Topoisomerase I (TOP1) is a functional mitotic interactor of the bookmarking factor HNF1B [ChIPseq_786O]

HNF1B (Hepatocyte Nuclear Factor 1-Beta) is a POU-homeobox transcription factor expressed in kidney and frequently mutated in patients suffering from Congenital Anomalies of the Kidney and the Urinary Tract (CAKUT). HNF1B is a bookmarking factor, able to bind mitotic chromatin and necessary for the post-mitotic reactivation of gene expression. In order to characterize the molecular functions of HNF1B as a bookmarking factor, we performed ChIPseq on asynchronous and mitotic renal cells. We developed a novel ChIP method with a non-aqueous crosslinking (NAQC) to circumvent the well-known artefactual effects of formaldehyde crosslinking of mitotic chromosomes. NAQC-ChIP allowed the retention of the mitotic signal that was lost with a regular ChIP. With this novel methodology, we show that the vast majority HNF1B binding sites detected in asynchronous cells are also bound in mitosis. HNF1B-ChIPseq was performed in asynchronous and mitotic 786-O cells fixed with NAQC (non-aqueous crosslinking) or AQC (aqueous crosslinking) methods. Free cycling mIMCD3 cells were admixed either to asynchronous or mitotic 786-O cells just before the crosslinking step as a calibrating internal control.