FIGURE 5.

Genomic distributions of novel lncRNAs. (A) Distances between genomic loci transcribing unique novel lncRNAs. The X-axis ranks novel lncRNA loci according to distance to the next novel lncRNA loci and the Y-axis shows the actual distance in bp between neighboring lncRNA loci. (B) Characteristics of genomic ‘bins’ transcribing multiple novel lncRNAs. (C, D, & E) Examples of genomic bins selectively transcribing multiple novel lncRNAs in (C) T_N relative to T_M, D) T_CM relative to T_N and T_EM, and (E) T_EM relative to T_N and T_CM. X-axes show genomic positions from which novel lncRNAs are transcribed; lines illustrate sizes of the transcribed novel lncRNA. Y-axes are mean expression ratios, log2, between the indicated T cell lineages. (F) Genomic bins transcribing novel lncRNAs co-localize with T_N and T_M typical and super transcriptional enhancers (from ref. 20). We considered that the genomic bins may not exactly overlap with enhancers so we performed the analysis to include the proportion of bins that co-localize with an enhancer (0), and the proportion of bins that co-localized with enhancers if we extended bin size by 5, 10, 15, 20 or 30 kb in both 5’ and 3’ directions, X-axis. The Y-axis is the proportion of total bins with a T_N or T_M enhancer. P values, -log₁₀, were determined by c² analysis. (G) Number of bins within T_M SE or TE (CD4MSE, CD4MTE) structures or T_N SE or TE structures. X-axis is as in (F), Y axis is the number of bins with enhancers. (H&I) Re-analysis of RNA-seq data using ‘bins’ as definition lists. (H) After FDR correction, bins were identified that were over-expressed (blue lines) or under-expressed (brown lines) in T_CM and T_EM cells compared to T_N cells. (I) Expression levels of bins differentially expressed in T_CM relative to T_N and T_EM after FDR correction. Y-axes are expression ratios, log₂, X-axes identify ratios; Tn=T_N/T_N, Tcm=T_CM/T_N, Tem=T_EM/T_N.