Journal: Nature Communications
Article Title: A searchable atlas of pathogen-sensitive lncRNA networks in human macrophages
doi: 10.1038/s41467-025-60084-x
Figure Lengend Snippet: A Left: Evolutionary tree of selected mammalian species. Right: Percent base conservation of human LPS-inducible macrophage lncRNA sequences across the genomes of indicated species, sorted by evolutionary distance; top panel includes all 24 lncRNAs from Fig. and data are shown as box plots (median and 75th-25th percentile interquartile range, whiskers indicate minimum and maximum data values), with species generation time overlayed; bottom panel focuses on specific lncRNAs. B Illustration of genomic locations of specified lncRNAs relative to nearest neighboring genes (distance in kilobases [kb] provided). Red triangles indicate transcriptional start site positions targeted by CRISPRi for lncRNA silencing. C Volcano plots from CRISPRi-based lncRNA loss-of-function experiments in THP1 cells stimulated with LPS for 8 h. Fold-changes (fc) compare lncRNA-knockdown cells to empty vector control cells. Results from three independent experiments. Two-tailed Student’s t-test p -values are shown. D Cytoscape network of lncRNAs (blue) and mRNAs from panel C , regulated upon lncRNA silencing (≥2-fold up or down, p ≤ 0.05, two-tailed Student’s t-test). E Pie charts showing proportions of all expressed mRNAs or LPS-responsive mRNAs (≥2-fold up or down, p ≤ 0.05, two-tailed Student’s t-test) affected by silencing of one or more lncRNAs. C – E: 8 h LPS-stimulated THP1 cells and three independent replicates.
Article Snippet: Stable knockdown cell lines were generated using the CRISPR interference (CRISPRi) vector pLV-hU6-sgRNA-hUbC-dCas9-KRAB-T2a-GFP (Addgene #71237).
Techniques: Knockdown, Plasmid Preparation, Control, Two Tailed Test
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![A Left: Evolutionary tree of selected mammalian species. Right: Percent base conservation of human LPS-inducible macrophage lncRNA sequences across the genomes of indicated species, sorted by evolutionary distance; top panel includes all 24 lncRNAs from Fig. and data are shown as box plots (median and 75th-25th percentile interquartile range, whiskers indicate minimum and maximum data values), with species generation time overlayed; bottom panel focuses on specific lncRNAs. B Illustration of genomic locations of specified lncRNAs relative to nearest neighboring genes (distance in kilobases [kb] provided). Red triangles indicate transcriptional start site positions targeted by <t>CRISPRi</t> for lncRNA silencing. C Volcano plots from CRISPRi-based lncRNA loss-of-function experiments in THP1 cells stimulated with LPS for 8 h. Fold-changes (fc) compare lncRNA-knockdown cells to empty vector control cells. Results from three independent experiments. Two-tailed Student’s t-test p -values are shown. D Cytoscape network of lncRNAs (blue) and mRNAs from panel C , regulated upon lncRNA silencing (≥2-fold up or down, p ≤ 0.05, two-tailed Student’s t-test). E Pie charts showing proportions of all expressed mRNAs or LPS-responsive mRNAs (≥2-fold up or down, p ≤ 0.05, two-tailed Student’s t-test) affected by silencing of one or more lncRNAs. C – E: 8 h LPS-stimulated THP1 cells and three independent replicates.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_5776/pmc12095776/pmc12095776__41467_2025_60084_Fig3_HTML.jpg)