Chromatin accessibility profiling methods

Abstract

Chromatin accessibility refers to the level of physical compaction of chromatin, a complex formed by DNA and associated proteins consisting mainly of histones, transcription factors (TFs), chromatin-modifying enzymes and chromatin-remodelling complexes 1-3. Although eukaryotic genomes are generally packed into nucleosomes, which comprise ~147 bp of DNA wrapped around an octamer of histones 4,5 , nucleosome occupancy is not uniform in the genome, and varies across tissues and cell types. Nucleosomes are typically depleted at genomic locations that represent cis-regulatory elementsenhancers and promoters, among others-that interact with transcriptional regulators (for example, TFs), resulting in accessible chromatin 6-10. Profiling chromatin accessibility on a genome-wide scale is an excellent tool to map putative regulatory elements in a cell type or cell state. Post-translational chemical modifications of chromatin, including DNA methylation (in vertebrates) and histone methylation and acetylation, are dynamic and change between different cell states, similar to nucleosome positioning. These post-translational modifications are often correlated with chromatin accessibility and can reflect specific functionalities of genomic regions related to the regulation of gene expression 11,12. Changes in these post-translational modifications, such as increased or decreased histone methylation and acetylation, are affected by a large set of chromatin-modifying enzymes that can be recruited to chromatin regions by TFs. These modifications alter the physico-chemical properties of the chromatin, which in turn can influence the formation of transcriptional condensates 13,14. In addition, active chromatin remodelling impacts nucleosome occupancy; for example, the SWI/SNF complexes use ATP hydrolysis to alter histone-DNA contacts, thereby repositioning or removing nucleosomes 15. Dynamic changes in the chromatin structure, chemical modifications and nucleosome positioning form a crucial interplay with the TFs that drive differentiation of cells during development 16,17. Initial changes in chromatin accessibility are caused by the binding of TFs, which outcompete histones and recruit cofactors, including ATP-dependent chromatin remodellers 18,19 , or by TFs that preferentially bind to their recognition sequence in nucleosomal DNA 20,21. The binding of these initial TFs, known as pioneer factors, can recruit other TFs to co-bind and further stabilize the nucleosome-depleted

Profiling single-cell chromatin accessibility in plants

“…Profiling chromatin accessibility requires isolating nuclei from heterogenous tissues ( Minnoye et al., 2021 ). Tn5 can tagment organellar genomes with high efficiency due to a lack of nucleosomes on chloroplast and mitochondrial DNA ( Lu et al., 2017 ).…”

Immunotherapy in the Treatment of Urothelial Bladder Cancer: Insights From Single-Cell Analysis

“…For example, surface protein levels can also be measured in single cells by oligonucleotide-barcoded antibodies, as illustrated by various methods including CITE-seq and REAP-seq ( 92 , 93 ). Another relevant knowledge tier is the cellular epigenetic state, and recently described scATAC-seq and scDNase-seq, among others, enable high-throughput examination of chromatin accessibility at single-cell resolution ( 94 ). One key attribute of tumor ecosystem is the spatial distribution of cellular niches which directly determines physical cell-cell interactions and intercellular signaling communications ( 95 ).…”

HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

“…median of 250-500 genes per cell in primary tissues 1,5 ), and relatively lengthy workflows compared to commercial solutions such as 10x Genomics, generic protocols such as Drop-seq 6 and InDrop 7 have been used much less than the commercial alternatives 5,8,9 . A second wave of droplet-based assays has provided the ability to profile chromatin accessibility of single cells, particularly using single-cell ATAC-seq 10 . To our knowledge, only one non-commercial droplet-based scATAC-seq protocol has been published so far 11 .…”