Extended Data Fig. 3: Binding proteins and repetitive elements expression changes in K non-rep KO and K rep KO versus WT HEK293T cells.
From: KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA–DNA triplexes and HP1 binding
a, Diagram showing regions of KCNQ1OT1 deleted in K non-rep KO and K rep KO cells. b, Strand-specific RNA-seq tracks show the expression of KCNQ1 and KCNQ1OT1 in WT, K non-rep KO, K rep KO, EV, and K KD HEK293T cells. c, Correlation analysis of the ChOP-MS dataset shows good correlation between biological replicates. Spearman’s rank correlation coefficient (rho) and p-value between two replicate samples are shown. KCNQ1OT1 denotes KCNQ1OT1 probe, LacZ denotes LacZ probe. d, Expression of randomly selected AluY elements that are targeted by KCNQ1OT1 assessed by RT-qPCR. e, Expression of randomly selected L1 elements that are targeted by KCNQ1OT1 assessed by RT-qPCR. f, Expression of L1HS in two different K rep KO clonal cell lines detected by RT-qPCR. g, DNA methylation status on a representative KCNQ1OT1 binding L1 element in WT, K rep KO clone-1, and K rep KO clone-2 cells detected by MeDIP-qPCR. The qPCR primers amplify unique sequence within the repetitive element (chr1:65,797,529-65,797,674). h, Significance of DNMT1, DNMT3A and HP1α in WT, K non-rep KO and K rep KO cells (use NSAF for one-tailed paired Student’s t-test). Data in d, e, f, and g are mean ± s.e.m. (n = 3 independent experiments). Statistical significance was determined by two-tailed Student’s t-test, *p < 0.05, **p < 0.01, ***p < 0.001. Source numerical data are available in Source Data.
