DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

Abstract

DNase-seq is primarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that correspond to active regulatory elements. However,~40 yr ago it was demonstrated that DNase I also digests with a~10-bp periodicity around nucleosomes matching the exposure of the DNA minor groove as it wraps around histones. Here, we use DNase-seq data from 49 samples representing diverse cell types to reveal this digestion pattern at individual loci and predict genomic locations where nucleosome rotational positioning, the orientation of DNA with respect to the histone surface, is stably maintained. We call these regions DNase I annotated regions of nucleosome stability (DARNS). Compared to MNase-seq experiments, we show DARNS correspond well to annotated nucleosomes. Interestingly, many DARNS are positioned over only one side of annotated nucleosomes, suggesting that the periodic digestion pattern attenuates over the nucleosome dyad. DARNS reproduce the arrangement of nucleosomes around transcription start sites and are depleted at ubiquitous DHS sites. We also generated DARNS from multiple lymphoblast cell line (LCL) samples. We found that LCL DARNS were enriched at DHS sites present in most of the original 49 samples but absent in LCLs, while multi-cell-type DARNS were enriched at LCL-specific DHS sites. This indicates that variably open DHS sites are often occupied by rotationally stable nucleosomes in cell types where the DHS site is closed. DARNS provide additional information about precise DNA orientation within individual nucleosomes not available from other nucleosome positioning assays and contribute to understanding the role of chromatin in gene regulation.

Mapping nucleosome positions using DNase-seq

“…This is most likely due to dynamic nucleosome wrapping and unwrapping (DNA breathing) (Li and Widom 2004;Li et al 2005). Overlaid on this quadratic shape, we also observe a signature oscillatory cleavage pattern, which has been previously wellestablished (Noll 1974;Boyle et al 2008;Winter et al 2013). Since DNase I binds within the minor groove, it can more easily nick nucleosomal DNA when the minor groove is exposed.…”

“…This indicates that if a DNase-based nucleosome center does not coincide with a reference nucleosome center, it is far more likely to be a multiple of 10.3 bp away from it. Many have reported that nucleosomes exhibit this translational positioning offset property, in which a nucleosome is likely to position itself at "rotationally in-phase" positions that are multiples of 10.3 bp away from each other (Albert et al 2007;Brogaard et al 2012;Gaffney et al 2012;Winter et al 2013). We believe that our DNase-seqbased approach identifies genuine nucleosome centers, and where the map does not perfectly coincide with the reference, the differences appear to represent translational offsets with respect to reference nucleosome centers.…”

“…In comparison with other work, several recent studies have noted a similar oscillatory cleavage pattern of DNase I in highthroughput DNase-seq data (Boyle et al 2008;Gaffney et al 2012;Winter et al 2013;Vierstra et al 2014). However, none of them utilized this pattern to map genome-wide nucleosome positions.…”

“…The superior ability of our approach to produce an accurate nucleosome map is most likely due to the fact that it uses DNase I cuts both within and outside the nucleosome. The oscillatory cut information can be maintained even at fuzzy nucleosomes because of the stability of nucleosome rotational positioning Winter et al 2013). However, MNase-seq methods rely primarily on the digestion signals from within nucleosome linkers, which are weaker when nucleosomes are not well positioned.…”

“…However, none of them utilized this pattern to map genome-wide nucleosome positions. Winter et al (2013) used an oscillatory pattern to identify regions called "DNase I annotated regions of nucleosome stability" (DARNS), which are not individual nucleosome positions but rather genomic regions representing typically small portions of nucleosomes that maintain their rotational phasing. Vierstra et al (2014) use DNase I to identify "nucleosome architecture" around TF binding sites, but their method requires pairedend sequencing and relies on the size of reads to distinguish nucleosome-associated fragments from those within DHSs.…”