Nucleosome repositioning during differentiation of a human myeloid leukemia cell line

Abstract

Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope). Nucleosome positions changed genome-wide, exhibiting a specific class of alterations involving nucleosome loss in extended (∼1kb) regions, pronounced in enhancers and promoters. Genes that lost nucleosomes at their promoters showed a tendency to be upregulated. On the other hand, nucleosome gain did not show simple effects on transcript levels. The average genome-wide nucleosome repeat length (NRL) did not change significantly with differentiation. However, we detected an approximate 10 bp NRL decrease around the haematopoietic transcription factor (TF) PU.1 and the architectural protein CTCF, suggesting an effect on NRL proximal to TF binding sites. Nucleosome occupancy changed in regions associated with active promoters in differentiated cells, compared with untreated HL-60/S4 cells. Epichromatin regions revealed an increased GC content and high nucleosome density compared with surrounding chromatin. Epichromatin showed depletion of major histone modifications and revealed enrichment with PML body-associated genes. In general, chromatin changes during HL-60/S4 differentiation appeared to be more localized to regulatory regions, compared with genome-wide changes among diverse cell types studied elsewhere.

Resolution of Complex Issues in Genome Regulation and Cancer Requires Non-Linear and Network-Based Thermodynamics

“…The exit from the circulus vicious of cancer treatments might be searched either in interruption of reprogramming (that might be difficult or even impossible) or in the opposite direction, while using the toti-pluripotent reprogrammed state of cancer cells for their channelled normalisation (differentiation, which epigenetically can take over the mutations [157]). For this purpose, the appropriate morphogenic embryonal inducers, regeneration fields [158], and the structured 3D environment-putting tumours in context [159] and changing the chromatin folding-can be used [160]. This approach can, at least, stop the invasion and metastatic spread of cancer, which is the main cause of patient mortality.…”

Differential staining of peripheral nuclear chromatin with Acridine orange implies an A-form epichromatin conformation of the DNA

“…The participation of epichromatin, and its derived nuclear envelope sheets, in providing anchorage of decondensing mitotic chromosomes to the restituting nuclear envelope in normal telophase, and in mitotic slippage, was evidenced by electron microscopy [ 8 , 14–16 ]. The latest papers from Olins, Teif and colleagues [ 13 , 17 ] revealed enrichment of epichromatin constituting 5% of the nuclear DNA with GC stretches, methylated CpGs, ALU transposons, poverty with AT stretches, preservation of the nucleosome repeats, and more dense nucleosome packaging than in general chromatin.…”

Nucleosome dynamics of human iPSC during neural differentiation

“…A recent report using an alternative method based on Histone 3 ChIP-seq also showed a nucleosome array centred on CTCF of human myeloid leukaemia cells (HL60) and altered nucleosome spacing following retinoic acid-induced differentiation [39]. In Dictyostelium, loss of ChdC increases nucleosome spacing, indicating a capacity to specifically regulate spacing within nucleosomes [12].…”