Direct regulatory function for Ldb1 complexes in the induced expression of erythroid genes in MEL cells. (A) Ldb1 complex–bound genes are more highly expressed in differentiated MEL cells. (Left) All Ldb1-bound genes (yellow, upper panel) compared with all unbound genes (gray, lower panel), P < 7.7 × 10−74. (Right) Erythroid Ldb1 complex–bound genes (yellow, upper panel) compared with unbound erythroid genes (gray, lower panel), P < 1.4 × 10−9. (B) Ldb1 complex–bound genes are more strongly induced in differentiated MEL cells. (Left) All Ldb1 complex–bound genes (yellow, upper panel) compared with all unbound genes (gray, lower panel), P < 1.0 × 10−32. (Right) Ldb1 complex–bound erythroid genes (yellow, upper panel) compared with unbound erythroid genes (gray, lower panel), P < 7.9 × 10−11. Significance for all comparisons was calculated by Mann-Whitney U. (C-D) Ldb1-complexes directly regulate the expression of erythroid genes. Stable clones of MEL cells expressing Ldb1 shRNA or control shRNA were treated with 1.5% dimethylsulfoxide to induce erythroid differentiation. Total RNA was isolated and gene expression was assayed by microarray. (C) Highly expressed erythroid genes are the most strongly down-regulated in Ldb1 KD MEL cells. Genes bound by Ldb1 complexes are depicted in yellow; unbound genes are in gray. Zero line is indicated (dotted line). (D) Erythroid genes that are most strongly induced in differentiated control MEL cells are the most strongly down-regulated in Ldb1 KD MEL cells. Erythroid genes bound by Ldb1 complex are shown in yellow; unbound genes are shown in gray. Zero lines are indicated (dotted lines). y-axis histograms show stronger KD of Ldb1 complex–bound erythroid genes relative to all erythroid unbound genes, respectively (P < 6.7 × 10−10; Mann-Whitney U).
