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Additional file 1: Fig. S1. of Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions

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posted on 2015-08-14, 05:00 authored by Elena Pugacheva, Samuel Rivero-Hinojosa, Celso Espinoza, Claudia Méndez-Catalá, Sungyun Kang, Teruhiko Suzuki, Natsuki Kosaka-Suzuki, Susan Robinson, Vijayaraj Nagarajan, Zhen Ye, Abdelhalim Boukaba, John Rasko, Alexander Strunnikov, Dmitri Loukinov, Bing Ren, Victor Lobanenkov
CTCF and BORIS occupancy in human cancer cell lines. a CTCF and BORIS expression in different cell types determined by quantitative PCR. b Western blot depicts the relative levels of CTCF and BORIS proteins in nuclear lysates extracted from different cell types. c K562 and OVCAR8 cells immunostained with antibodies against CTCF (green) and BORIS (red). The merge panel shows co-localization of CTCF and BORIS proteins in the nucleus. d EMSA: either in vitro translated CTCF (CTCF TNT) or BORIS (BORIS TNT) were incubated with 32P-labeled probe. The first lane is a negative control, containing no protein (Free-F). The appearance of a shifted band (Super Shift) after adding specific antibodies demonstrated the specificity of DNA–protein interaction and the absence of cross-reactivity between CTCF and BORIS antibodies. e, f Venn diagrams depict the numbers and percentages of CTCF (e) and BORIS (f) bound regions overlapping in K562, OVCAR8 and Delta47 cells. Heatmap shows BORIS (e) or CTCF (f) occupancy at the invariant CTCF (47,531) or BORIS (17,536) bound regions in three cancer cell types. The tag density was subjected to k-means ranked clustering with two clusters expected. BORIS binds to roughly 30 % of invariant CTSes, while the remaining 70 % of CTSes belong to CTCF-only binding regions. e Similar analysis revealed that nearly 70 % of BORIS bound regions showed CTCF occupancy in all three cell lines. f Invariant BORIS-only regions mapped in K562 and Delta47 cells were generally occupied by CTCF in OVCAR8 cells (f), marked by bracket. g Venn diagram depicts the overlapping CTCF bound regions mapped in 38 human cell lines (ENCODE) with BORIS-only bound regions mapped in K562 cells. h ChIP-seq tracks show the genomic regions occupied by BORIS alone in K562 cells (BORIS-only) and by both CTCF and BORIS in OVCAR8 and Delta47 cells. (PPTX 1854 kb)

Funding

Division of Intramural Research, National Institute of Allergy and Infectious Diseases (US)

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