Journal: Nature Communications

Article Title: Nuclear microRNA 9 mediates G-quadruplex formation and 3D genome organization during TGF-β-induced transcription

doi: 10.1038/s41467-024-54740-x

Figure Lengend Snippet: a Visualization of selected SE with miR-9 enrichment using IGV genome browser showing enrichment miR-9 by ChIRP-seq (green), G4 by G4P ChIP-seq in NIH/3T3 cells (blue), G4 by CUT&Tag in Ctrl and miR-9 -specifc antagomiR transfected MLg cells (blue), MED1 (turquoise), KLF4 (magenta) and H3K27ac (purple) in by ChIP-seq in mouse embryonic fibroblasts, H3K27ac by CUT&Tag in Ctrl and miR-9 -specifc antagomiR transfected MLg cells (purple). Reads were normalized using reads per kilobase per million (RPKM). Images show the indicated gene loci with their genomic coordinates. Orange squares, regions with enrichment of miR-9 , G4 and SE markers; red lines, regions selected for single gene analysis in ( b ); dotted lines, regions shown at the bottom with high G content. Bottom, green line, miR-9 enrichment; blue line, G4 enrichment; purple line, H3K27ac enrichment. b Analysis of selected SE with miR-9 enrichment by ChIP using chromatin from MLg cells transfected with control (Ctrl) or miR-9 -specific antagomiR to induce miR-9 loss-of-function (LOF). Bar plots presenting data as means; error bars, s.e.m ( n = 3 biologically independent experiments); asterisks, P -values after two-tailed t-test, *** P ≤ 0.001; ** P ≤ 0.01; * P ≤ 0.05. See also Supplementary Figs. , . Source data are provided as a file.

Article Snippet: Mouse lung fibroblast cells MLg (ATCC CCL-206) and MFML4 were cultured in complete DMEM (4.5 g/L glucose, 10% FCS, 1% Pen-Strep, 2 mM L-glutamine) at 37 °C in 5% CO 2 .

Techniques: ChIP-sequencing, Transfection, Control, Two Tailed Test