect to 3D chromatin organization and genomic rearrangements, between normal and NAFLD mice, and revealed gene dysregulation frequently accompanied by these variations. Candidate target genes were identified in NAFLD, impacted by genetic rearrangements and spatial organization disruption. Our data provide a high-resolution 3D genome interaction resource for NAFLD investigations, revealed the relationship among genetic rearrangements, spatial organization disruption, and gene regulation, and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD. The newly findings offer insights into novel mechanisms of NAFLD pathogenesis and can provide a new conceptual framework for NAFLD therapy.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.