Extended Data Fig. 2: Depletion of the loop-extrusion loading factors NIPBL and MAU2 instructs cell-cycle arrest and orchestrates distinct neutrophil-specific gene programs.
From: Nuclear morphology is shaped by loop-extrusion programs
a, Flow cytometry analyses of propidium iodide staining for NIPBL-FKBP12F36V-EYFP ECOMG cells cultured for 72 h in the absence or presence of dTAG-13 are shown. b, Intracellular staining of the proliferation marker Ki-67 in NIPBL-FKBP12F36V-EYFP cells cultured for 72 h in the absence or presence of dTAG-13 is shown. c, Heat map indicating mRNA abundance encoding for factors involved in structuring the nuclear envelope in ECOMG progenitors and NIPBL-depleted ECOMG progenitors. d, Volcano plot represents the differential expression of transcripts in ECOMG progenitors carrying MAU2-FKBP12F36V-mScarlett cassettes were cultured for 72 h with β-oestradiol in the absence or presence of dTAG-13. Upregulated genes defined by Padj < 0.05 and log2-transformed fold change > 1 are represented in red. Downregulated genes defined by Padj < 0.05 and log2-transformed fold change < −1 are represented in blue. e, Depletion of MAU2 activates the expression of genes encoding for transcription factors that instruct neutrophil cell fate. f, GO-based functional classification of differentially expressed transcripts in MAU2-depleted cells. Representative pathways that relate to neutrophil differentiation and inflammation are shown. g, Depletion of both NIPBL plus MAU2 activates a neutrophil-specific transcription signature. Volcano plot shows differential transcript levels in ECOMG progenitors carrying both NIPBL-FKBP12F36V-EYFP and MAU2-FKBP12F36V-mScarlet cassettes that were cultured for 72 h with β-oestradiol and in the absence or presence of dTAG-13. Genes closely associated with a neutrophil-specific gene program are highlighted. Upregulated genes defined as Padj < 0.05 and log2-transformed fold change > 1 are represented in red. Downregulated genes defined as Padj < 0.05 and log2-transformed fold change < −1 are represented in blue. h. Volcano plot highlights transcripts encoding for neutrophil-signature transcription factors. i, GO-based functional classification of differentially expressed transcripts in cells depleted for both NIPBL and MAU2. Representative pathways that relate to neutrophil differentiation and inflammation are shown.
