Nucleosome landscape in HepG2 cells in relation to NFY, HNF4a and FOXA2 binding sites
(English)Manuscript (preprint) (Other academic)
Nucleosomes are the building blocks that compact the DNA in the nucleus, thereby regulating its accessibility. Here we report a genome-wide nucleosome positioning analysis on the HepG2 cell line, based on deep sequencing of mononucleosomal DNA. In concordance with other studies, we found nucleosomes to be well positioned at the TSS, with a nucleosome free region in the proximal promoter. Focusing on the importance of nucleosomal positioning at distal elements we found that TFBS sites often are flanked by well-positioning nucleosomes at a distance that indicate that the TF complexes replaces the nucleosome, and we also find that some transposable elements have distinct nucleosomal signatures. To build on previous regulatory data for HepG2 cells we also produced ChIP-seq reads for the transcription factors NF-Y and TCF7L2 and correlate this to the HepG2 transcriptome as defined by RNA-seq and Pol-II ChIP-seq. NF-Y was found primarily at promoters, contrary to what has been suggested from previous studies, and binds genes involved in cell cycle and chromatin organization.
ChIP-seq, NFY, Pol-II, TCF7L2, nucleosome positioning
Research subject Medical Genetics
IdentifiersURN: urn:nbn:se:uu:diva-132879OAI: oai:DiVA.org:uu-132879DiVA: diva2:359527