Chromatin accessibility: methods, mechanisms, and biological insights

Abstract

Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.

Keywords: ATAC-seq; Accessibility; HP1; MNase-seq; chromatin; compaction; heterochromatin; linker histones; phase separation; transcription.

Figure 1.

Types of accessibility. (a) Permeability of a nuclear volume (‘compartment’) determines whether proteins can diffuse into the same space as a genomic locus. (b) Broad-based accessibility of chromatin in a set of genomic loci determines the ability of proteins to nonspecifically access and scan the genomic DNA. Chromatin fiber compaction is shown as a mechanism for modulating broad-based accessibility, but many other mechanisms are possible. (c) Local hyper-accessible sites are narrow loci where proteins can access DNA with similar ease as de-chromatinized DNA. These sites are thought to have low nucleosome occupancy for several reasons, including competition from transcription factors (TFs) (illustrated, blue and red) that exclude nucleosomes.

Figure 2.

Models of accessibility control mechanisms by chromatin. (a) Steric occlusion at binding sites by nucleosomes or oligo-nucleosome contacts can prevent productive binding interactions and reduce the effective concentration of a TF or polymerase (blue circles) in a genomic region. If all binding sites are obscured, the protein is not concentrated in the genomic region, even though diffusion may be unaffected. (b) Liquid-liquid phase separation of chromatin and associated proteins can prevent proteins from entering three-dimensional regions of the nucleus (compartments) based on the proteins’ chemical properties such as charge. (c) If chromatin is crosslinked into a gel, it would exclude proteins larger than the pore size of the gel regardless of their chemical properties. (d) Volume exclusion due to crowding can reduce the concentration of soluble protein in a manner that depends more weakly on size than a gel (c).