Poly(ADP-ribosyl)ation dependent changes in CTCF-chromatin binding and gene expression in breast cells

CTCF is an evolutionary conserved and ubiquitously expressed architectural protein, which regulates a plethora of cellular functions using different molecular mechanisms. The main form of CTCF with an apparent molecular mass of 130 kDa (CTCF130) has been extensively studied, however the properties of CTCF180, highly modified by poly(ADP-ribosyl)ation (PARylation) are not well understood. In this study we performed ChIP-seq and RNA-seq analyses in breast cells 226LDM, proliferating (with CTCF130 as the most abundant CTCF form) and arrested in the cell cycle (with only CTCF180). A dramatic reorganization of CTCF binding was observed during this transition, whereby CTCF was evacuated from many sites ("lost" group), although some sites retained modified CTCF ("common") and others acquired CTCF180 ("gained"). The classic CTCF binding motifs were identified for the former two groups, whereas the latter had no CTCF binding motif. Changes in CTCF occupancies in lost/common (but not gained) sites were associated with increased chromatin densities and altered expression from the neighboring genes. We propose a model integrating CTCF130/180 transition with CTCF-DNA binding and gene expression patterns, and functional outcomes. This study issues an important cautionary note concerning design and interpretation of any experiments using cells and tissues where CTCF180 may be present. ChIP-Seq and RNA-Seq analyses to investigate CTCF binding, histone patterns and gene expression profiles in breast cells, 226LDM, proliferating (with CTCF130 as the most abundant CTCF form) and chemically arrested in the cell cycle (with only CTCF180)