Dynamic expression patterns of lncRNAs during erythroid differentiation. (A) Abundance of mRNAs and lncRNAs that are differentially expressed during erythropoiesis, as determined by DESeq at a 5% false discovery threshold. Shown are absolute gene expression estimates (FPKM) from poly(A)⁺ RNA-seq of FACS-purified BFU-Es, CFU-Es, and TER119⁺ erythroblasts (ERY) (2 replicates each), based on gene models from our de novo assembly using Cufflinks. (B) Examples of differentially expressed lncRNA loci, the same RNAs as in Figure 2B. Images from the UCSC Genome Browser depict RNA-seq signal as the density of mapped RNA-seq reads and chromatin immunoprecipitation sequencing (ChIP-seq) signal as the density of processed signal enrichment. Tracks 1 to 3 show in red the non–strand-specific RNA-seq signal of poly(A)⁺ RNA from FACS-purified fetal liver BFU-Es, CFU-Es, and TER119⁺ erythroblasts (ERY). Tracks 4 to 12 depict the ChIP-seq signal for H3K4me1, a chromatin mark enriched in promoter and enhancer regions, in ERY (dark red); H3K4me2, associated with transcriptional activation, in erythroid progenitor-enriched fetal liver cells (PROG) and ERY (dark and light blue); serine 5 phosphorylated RNA Pol II, enriched at the TSS of active genes, in PROG and ERY (dark and light green); H3K79me2, associated with transcriptional elongation, in PROG and ERY (dark and light purple); and H3K27me3, associated with transcriptional repression, in PROG and ERY (black). The bottom tracks depict lncRNA transcript models and Ensembl gene annotations as in Figure 2B.