Skip to main content
. Author manuscript; available in PMC: 2023 May 19.
Published in final edited form as: Mol Cell. 2022 Apr 6;82(10):1894–1908.e5. doi: 10.1016/j.molcel.2022.03.018

Figure 3. Knock-down of HOXD-AS2 or LINC01116 lncRNAs reduces gene expression, looping, and CTCF and Rad21 binding in the HOXD/miR-10b TAD in glioma.

Figure 3.

A and B. Correlation heatmaps for individual HOXD RNAs expressed in LGG (A) and GBM (B). Pearson correlation coefficient for each pair of transcripts is indicated by color and value.

C. KD of either HOXD-AS2 or LINC01116 reduces the levels of miR-10b and HOXD mRNAs in glioma cells. The lncRNAs were inhibited with targeting shRNAs, and relative levels of indicated transcripts quantified by qRT-PCR in control (non-targeting shRNA, blue bars), LINC01116 KD (orange bars) and HOXD-AS2 KD (grey bars) groups 48 hours post-transfection (mean+SD, n=3).

D. KD of either HOXD-AS2 or LINC01116 in GBM8 reduces interactions between HOXD3/D4/miR-10b and LINC01116 regions, abolishing loop formation within TADs, and CTCF and Rad21 binding. Representative 4C-Seq and ChIP-Seq tracks are shown. The HOXD3/D4/miR10b bait used in 4C-Seq (arrowhead), and major glioma-enriched interactions and CTCF/Rad21 binding sites lost upon the KD are highlighted in green and yellow. CTCF motif orientation is indicated in green (forward) and red (reverse).