Fig. 5
From: LSD1 is required for euchromatic origin firing and replication timing
LSD1 regulates genome-wide replication timing. a Comparison of genome-wide replication timing after LSD1 was depleted or inhibited. HeLa cells were transfected with LSD1 siRNAs or treated with GSK-LSD1 prior to synchronization in early S phase for Repli-seq. The results from a representative region of chromosome 2 spanning 49 Mb are illustrated. Regions with decreased Repli-seq reads density after LSD1 depletion/inhibition are shaded in pink, and regions with increased reads density shaded in gray. Replication profiles from public data representing early (G1b) and late (G2) S phases and the distribution of H3K4me2 and H3K27ac are shown. Numbers in square brackets indicate the data range of corresponding track. Statistical analysis of Repli-seq reads density around the summits of LSD1 binding sites is shown (right panel). b Different time points of synchronized LSD1-depleted HeLa cells were analyzed by Repli-seq. Replication profiles from public data representing early (G1b and S1), middle (S2 and S3), and late (S4 and G2) S phases (dark blue) are shown. Statistical analysis of Repli-seq reads density around the summits of LSD1 is shown (lower panel). Full cell cycle plots of LSD1-deficient HeLa cells for Repli-seq (right). c HeLa cells were synchronized via double-thymidine block followed by release for 0.5 or 2.5 h to enrich cells in early S phase. Genomic distributions of LSD1, CDC45, and H3K4me2 were determined by ChIP-seq analysis. A representative region spanning 30 Mb in chromosome 3 is shown. Origins and ORC1 ChIP-seq data in HeLa cells were from published data. Public Repli-seq data of early S phase (G1b) is shown below. Co-occurrence of LSD1, CDC45 and H3K4me2 on early-replication regions are shaded. d Whole-genome analysis of the distribution of LSD1 and CDC45. r, Pearson’s correlation coefficient. e The changes in H3K4me2 were quantitated by ChIP-seq with exogenous Drosophila melanogaster genome as a reference. Scale factors for 0.5 and 2.5 h are 24.8 and 11, respectively (left). Log2-based ratio of H3K4me2 signal density at 2.5 and 0.5 h of 3000-bp up- and down-stream of TSS of all genes are indicated (right)
