title: HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.
abstract: BACKGROUND
  Small molecule inhibitors of histone deacetylases (HDACi) hold promise as anticancer agents for particular malignancies. However, clinical use is often confounded by toxicity, perhaps due to indiscriminate hyperacetylation of cellular proteins. Therefore, elucidating the mechanisms by which HDACi trigger differentiation, cell cycle arrest, or apoptosis of cancer cells could inform development of more targeted therapies. We used the myelogenous leukemia line K562 as a model of HDACi-induced differentiation to investigate chromatin accessibility (DNase-seq) and expression (RNA-seq) changes associated with this process.
  
  
  RESULTS
  We identified several thousand specific regulatory elements [~10 % of total DNase I-hypersensitive (DHS) sites] that become significantly more or less accessible with sodium butyrate or suberanilohydroxamic acid treatment. Most of the differential DHS sites display hallmarks of enhancers, including being enriched for non-promoter regions, associating with nearby gene expression changes, and increasing luciferase reporter expression in K562 cells. Differential DHS sites were enriched for key hematopoietic lineage transcription factor motifs, including SPI1 (PU.1), a known pioneer factor. We found PU.1 increases binding at opened DHS sites with HDACi treatment by ChIP-seq, but PU.1 knockdown by shRNA fails to block the chromatin accessibility and expression changes. A machine-learning approach indicates H3K27me3 initially marks PU.1-bound sites that open with HDACi treatment, suggesting these sites are epigenetically poised.
  
  
  CONCLUSIONS
  We find HDACi treatment of K562 cells results in site-specific chromatin remodeling at epigenetically poised regulatory elements. PU.1 shows evidence of a pioneer role in this process by marking poised enhancers but is not required for transcriptional activation.
authors.affiliation: Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708 USA ; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA.
authors.forename: Christopher L
authors.initials: CL
authors.lastname: Frank
authors.affiliation: Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA ; Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708 USA.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Manandhar
authors.affiliation: Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA ; Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708 USA.
authors.forename: Raluca
authors.initials: R
authors.lastname: Gordân
authors.affiliation: Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA ; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708 USA.
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Crawford
keywords: Acetylation; Chromatin accessibility; Enhancer; Histone deacetylase inhibitor; Pioneer factor