Transcriptome measurements after knocking out the UMLILO lncRNA

Purpose: Assess whether knocking out the UMLILO lncRNA altered the expression of genes transcribed within the CXCL chemokine TAD Outcome: To confirm whether the effect of UMLILO was limited to the CXCL TAD. Adeno-associated viral vectors (AAVs) were constructed that contain CRISPR/Cas9 and guides targeting UMLILO to delete the full length UMLILO transcript. RNAseq was performed on a transduced THP-1 population to verify genome-wide effects of UMLILO depletion. This revealed that IL8, CXCL1, 2, 3 transcription was abrogated, but a similar effect was not seen for genes located outside of the CXCL TAD boundary AAVs were constructed that contain CRISPRs that harness non homologous end joining (NHEJ) to target UMLILO by deleting the genomic region encoding UMLILO, but not its promoter. The THP-1 monocytic cell line was transduced with the AAVs containing the CRISPRs for 1.5 weeks. Controls were transduced with AAV vector plasmids expressing SpCas9.