Nucleosome repositioning in chronic lymphocytic leukaemia

Abstract

The location of nucleosomes in the human genome determines the primary chromatin structure and regulates access to regulatory regions. However, genome-wide information on deregulated nucleosome occupancy and its implications in primary cancer cells is scarce. Here, we performed a systematic comparison of high-resolution nucleosome maps in peripheral-blood B-cells from patients with chronic lymphocytic leukaemia (CLL) and healthy individuals at single base pair resolution. Our investigation uncovered significant changes of both nucleosome positioning and packing in CLL. Globally, the spacing between nucleosomes (the nucleosome repeat length, NRL) was shortened in CLL. This effect was stronger in the more aggressive IGHV-unmutated than IGHV-mutated CLL subtype. Changes in nucleosome occupancy at specific sites were linked to active chromatin remodelling and reduced DNA methylation. Nucleosomes lost or gained in CLL in comparison with non-malignant B-cells marked differential binding of 3D chromatin organisers such as CTCF as well as immune response-related transcription factors, allowing delineating epigenetic mechanisms affected in CLL. Furthermore, patients could be better assigned to CLL subtypes according to nucleosome occupancy at cancer-specific sites than based on DNA methylation or gene expression. Thus, nucleosome positioning constitutes a novel readout to dissect molecular mechanisms of disease progression and to stratify patients. Furthermore, we anticipate that the global nucleosome positioning changes detected in our study, like the reduced NRL, can be exploited for liquid biopsy applications based on cell-free DNA to monitor disease progression.

Nucleosome reorganisation in breast cancer tissues

“…The global NRL decrease reported here for breast cancer may also take place in other cancers. Indeed, we have also found a similar genome-wide NRL shortening effect in B-cells from patients with chronic lymphocytic leukaemia, which was more pronounced for more aggressive cancer subtypes (20).…”

“…NucTools (Vainshtein et al 2017) was used to split the regions into chromosomes and 5mC occurrence per CpG was calculated with a cfDNAtools script bed2occupancy.v3d.methyl.pl as in (Piroeva et al 2023). Aggregate DNA methylation profiles were calculated around centres of common and shifted nucleosomes defined above using NucTools, summing up the methylation beta-values for each CpG located at a given distance from the genomic feature of interest as in (Wiehle et al 2019).…”

“…Our recent study in chronic lymphocytic leukaemia uncovered some of the rules of cancer-specific nucleosome repositioning in B-cells from peripheral blood (Piroeva et al 2023), but nucleosome repositioning in solid tissues remains enigmatic. One of the reasons for this is that chromatin in solid tissues may have vastly different properties than chromatin from immortalised cell lines, which have been used historically as model systems for nucleosome positioning.…”

Detection of new pioneer transcription factors as cell-type specific nucleosome binders

“…Using open chromatin regions from the DNase-seq data, we identified differentially and conserved open chromatin regions using the “intersect” command from the BEDTools suite 39 . Conserved open chromatin regions represent open chromatin regions that are more than 80% shared between embryonic H1 and at least one other differentiated cell line used in this study 45 (Supplementary Figure 1). Chromatin regions with differential accessibility (“ differentially open chromatin regions ”) are defined as those that have less than 20% overlap between open regions in H1 embryonic cell line and any other differentiated cell line 45 (Supplementary Figure 1).…”

“…Conserved open chromatin regions represent open chromatin regions that are more than 80% shared between embryonic H1 and at least one other differentiated cell line used in this study 45 (Supplementary Figure 1). Chromatin regions with differential accessibility (“ differentially open chromatin regions ”) are defined as those that have less than 20% overlap between open regions in H1 embryonic cell line and any other differentiated cell line 45 (Supplementary Figure 1). For motif enrichment analysis of transcription factors, we selected two sets of NRs and NDRs: 1) NDRs located in the open chromatin regions and all identified NRs using the MNase-seq data; 2) NDRs located in conserved open chromatin regions and NRs located in the differentially open regions so that their accessibility may be associated with TF binding.…”