Fig. 9: Linc00899 binds to and represses transcription of TPPP.

a CUT&RUN profiling of H3K4me3 enrichment after depletion of linc00899 with RNAi and LNAs at the TPPP locus in HeLa cells. An increase in H3K4me3 (arrow) was observed at the TPPP promoter upon depletion of linc00899 with both LOF methods. Tracks were constructed from averages of two biological replicates for each condition. TSS, transcriptional start site. b Enrichment of linc00899 using a cocktail of four oligonucleotides complementary to accessible regions of linc00899 (as determined by RNase H mapping, Supplementary Fig. 14a), compared to a mixture of two control oligonucleotides containing parts of the linc00899 sense sequence, as measured by qPCR. The 5.8S was used as a negative control region. Data are shown mean ± S.E.M. n = 4 biological replicates. **P < 0.01 by two-tailed Student t test. c Profiling of linc00899 binding by CHART-seq after RNase H elution at the TPPP locus in HeLa cells. The region with the most significant increase in linc00899 binding compared to the sense control was present in the second intron of TPPP (arrow). All binding sites were detected using an empirical FDR threshold of 30%. d Validation of linc00899 colocalisation with the TPPP locus by co-RNA FISH in HeLa cells. Linc00899 (exonic probes against the mature transcript) colocalised to the genomic region of TPPP (intronic probes against the premature transcript) in ~3% of the cells (n = 376). The nucleus was stained with DAPI (blue). Scale bar, 5 μm. Source data are provided as a Source Data file.