American Society of Hematology

Figure 7

$Figure 7. alncRNA-EC7 is an enhancer RNA needed for expression of neighboring BAND 3. (A) alncRNA-EC7 marks an enhancer site proximal to BAND 3. Images from the UCSC Genome Browser depict 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 4 show in black the strand-specific RNA-seq signal in the plus strand or minus strand (denoted to the left of the tracks) of poly(A)− or poly(A)+ RNA from fetal liver TER119+ erythroblasts (ERY). Track 5 depicts in red the signal for DNase I HS, associated with open chromatin, in ERY. Tracks 6 to 8 show in red the ChIP-seq signal for GATA1, TAL1, and KLF1, respectively, in ERY. Tracks 9 and 10 depict the ChIP-seq signal for H3K4me1, enriched along promoter and enhancer regions, in ERY (dark red), and H3K27Ac, associated with active promoters and enhancers, in fetal liver cells (yellow). Peaks of signal enrichment are shown in gray under the DNase I HS track (determined by I-max, empirical FDR <1%) and under the GATA1, TAL1, KLF1, H3K4me1, and H3K27Ac tracks (determined by MACS, empirical FDR <5%). The bottom tracks depict lncRNA transcript models inferred by de novo assembly using Cufflinks (black) and Ensembl gene annotations (red). Shown at the top are the target sites of 3 shRNAs designed against the transcripts from the enhancer site. (B) The alncRNA-EC7 locus is conserved in human. Images from the UCSC Genome Browser depict RNA-seq signal, DNase I HS signal, and ChIP-seq signal in K562 cells as in A. Track 1 shows in blue the non–strand-specific RNA-seq signal of poly(A)+ RNA. Tracks 2 and 3 depict in light blue the ChIP-seq signal for H3K4me1, enriched along promoter and enhancer regions, and H3K27Ac, associated with active promoters and enhancers. Track 4 depicts in dark blue the signal for DNase I HS, associated with open chromatin. Tracks 5 to 8 show in dark blue the ChIP-seq signal for RNA Pol II, GATA1, TAL1, and p300 (enriched at promoter and enhancer sites), respectively. Shown at the bottom are lncRNA transcript models based on our detection of orthologous genomic regions from local alignment and synteny to the mouse genome (black; supplemental Methods) and Ensembl gene annotations (red). The last track depicts in red chromatin interactions associated with binding of the CTCF binding factor, determined by ChIA-PET. (C) Relative abundance of alncRNA-EC7 and Band 3 mRNA across 30 mouse primary tissue and cell types from ENCODE, determined as in Figure 2. Color intensity represents the fractional expression level across all tissues examined. ERY_1 and ERY_2 (red) are TER119+ fetal liver erythroblast biological replicate experiments. (D) (Top) Band 3 expression is coordinated with that of neighboring alncRNA-EC7 during differentiation. (Bottom) Inhibiting alncRNA-EC7 with the shRNAs shown in A abolishes expression of BAND 3 relative to scramble shRNA control (data are mean ± SEM; n = 3).$

alncRNA-EC7 is an enhancer RNA needed for expression of neighboring BAND 3. (A) alncRNA-EC7 marks an enhancer site proximal to BAND 3. Images from the UCSC Genome Browser depict 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 4 show in black the strand-specific RNA-seq signal in the plus strand or minus strand (denoted to the left of the tracks) of poly(A)⁻ or poly(A)⁺ RNA from fetal liver TER119⁺ erythroblasts (ERY). Track 5 depicts in red the signal for DNase I HS, associated with open chromatin, in ERY. Tracks 6 to 8 show in red the ChIP-seq signal for GATA1, TAL1, and KLF1, respectively, in ERY. Tracks 9 and 10 depict the ChIP-seq signal for H3K4me1, enriched along promoter and enhancer regions, in ERY (dark red), and H3K27Ac, associated with active promoters and enhancers, in fetal liver cells (yellow). Peaks of signal enrichment are shown in gray under the DNase I HS track (determined by I-max, empirical FDR <1%) and under the GATA1, TAL1, KLF1, H3K4me1, and H3K27Ac tracks (determined by MACS, empirical FDR <5%). The bottom tracks depict lncRNA transcript models inferred by de novo assembly using Cufflinks (black) and Ensembl gene annotations (red). Shown at the top are the target sites of 3 shRNAs designed against the transcripts from the enhancer site. (B) The alncRNA-EC7 locus is conserved in human. Images from the UCSC Genome Browser depict RNA-seq signal, DNase I HS signal, and ChIP-seq signal in K562 cells as in A. Track 1 shows in blue the non–strand-specific RNA-seq signal of poly(A)⁺ RNA. Tracks 2 and 3 depict in light blue the ChIP-seq signal for H3K4me1, enriched along promoter and enhancer regions, and H3K27Ac, associated with active promoters and enhancers. Track 4 depicts in dark blue the signal for DNase I HS, associated with open chromatin. Tracks 5 to 8 show in dark blue the ChIP-seq signal for RNA Pol II, GATA1, TAL1, and p300 (enriched at promoter and enhancer sites), respectively. Shown at the bottom are lncRNA transcript models based on our detection of orthologous genomic regions from local alignment and synteny to the mouse genome (black; supplemental Methods) and Ensembl gene annotations (red). The last track depicts in red chromatin interactions associated with binding of the CTCF binding factor, determined by ChIA-PET. (C) Relative abundance of alncRNA-EC7 and Band 3 mRNA across 30 mouse primary tissue and cell types from ENCODE, determined as in Figure 2. Color intensity represents the fractional expression level across all tissues examined. ERY_1 and ERY_2 (red) are TER119⁺ fetal liver erythroblast biological replicate experiments. (D) (Top) Band 3 expression is coordinated with that of neighboring alncRNA-EC7 during differentiation. (Bottom) Inhibiting alncRNA-EC7 with the shRNAs shown in A abolishes expression of BAND 3 relative to scramble shRNA control (data are mean ± SEM; n = 3).

This Feature Is Available To Subscribers Only