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From profiles to function in epigenomics

Key Points

  • Many epigenetic approaches contribute to our understanding of gene regulation and cell identity. By pursuing these epigenetic approaches, different levels of functionality can be proven for epigenomic features.

  • Epigenomic profiling is providing a descriptive view of the chromatin landscape, and data integration enables us to 'infer' functionality from complex data sets.

  • Genetic manipulations are crucial to show the relevance of chromatin-modifying enzymes (and genomic domains that harbour epigenomic features); however, they can sometimes fall short of distinguishing the effect of an epigenomic feature from other induced changes.

  • Epigenome editing provides a new possibility to test the functionality of epigenomic features directly. Numerous recent publications have indicated a ubiquitous applicability of epigenome editing and its potential in manipulating gene expression.

  • Once current limitations are overcome, epigenetic screens — using large-scale epigenome editing approaches across the epigenome — will allow functional epigenomic features to be distinguished from non-functional counterparts.

Abstract

Myriads of epigenomic features have been comprehensively profiled in health and disease across cell types, tissues and individuals. Although current epigenomic approaches can infer function for chromatin marks through correlation, it remains challenging to establish which marks actually have causative roles in gene regulation and other processes. After revisiting how classical approaches have addressed this question in the past, we discuss the current state of epigenomic profiling and how functional information can be indirectly inferred. We also present new approaches that promise definitive functional answers, which are collectively referred to as 'epigenome editing'. In particular, we explore CRISPR-based technologies for single-locus and multi-locus manipulation. Finally, we discuss which level of function can be achieved with each approach and introduce emerging strategies for high-throughput progression from profiles to function.

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Figure 1: Evolving views on the Waddington landscape.
Figure 2: Experimental approaches and the level of function that they report.
Figure 3: Multi-dimensional epigenome profile integration.
Figure 4: Strategies for epigenome editing.

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Acknowledgements

S.H.S. was supported by DFG (STR 1385/1-1). A.K. was supported by a CRUK Ph.D. Fellowship. S.B. was supported by the EU-FP7 BLUEPRINT Project (282510) and the NIHR UCLH Biomedical Research Centre (BRC84/CN/SB/5984).

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Supplementary information

Supplementary Video 1

http://www.paulliamharrison.co.uk/movies/Genetic%20landscape%20model_0224.mov Contemporary version of the Waddington landscape (see also FIG. 1). Epigenetic and epigenomic manipulation promises to dynamically change the landscape and thus cellular phenotypes. This movie is from 'EpiGeneScapes' by Paul Liam Harrison (2015). EpigeneScapes is a body of work that includes animations, drawings, sculptures, interactive installations and a series of mixed media prints derived from the C. H. Waddington concept of the epigenetic landscape. The animated model was developed in collaboration with Mhairi Towler and Link Li and was undertaken as part of Paul Liam Harrison's role as Associate Artist with EpigeneSys European Network of Excellence. http://www.epigenesys.eu/en/science-and-you/art-and-science. Courtesy of P. L. Harrison, University of Dundee, UK, and EpiGeneSys. (MOV 26917 kb)

Glossary

Genome-wide association studies

(GWAS). Studies that aim to identify genetic loci associated with an observable trait, disease or condition.

Single-nucleotide polymorphisms

(SNPs). Single base-pair differences in the DNA sequence between individual members of a species.

DNase I-hypersensitive sites

(DHSs). Regions of chromatin that are sensitive to digestion with DNase I, indicating that these sites are accessible and free of nucleosomes.

Hi-C

Experimental method to map contacts formed between segments of DNA in three-dimensional space on a genome-wide scale.

CRISPR–Cas9

(Clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9). Components of a bacterial defence system against viruses.

COMETs

Blocks of co-methylation identified by methylome segmentation.

Chromatin immunoprecipitation followed by sequencing

(ChIP–seq). A method for mapping the distribution of histone modifications or chromatin-associated proteins or transcription factors along the genome. DNA and proteins are crosslinked and an antibody specific to the protein of interest is used to enrich for DNA sequences bound to this protein. These are then identified by sequencing, revealing the genome-wide profile of the protein of interest.

Assay for transposase-accessible chromatin sequencing

(ATAC-seq). A method to identify regions of open chromatin in cells using an engineered Tn5 transposase to both cleave DNA and integrate primer sequences into the cleaved DNA.

Formaldehyde-assisted isolation of regulatory elements followed by sequencing

(FAIRE–seq). A technique that uses the solubility of open chromatin in the aqueous phase during phenol–chloroform extraction to identify sites of open chromatin.

Chromosome conformation capture assays

A group of techniques (including 3C, 4C, 5C, Hi-C and ChIA-PET) that are used to map physical interactions between segments of DNA in three-dimensional space.

Topologically associating domains

(TADs). Regions of chromatin in which loci frequently interact with each other, usually based on evidence from chromosome conformation capture techniques. Loci located in different TADs do not frequently come into contact.

Zinc finger

A modular DNA-binding protein that can be engineered to bind to a sequence of choice.

Transcription activator-like effector

(TALE). DNA-binding protein that has a modular architecture, with each module (34 amino acids) recognizing a single nucleotide in a DNA sequence and that can therefore be engineered to bind to a DNA sequence of choice.

Cas9

(CRISPR-associated protein 9). Useful for genome engineering because it can be guided (by a guide RNA) to a particular site in the genome where it makes a DNA double-strand break.

dCas9

The nuclease-dead version of Cas9, which can no longer produce DNA double-strand breaks.

Guide RNA

(gRNA). An artificial fusion of CRISPR RNA (crRNA) and transactivating crRNA (tracrRNA) used to target the Cas9 protein to a target site in the genome.

Pooled screens

Approaches in which cells receiving the screening library (for example, pools of guide RNAs) are grown and selected together for a phenotypic change.

Fluorescence-activated cell sorting

(FACS). An experimental method that measures a fluorescence-based signal (from a reporter or antibody staining) emitted from individual cells of a population, and uses these fluorescence signals to isolate single cells of interest.

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Stricker, S., Köferle, A. & Beck, S. From profiles to function in epigenomics. Nat Rev Genet 18, 51–66 (2017). https://doi.org/10.1038/nrg.2016.138

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