S-phase lncRNAs

S-phase associated lncRNAs

Identification of temporally expressed lncRNAs across S-phase using nascent RNA capture assay. a) Cell cycle diagram showing Nascent RNA capture at three different time points (2, 3.5, and 5 h) of S-phase. b) Principle component analysis (PCA) of expression profiles by considering complete profile (noncoding and protein-coding), all noncoding RNas and only long noncoding RNAs (lncRNAs). c) Time-series analysis of S-phase associated lncRNAs with twofold enrichment at least in one time point over the unsynchronized sample. The S-phase lncRNAs show four significant temporal patterns with STEM clustering.

Pan-cancer analysis of s-phase associated lncRNAs

Characterization of S-phase lncRNAs as oncogenic drivers and independent prognostic markers using pan-cancer TCGA data sets. a) Heatmap of 570 S-phase lncRNAs showing significant differential expression at least in one cancer type from TCGA. The significance was considered based on log-fold change ± 2 and FDR < 1E–004 (Benjamini–Hochberg’s method). The highlighted lncRNAs are the ones selected for functional validation. The plot on the left side shows the frequency of individual lncRNAs differentially expressed across different cancer types. b) Heatmap of S-phase lncRNAs with anti-correlative promoter methylation status to the differential expression levels in corresponding cancer. Hypomethylated promoter associated with higher expression and hypermethylation to less expression compared to normal. The highlighted lncRNAs are differentially methylated in more than 100 patients (samples) supporting the methylation pattern in corresponding cancer. Box plots of highlighted lncRNAs denoting the anti-correlative relation between promoter methylation and transcript expression.

Molecular mechanism of S-phase cancer associated transcript 7 (SCAT7)

a) Heatmaps showing upregulated and downregulated genes with corresponding molecular pathways and biological processes upon silencing of to Sphase Cancer Associated Transcript, SCAT7 in HeLa cell line. b) Venn diagram showing SCAT7 interacting proteins in HeLa cells identified using ChOP-MS in two independent biological replicates. c) This shows that SCAT7 interacts with hnRNPK and YBX1 to regulate FGF signaling and downstream oncogenic pathways.

Note: Above findings are published in Nature communications, Issue 9 (Ali MM et al, 2018). Only computational analysis results contributed by me is included in above summary. For complete research, please have a look at this original article.