Recent advances in single-cell epigenetic sequencing technology
Basic Medicine|更新时间:2026-01-09
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Recent advances in single-cell epigenetic sequencing technology
Journal of Army Medical UniversityVol. 44, Issue 1, Pages: 74-78(2022)
作者机构:
1.400038 重庆,陆军军医大学(第三军医大学)高原军事医学系病理生理学教研室
2.2400038 重庆,陆军军医大学(第三军医大学)基础医学院全军免疫学研究所
作者简介:
基金信息:
the Young Talent Promotion Project of China Association for Science and Technology(2019QNRC001);the Special Project for Scientific and Technological Innovation Ability Promotion of Army Medical University(2019XYY05);the Special Project for Scientific and Technological Innovation Ability Promotion of Army Medical University(2020XQN02)
Single-cell sequencing technologies are important hot tools for decoding the heterogeneity of tissues
organs
cells and molecules
mainly based on the next-generation sequencing technology. It mainly includes single-cell genome sequencing
single-cell epigenome sequencing and single-cell transcriptome sequencing
along with the multi-omics single-cell sequencing technology. Epigenetics is an important regulatory link between genomics and cell phenotype. It plays a role in transcriptional regulation through chromatin accessibility
DNA and histone modification
nucleosome arrangement and three-dimensional conformation of chromatin. At present
researchers have developed a variety of single-cell sequencing techniques at epigenetic level
plotted multiple heterogeneity atlases at epigenetic level for several tissues
organs and cells
and have also primarily illuminated the determinant mechanisms for the heterogeneity of cell transcription at epigenetic level. In the future
with the applications of new single-cell sequencing technologies and new algorithms in life science and medical sicences
it is expected that the heterogeneity and the underlying molecular mechanisms of tissues
organs
cells and molecules will be decoded deeply.
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references
TANG F, BARBACIORU C, WANG Y, et al . mRNA-Seq whole-transcriptome analysis of a single cell[J ] . Nat Methods, 2009, 6(5): 377-382. DOI: 10.1038/nmeth.1315.
KHARCHENKO P V. The triumphs and limitations of computational methods for scRNA-seq[J]. Nat Methods, 2021, 18(7): 723-732. DOI: 10.1038/s41592-021-01171-x.
ZONG C H, LU S J, CHAPMAN A R, et al . Genome-wide detection of single-nucleotide and copy-number variations of a single human cell[J ] . Science, 2012, 338(6114): 1622-1626. DOI: 10.1126/science.1229164.
JIN W F, TANG Q S, WAN M M, et al . Genome-wide detect ion of DNase I hypersensitive sites in single cells and FFPE tissue samples[J ] . Nature, 2015, 528(7580): 142-146. DOI: 10.1038/nature15740.
BUENROSTRO J D, WU B J, LITZENBURGER U M, et al . Single-cell chromatin accessibility reveals principles of regulatory variation[J ] . Nature, 2015, 523(7561): 486-490. DOI: 10.1038/nature14590.
ROTEM A, RAM O, SHORESH N, et al . Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state[J ] . Nat Biotechnol, 2015, 33(11): 1165-1172. DOI: 10.1038/nbt.3383.
CARTER B, ZHAO K J. The epigenetic basis of cellular heterogeneity[J]. Nat Rev Genet, 2021, 22(4): 235-250. DOI: 10.1038/s41576-020-00300-0.
RODRIGUEZ J, REN G, DAY C R, et al . Intrinsic dynamics of a human gene reveal the basis of expression heterogeneity[J ] . Cell, 2019, 176(1/2): 213-226. e18. DOI: 10.1016/j.cell.2018.11.026.
GAO W, KU W L, PAN L, et al . Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells[J ] . Nucleic Acids Res, 2021, 49(10): e56. DOI: 10.1093/nar/gkab102.
LAI B B, GAO W W, CUI K R, et al . Principles of nucleosome organization revealed by single-cell micrococcal nuclease sequencing[J ] . Nature, 2018, 562(7726): 281-285. DOI: 10.1038/s41586-018-0567-3.
GAO W, LAI B, NI B, et al . Genome-wide profiling of nucleosome position and chromatin accessibility in single cells using scMNase-seq[J ] . Nat Protoc, 2020, 15(1): 68-85. DOI: 10.1038/s41596-019-0243-6.
KU W L, NAKAMURA K, GAO W W, et al . Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification[J ] . Nat Methods, 2019, 16(4): 323-325. DOI: 10.1038/s41592-019-0361-7.
SKENE P J, HENIKOFF S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites[J]. Elife, 2017, 6: e21856. DOI: 10.7554/eLife.21856.
CARTER B, KU W L, KANG J Y, et al . Mapping histone modifications in low cell number and single cells using antibody-guided chromatin tagmentation (ACT-seq)[J ] . Nat Commun, 2019, 10(1): 3747. DOI: 10.1038/s41467-019-11559-1.
XIONG H, LUO Y, WANG Q, et al . Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions[J ] . Nat Methods, 2021, 18(6): 652-660. DOI: 10.1038/s41592-021-01129-z.
BARTOSOVIC M, KABBE M, CASTELO-BRANCO G. Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues[J]. Nat Biotechnol, 2021, 39(7): 825-835. DOI: 10.1038/s41587-021-00869-9.
HAINER S J, BOŠKOVIĆA, MCCANNELL K N, et al . Profiling of pluripotency factors in single cells and early embryos[J ] . Cell, 2019, 177(5): 1319-1329. e11. DOI: 10.1016/j.cell.2019.03.014.
KU W L, PAN L X, CAO Y Q, et al . Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing[J ] . Genome Res, 2021. DOI: 10.1101/gr.260893.120.[Onlineahead of print ] .