Advances in Single-cell Multi-omics Profiling

Overview

Journal RSC Chem Biol

Publisher Royal Society of Chemistry

Specialty Biology

Date 2021 Aug 30

PMID 34458793

Citations 12

Authors

Dongsheng Bai

Jinying Peng

Chengqi Yi

Affiliations

Soon will be listed here.

Abstract

Single-cell profiling methods are developed to dissect heterogeneity of cell populations. Recently, multiple enzymatic or chemical treatments have been integrated into single-cell multi-omics profiling methods with high compatibility. These methods have been verified to identify rare or new cell types with high confidence. Single-cell multi-omics analysis can also provide tools to solve the complex regulatory network associated with genome coding, epigenome regulation, and transcripotome expression in a single cell. However, acquiring high-quality single-cell data still faces inherent technical challenges, and co-assays with some other layers of cell identify such as transcription factors binding, histone modifications ., profiles need new technological breakthroughs to facilitate a more thorough understanding of a single cell. In this review, we summarize the recent advances of single-cell multi-omics methods and discuss the challenges and opportunities in this filed.

Citing Articles

Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine.

Chu L, Wang W, Gu X, Wu P, Gao C, Zhang Q Mil Med Res. 2024; 11(1):31.

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moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud.

Choi J, Park C, Chae H PeerJ. 2024; 12:e17006.

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Oncogenes and cancer associated thrombosis: what can we learn from single cell genomics about risks and mechanisms?.

Tawil N, Mohammadnia A, Rak J Front Med (Lausanne). 2024; 10:1252417.

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CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification.

Liu J, Zeng W, Kan S, Li M, Zheng R Brief Bioinform. 2023; 25(1).

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Application of single-cell multi-omics approaches in horticulture research.

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References

Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A . Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289-93. PMC: 2858594. DOI: 10.1126/science.1181369. View

Zeng H, He B, Xia B, Bai D, Lu X, Cai J . Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution. J Am Chem Soc. 2018; 140(41):13190-13194. PMC: 6423965. DOI: 10.1021/jacs.8b08297. View

Liu Y, Siejka-Zielinska P, Velikova G, Bi Y, Yuan F, Tomkova M . Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat Biotechnol. 2019; 37(4):424-429. DOI: 10.1038/s41587-019-0041-2. View

Duan Z, Andronescu M, Schutz K, Lee C, Shendure J, Fields S . A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes. Methods. 2012; 58(3):277-88. PMC: 3477625. DOI: 10.1016/j.ymeth.2012.06.018. View

Buenrostro J, Wu B, Litzenburger U, Ruff D, Gonzales M, Snyder M . Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015; 523(7561):486-90. PMC: 4685948. DOI: 10.1038/nature14590. View

Patti G, Yanes O, Siuzdak G . Innovation: Metabolomics: the apogee of the omics trilogy. Nat Rev Mol Cell Biol. 2012; 13(4):263-9. PMC: 3682684. DOI: 10.1038/nrm3314. View

Zhu C, Yu M, Huang H, Juric I, Abnousi A, Hu R . An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome. Nat Struct Mol Biol. 2019; 26(11):1063-1070. PMC: 7231560. DOI: 10.1038/s41594-019-0323-x. View

Cusanovich D, Daza R, Adey A, Pliner H, Christiansen L, Gunderson K . Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015; 348(6237):910-4. PMC: 4836442. DOI: 10.1126/science.aab1601. View

Angermueller C, Clark S, Lee H, Macaulay I, Teng M, Hu T . Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity. Nat Methods. 2016; 13(3):229-232. PMC: 4770512. DOI: 10.1038/nmeth.3728. View

10.

Ai S, Xiong H, Li C, Luo Y, Shi Q, Liu Y . Profiling chromatin states using single-cell itChIP-seq. Nat Cell Biol. 2019; 21(9):1164-1172. DOI: 10.1038/s41556-019-0383-5. View

11.

Meissner A, Gnirke A, Bell G, Ramsahoye B, Lander E, Jaenisch R . Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005; 33(18):5868-77. PMC: 1258174. DOI: 10.1093/nar/gki901. View

12.

Dey S, Kester L, Spanjaard B, Bienko M, van Oudenaarden A . Integrated genome and transcriptome sequencing of the same cell. Nat Biotechnol. 2015; 33(3):285-289. PMC: 4374170. DOI: 10.1038/nbt.3129. View

13.

Nagano T, Lubling Y, Stevens T, Schoenfelder S, Yaffe E, Dean W . Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature. 2013; 502(7469):59-64. PMC: 3869051. DOI: 10.1038/nature12593. View

14.

Liu L, Liu C, Quintero A, Wu L, Yuan Y, Wang M . Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity. Nat Commun. 2019; 10(1):470. PMC: 6349937. DOI: 10.1038/s41467-018-08205-7. View

15.

Chen S, Lake B, Zhang K . High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. Nat Biotechnol. 2019; 37(12):1452-1457. PMC: 6893138. DOI: 10.1038/s41587-019-0290-0. View

16.

Zeng H, He B, Yi C . Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA. Chembiochem. 2019; 20(15):1898-1905. DOI: 10.1002/cbic.201900035. View

17.

Roundtree I, Evans M, Pan T, He C . Dynamic RNA Modifications in Gene Expression Regulation. Cell. 2017; 169(7):1187-1200. PMC: 5657247. DOI: 10.1016/j.cell.2017.05.045. View

18.

Picelli S, Faridani O, Bjorklund A, Winberg G, Sagasser S, Sandberg R . Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc. 2014; 9(1):171-81. DOI: 10.1038/nprot.2014.006. View

19.

Zong C, Lu S, Chapman A, Xie X . Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science. 2012; 338(6114):1622-6. PMC: 3600412. DOI: 10.1126/science.1229164. View

20.

Kelly T, Liu Y, Lay F, Liang G, Berman B, Jones P . Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 2012; 22(12):2497-506. PMC: 3514679. DOI: 10.1101/gr.143008.112. View