Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions
Although emerging evidence indicates that alterations in proteins within nuclear compartments elicit changes in chromosomal architecture and differentiation, the underlying mechanisms are not well understood. Here we investigate the direct role of the abundant nuclear complex protein Matrin3 (Matr3) in chromatin architecture and development in the context of myogenesis. Using an acute targeted protein degradation platform (dTAG-Matr3), we reveal the dynamics of development-related chromatin reorganization. Upon acute depletion of Matr3, gains in chromatin accessibility and MyoD binding were observed, prior to widespread loss in the steady-state Matr3-knockout. These initial changes correlated with gene expression changes later in development. High-throughput chromosome conformation capture (Hi-C) experiments revealed substantial chromatin loop rearrangements soon after Matr3 depletion. Notably, YY1 binding was detected in close proximity to enhancer and promoter regions, accompanied by the emergence of novel YY1-mediated enhancer-promoter loops, which occurred concurrently with changes in histone modifications and chromatin-level binding patterns. Overall, our results suggest that Matr3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and highlight a conserved and direct role for Matr3 in maintenance of chromosomal architecture. Overall design: In order to track chromatin accessiblity and transcription factor binding in absence of Matr3 in myoblasts derived from the skeletal muscle line C2C12, we have designed an inducible targeted degradation system to target Matr3 protein expression. We performed ATAC-seq at 4 hrs., 8 hrs. post Matr3 depletion (by the addition of dTAG treatment) and compared those with DMSO-treated cells. We also performed MyoD CUT&RUN at the 4hr and 8hr post Matr3 depletion, and CTCF, Rad21, and YY1 CUT&RUN in the same time points. We measured the gene expression by RNAseq and SLAMseq at 4hr and steady state. This dataset contains the ATACseq, CUT&RUN, RNAseq portion. A separate dataset contains the HiC portion of the experiments.