Long-range single-molecule mapping of chromatin accessibility in eukaryotes

Shipony, Zohar; Marinov, Georgi K.; Swaffer, Matthew P.; Sinnott‐Armstrong, Nicholas A.; Skotheim, Jan M.; Kundaje, Anshul; Greenleaf, William J.

doi:10.1038/s41592-019-0730-2

Cited by 104 publications

(106 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…SAMOSA adds to the growing list of technologies that use high-throughput single-molecule sequencing to explore the epigenome (Baldi et al, 2018;Lee et al, 2019;Shipony et al, 2020;Wang et al, 2019;Stergachis et al, 2020). We foresee the broad applicability of this and similar approaches to dissect gene regulatory processes at previously intractable length-scales.…”

Section: Discussionmentioning

confidence: 99%

Massively multiplex single-molecule oligonucleosome footprinting

Abdulhay

McNally

Hsieh

et al. 2020

eLife

View full text Add to dashboard Cite

Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular 'states' of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across both active and silent human epigenomic domains. Our analyses suggest that chromatin is comprised of a diverse array of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution, and offers up new avenues for modeling and visualizing higher-order chromatin structure.

show abstract

Section: Discussionmentioning

confidence: 99%

Massively multiplex single-molecule oligonucleosome footprinting

Abdulhay

McNally

Hsieh

et al. 2020

eLife

View full text Add to dashboard Cite

show abstract

“…(ii) For diploid cells it is not usually possible to tell which chromosome copy each nucleosome came from. Another exciting technology making an entrance is long-read sequencing, which can be used to map nucleosome footprints on the same long DNA molecule, obtained using DNA methylases which can only methylate linker DNA [39].…”

Section: Nucleosome Mapping: Mnase-seq and Chemical Mappingmentioning

confidence: 99%

Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast

Prajapati

Ocampo

Clark

2020

Biology

View full text Add to dashboard Cite

Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent remodeling enzymes that are capable of moving nucleosomes along DNA, or of evicting nucleosomes altogether. In yeast, the nucleosome-spacing enzymes are ISW1 (Imitation SWitch protein 1), Chromodomain-Helicase-DNA-binding (CHD)1, ISW2 (Imitation SWitch protein 2) and INOsitol-requiring 80 (INO80); the nucleosome eviction enzymes are the SWItching/Sucrose Non-Fermenting (SWI/SNF) family, the Remodeling the Structure of Chromatin (RSC) complexes and INO80. We discuss the contributions of each set of enzymes to chromatin organisation. ISW1 and CHD1 are the major spacing enzymes; loss of both enzymes results in major chromatin disruption, partly due to the appearance of close-packed di-nucleosomes. ISW1 and CHD1 compete to set nucleosome spacing on most genes. ISW1 is dominant, setting wild type spacing, whereas CHD1 sets short spacing and may dominate on highly-transcribed genes. We propose that the competing remodelers regulate spacing, which in turn controls the binding of linker histone (H1) and therefore the degree of chromatin folding. Thus, genes with long spacing bind more H1, resulting in increased chromatin compaction. RSC, SWI/SNF and INO80 are involved in NDR formation, either directly by nucleosome eviction or repositioning, or indirectly by affecting the size of the complex that resides in the NDR. The nature of this complex is controversial: some suggest that it is a RSC-bound “fragile nucleosome”, whereas we propose that it is a non-histone transcription complex. In either case, this complex appears to serve as a barrier to nucleosome formation, resulting in the formation of phased nucleosomal arrays on both sides.

show abstract

“…We and others have previously shown that endogenous CpG methylation can be accurately called with nanopore data 7 , 8 . More recently, this technology was applied to exogenous labeling of chromatin accessibility in S. Cerevisiae , a unicellular eukaryotic model organism without endogenous methylation 9 , 10 . Others have demonstrated this application on the PacBio platform even in human cells, though they did not capture endogenous methylation 11 , 12 .…”

Section: Introductionmentioning

confidence: 99%

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

et al. 2020

View full text Add to dashboard Cite

Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore sequencing to evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA by applying GpC methyltransferase to exogenously label open chromatin. We performed nanopore sequencing of Nucleosome Occupancy and Methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7, MDA-MB-231). The single-molecule resolution allows footprinting of protein and nucleosome binding and determining the combinatorial promoter epigenetic signature on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, allowing us to generate the first fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility. We further apply this to a breast cancer model to evaluate differential methylation and accessibility between cancerous and non-cancerous cells.

show abstract

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

Cited by 104 publications

References 66 publications

Massively multiplex single-molecule oligonucleosome footprinting

Massively multiplex single-molecule oligonucleosome footprinting

Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

Contact Info

Product

Resources

About