YY1 regulates B cell lineage plasticity via transcriptional, miRNA post-transcriptional, and epigenetic mechanisms 2299696
TL;DR
Multi-omics integration across RNA-seq, miRNA, scRNA-seq, and scATAC-seq datasets allowed the construction of YY1-dependent regulatory networks that reveal how YY1 influences B-cell lineage plasticity.
Abstract
YY1 is essential for embryogenesis, cell proliferation, and lineage differentiation. It regulates genes via co-activators, co-repressors, or PcG complexes. In hematopoiesis, YY1 controls stem cell differentiation, and its loss at the pro-B stage halts B-cell development. Bulk RNA-seq of WT and YY1-KO pro-B cells was analyzed for QC, alignment, and differential expression (edgeR), and their miRNA list was identified via miRDeep2, targets were predicted with TargetScan, and their functional enrichment and pathways were performed through the clusterProfiler package. Further, scRNA-seq and scATAC-seq (Seurat and Signac) confirmed lineage-specific changes in expression and chromatin accessibility at these targets. Upregulated miRNAs in YY1-KO pro-B cells (miR-1194, miR-714, miR-712-5p, and miR-712-3p) target key genes involved in B-cell regulation. Their elevated expression is associated with repression of B-cell-related signaling, suggesting a role in the reduced B-cell commitment observed in YY1-deficient cells. Consistently, scRNA-seq analysis of YY1-KO pro-B cells cultured on OP9-DL4 feeders showed decreased expression of B-lineage genes such as Pla2g12a and Map3k4, which was further supported by reduced chromatin accessibility in scATAC-seq data. In contrast, downregulated miRNAs (miR-3473, miR-696, and miR-762) regulate genes involved in monocyte, macrophage, and T-cell pathways. Their reduced expression in YY1-KO pro-B cells correlated with increased expression of alternative-lineage genes, including Cxcl2, Fhl2, and Il1b miRNA targets. Consistent with increased expression for downregulated miRNA targets in YY1-KO pro-B cells, scATAC-seq also revealed increased chromatin accessibility at these loci, indicating activation of non-B-lineage differentiation programs. Multi-omics integration across RNA-seq, miRNA, scRNA-seq, and scATAC-seq datasets allowed the construction of YY1-dependent regulatory networks that reveal how YY1 influences B-cell lineage plasticity. n/a Computational and Systems Immunology (COMP)