Tissue specificity of fetal liver and erythroid lncRNAs. (A) Relative abundance of mRNA and lncRNA genes (rows) expressed in fetal liver across 30 primary cell and tissue types from the mouse ENCODE consortium (columns). Color intensity represents the fractional gene-level expression across all tissues examined. ERY_1 and ERY_2 (red) are fetal liver TER119⁺ erythroblast replicates. Tissue expression was quantified based on gene models from our de novo assembly using Cufflinks. Black bars in the left panels highlight empirically defined erythroid-restricted genes. (B) Examples of erythroid-enriched lncRNA loci. These loci were selected based on their expression, regulation, and tissue specificity features (see text). Images from the UCSC Genome Browser depict RNA-seq signal as the density of mapped strand-specific RNA-seq reads. The plus strand (transcribed left to right) and minus strand (transcribed right to left) are denoted to the left of the tracks. Tracks 1 to 6 show in black the RNA-seq signal of total, poly(A)⁻, or poly(A)⁺ RNA from fetal liver TER119⁺ erythroblasts (ERY). Tracks 7 to 12 depict in light blue the RNA-seq signal of poly(A)⁺ RNA from other hematopoietic cells: adult megakaryocyte-erythroid progenitors (MEP), fetal megakaryocytes (MEG), and adult T-naïve cells (T-cell), all from the ENCODE consortium. Tracks 13 to 20 show the RNA-seq signal of poly(A)⁺ RNA from other tissues from the ENCODE consortium: adult liver (yellow), adult heart (red), adult lung (black), and E14.5 whole brain (gray). The bottom tracks depict lncRNA transcript models inferred by de novo assembly using Cufflinks (black) and Ensembl gene annotations (red). Left-to-right arrows indicate transcripts in the plus strand; right-to-left arrows indicate transcripts in the minus strand. Note that all lncRNA transcripts shown are transcribed in the minus strand.