Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin. Tremendous progress has been made in cataloguing CREs in the human genome using bulk transcriptomic and epigenomic methods. However, single-cell epigenomic and multi-omic technologies have the potential to provide deeper insight into cell type-specific gene regulatory programmes as well as into how they change during development, in response to environmental cues and through disease pathogenesis. Here, we highlight recent advances in single-cell epigenomic methods and analytical tools and discuss their readiness for human tissue profiling.
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We apologize to those authors whose work we fail to include in this Review due to space constraints. Research in the Ren lab is funded by the Ludwig Institute and the National Institutes of Health (NIH) grants 1UM1HG009402, 1U19MH114831, 1U01MH121282, 1R01AG066018, R01AG067153, U01DA052769, 1UM1HG011585, RF1MH124612, 1R56AG069107, R01EY031663, 1U01HG012059, R24AG073198 and RF1MH128838. The Center for Epigenomics was supported, in part, by the UC San Diego School of Medicine and by NIH grants R01EY030591, U01HL148867, U01DK120429 and R01HD102534. The Gaulton lab is funded by NIH grants DK114650, DK120429, DK122607, DK105554 and HG012059.
B.R. is a shareholder and consultant of Arima Genomics, Inc., and a co-founder of Epigenome Technologies, Inc. K.J.G. is a consultant of Genentech and a shareholder in Vertex Pharmaceuticals and Neurocrine Biosciences. These relationships have been disclosed to and approved by the UCSD Independent Review Committee. S.P. declares no competing interests.
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- Cis-regulatory elements
(CREs). Non-coding DNA sequences that regulate transcription of genes located on the same chromosome. They include enhancers, promoters, insulators, silencing elements and tethering elements. Different classes of CREs can be identified using a combination of molecular markers, including chromatin accessibility and epigenetic modifications.
CREs located at the transcriptional start site of a gene.
CREs that can activate target gene expression from a large genomic distance, ranging from several kilobases to even millions of base pairs. They can be found either upstream or downstream of the target gene promoter.
CREs that prevent an enhancer from activating a target gene when placed between the enhancer and gene promoter but not when placed outside. An insulator also refers to a boundary element that can prevent the spreading of heterochromatin into euchromatic regions.
- Silencer elements
CREs that can be located close or distal to the transcriptional start site of the target gene. Silencers are bound by repressive transcription factors to inactivate gene expression.
- Tethering elements
CREs that can bring together promoters and enhancers for gene activation.
A complex of DNA and histone proteins. The basic unit of chromatin is the nucleosome.
- Histone modifications
Covalent modifications to histone proteins, such as methylation, acetylation, phosphorylation, ubiquitylation and sumoylation, that take place at lysine, serine, threonine, arginine and other residues. Histone modifications are catalysed by a diverse panel of enzymes referred to as writers, removed by a different set of proteins known as erasers, and recognized by chromatin-binding proteins known as readers. Activity of CREs is directly linked to distinct histone modifications due to the activities of writers, erasers and readers.
The combined features that enable stable propagation of different gene expression patterns from the same genome sequence. These include methylation of DNA at cytosine bases (mC), chemical modification of the histone proteins, chromatin accessibility and higher-order chromatin structures.
The process by which double-stranded DNA is cleaved by the transposase Tn5, creating short DNA fragments that are simultaneously tagged with PCR adapters. Tagmentation using Tn5 preferentially occurs at accessible or open chromatin and this property is used in ATAC-seq and other related assays.
- 3D-chromatin organization
Folding of the chromatin fibres inside the nucleus governs the spatial proximity between genes and CREs. While complex and variable between cells, the chromatin organization exhibits certain common features, including A/B compartments, topologically associating domains and loops.
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Preissl, S., Gaulton, K.J. & Ren, B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet (2022). https://doi.org/10.1038/s41576-022-00509-1
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