lncRNAs are targeted by core erythroid transcription factors. (A) Binding of GATA1, TAL1, and KLF1 transcription factors within promoter-proximal regions (TSS ± 1 kb) of (left) mRNAs and (right) lncRNAs that are differentially expressed during erythropoiesis (see text). (B) Changes in expression and promoter-proximal (TSS ± 1 kb) H3K4me2 levels for all differentially expressed mRNA or lncRNA genes, for the subset of genes bound by KLF1 or for those bound by both GATA and TAL1. Changes are shown as the log2 ratio of the levels in TER119⁺ erythroblasts (ERY) to the levels in erythroid progenitor-enriched fetal liver cells (PROG). (C) Examples of differentially expressed lncRNA loci that are bound proximally by GATA1, TAL1, or KLF1, the same RNAs as in Figures 2B and 3B. Images from the UCSC Genome Browser depict the RNA-seq signal as the density of mapped RNA-seq reads, DNase I hypersensitivity (HS) signal as the density of mapped sequencing tags, and ChIP-seq signal as the density of processed signal enrichment. Tracks 1 to 6 show in black the strand-specific RNA-seq signal in the plus strand or minus strand (denoted to the left of the tracks) of total, poly(A)⁻, or poly(A)⁺ RNA from fetal liver TER119⁺ erythroblasts (ERY). Tracks 7 to 9 depict in red the signal for DNase I HS, associated with open chromatin, in BFU-Es, CFU-Es, and ERY. Tracks 10 to 12 show in red the ChIP-seq signal for GATA1, TAL1, and KLF1, respectively, in ERY. Peaks of signal enrichment are shown in gray under the DNase I HS tracks (determined by I-max, empirical FDR <1%) and under the GATA1, TAL1, and KLF1 tracks (determined by MACS, empirical FDR <5%). The bottom tracks depict lncRNA transcript models and Ensembl gene annotations as in Figure 2B.