Xenbase Image ID: 128051

Figure 6. Depletion of KDM2B causes a reduction in RING1B occupancy.(A) KDM2B ChIP-seq signal was plotted at CGIs in the control (solid blue line) and knockdown cell line (dotted blue line). Sequencing signal in the input samples over the same regions are indicated as solid or dotted black lines. KDM2B ChIP-seq signal is specifically lost over CGIs genome-wide in the KDM2B knockdown cell line. (B) A snapshot showing RING1B ChIP-seq signal in the control cell line illustrating a previously identified high magnitude RING1B binding sites (i.e. Atf3) and novel low magnitude RING1B binding sites. Input sequencing traces over the same region are shown in black. Bio-CAP-seq signal indicates regions containing non-methylated DNA. Above the sequencing traces gene promoters are show by black arrows and exons by vertical black lines. CGIs are shown as green bars with previously identified RING1B peaks and novel RING1B peaks indicated with purple boxes. (C) RING1B ChIP-seq signal from the control (solid purple line) and KDM2B knockdown cell line (dotted purple line) were plotted over previously identified CGI associated RING1B binding sites. Input sequencing signal was plotted over same regions. In the KDM2B knockdown line there is a specific reduction of RING1B binding over the CGI. (D) The same ChIP-seq signal as in part (C) was plotted over novel low magnitude binding sites identified in part (B). In the KDM2B knockdown cell line there is an even more severe loss of RING1B binding at these novel RING1B occupied sites. (E),(F) Examples of ChIP-seq profiles at individual high (E) and low (F) magnitude RING1B binding sites showing clear reduction of RING1B following KDM2B knockdown.DOI: http://dx.doi.org/10.7554/eLife.00205.011Figure 6—figure supplement 1. Conditional removal of RING1B validates the identity of novel peaks identified in the RING1B ChIP-seq.Eight genes corresponding to novel RING1B peaks identified in ChIP-seq were examined by ChIP quantitative-PCR (bar graphs) in the RING1B conditional ESC cells before (blue bars) and after (red bars) deletion of RING1B by addition of tamoxifen. In all cases deletion of RING1B leads to a loss of RING1B ChIP signal by quantitative-PCR, indicating that these are bona fide RING1B occupied sites. RING1B ChIP-seq traces are shown in each case for comparison. Error bars indicate the SEM for three biological replicates.DOI: http://dx.doi.org/10.7554/eLife.00205.012 Image published in: Farcas AM et al. (2012) Copyright © 2012, Farcas et al. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View

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