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Lineage-specific rearrangement of chromatin loops and epigenomic features during adipocytes and osteoblasts commitment

Abstract

Human mesenchymal stem cells (hMSCs) can be differentiated into adipocytes and osteoblasts. The processes are driven by the rewiring of chromatin architectures and transcriptomic/epigenomic changes. Here, we induced hMSCs to adipogenic and osteogenic differentiation, and performed 2 kb resolution Hi-C experiments for chromatin loops detection. We also generated matched RNA-seq, ChIP-seq and ATAC-seq data for integrative analysis. After comprehensively comparing adipogenesis and osteogenesis, we quantitatively identified lineage-specific loops and screened out lineage-specific enhancers and open chromatin. We reveal that lineage-specific loops can activate gene expression and facilitate cell commitment through combining enhancers and accessible chromatin in a lineage-specific manner. We finally proposed loop-mediated regulatory networks and identified the controlling factors for adipocytes and osteoblasts determination. Functional experiments validated the lineage-specific regulation networks towards IRS2 and RUNX2 that are associated with adipogenesis and osteogenesis, respectively. These results are expected to help better understand the chromatin conformation determinants of hMSCs fate commitment.

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Fig. 1: Chromatin conformation features of hMSCs and differentiated adipocytes and osteoblasts.
Fig. 2: Chromatin 3D structure is coupled with active gene expression, and lineage-specific loops are closely related to gene activation during adipogenic and osteogenic differentiation.
Fig. 3: Adipogenesis and osteogenesis are achieved by lineage-specific loops featured with lineage-specific enhancers.
Fig. 4: Chromatin accessibility reveals loop-mediated transcription network reprogramming during hMSCs differentiation.
Fig. 5: Regulatory networks identify loop-mediated gene regulation cascades for cell fate determination.
Fig. 6: Functional experiments validate the lineage-specific long-range regulation cascades for IRS2 and RUNX2.
Fig. 7: eQTL variants are linked to target genes through chromatin loop structures.

Data availability

All data needed to evaluate the conclusions in the paper are present in the paper and the Supplementary data files. The raw and processed data generated in this study are deposited in the Gene Expression Omnibus under accession number GSE151324.

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Acknowledgements

We would like to thank the GTEx Consortium. We obtained GTEx data through dbGaP authorized access at https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login with the accession number of phs000424.v8.p2. This study is also supported by the High-Performance Computing Platform and Instrument Analysis Center of Xi’an Jiaotong University. This work was supported by grants from the National Natural Science Foundation of China (82170896, 32170616, 31970569, 32100416, 31871264), the Natural Science Basic Research Program of Shaanxi Province (2021JC-02), Innovation Capability Support Program of Shaanxi Province (2022TD-44), China Postdoctoral Science Foundation (2021M702618), and the Fundamental Research Funds for the Central Universities.

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TLY and YG conceived and supervised this project. RHH conducted the computational work. CW, CXD and FC performed the functional experiments. JG, RHH and QLC performed the cell culture experiments. YR performed visualization. SSD built the pipeline for Hi-C data analysis. HC and DLZ carried out the library construction experiments. SY and YXC participated in data analysis. RHH and YG wrote the manuscript with the assistance of other authors.

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Correspondence to Tie-Lin Yang.

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The authors declare no competing interests.

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The research was approved by the Ethics Committee of Xi’an Jiaotong University (Shaanxi, China). This study was performed in accordance with the Declaration of Helsinki.

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Hao, RH., Guo, Y., Wang, C. et al. Lineage-specific rearrangement of chromatin loops and epigenomic features during adipocytes and osteoblasts commitment. Cell Death Differ (2022). https://doi.org/10.1038/s41418-022-01035-7

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