Epigenetics reloaded: The single-cell revolution

Trends in Cell Biology

Volumn 24, Issue 11, 2014, Pages 712-723

  Bheda, Poonam ^a   Schneider, Robert ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Epigenetics; Epigenomics; Live cell; Microfluidics; Single cell

Indexed keywords

BISULFITE; CYTOSINE; DNA; DNA ADENINE METHYLTRANSFERASE; HISTONE; NUCLEIC ACID; PROTEIN; RESTRICTION ENDONUCLEASE; UNTRANSLATED RNA; CHROMATIN; NUCLEOSOME;

CELL DIVISION; CELL ISOLATION; CELL TRACKING; CHROMATIN; CHROMOSOME ANALYSIS; CHROMOSOME CONFORMATION ANALYSIS; DNA METHYLATION ASSAY; ENZYME ANALYSIS; EPIGENETICS; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE EXPRESSION; GENE LOCUS; GENE SEQUENCE; HISTONE MODIFICATION; IMMUNOPRECIPITATION; IN SITU HYBRIDIZATION; IN VIVO STUDY; INHERITANCE; MICROSCOPY; NONHUMAN; NUCLEOSOME; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN MODIFICATION; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA ANALYSIS; RNA SEQUENCE; SINGLE CELL ANALYSIS; ANIMAL; DEVICES; DNA METHYLATION; GENETIC EPIGENESIS; GENETICS; HUMAN; MICROFLUIDICS; PROCEDURES;

ANIMALS; CHROMATIN; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; GENE EXPRESSION; HUMANS; MICROFLUIDICS; NUCLEOSOMES; SINGLE-CELL ANALYSIS;

EID: 84927698129     PISSN: 09628924     EISSN: 18793088     Source Type: Journal    
DOI: 10.1016/j.tcb.2014.08.010     Document Type: Review

References (78)

1. Elgin S.C., Reuter G. Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb. Perspect. Biol. 2013, 5:a017780.
2. Saxena A., Carninci P. Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays 2011, 33:830-839.
3. Foster S.L., et al. Gene-specific control of inflammation by TLR-induced chromatin modifications. Nature 2007, 447:972-978.
4. Collins L.J., et al. The epigenetics of non-coding RNA. Handbook of Epigenetics 2011, 49-61. Elsevier. T.O. Tollefsbol (Ed.).
5. Rothbart S.B., Strahl B.D. Interpreting the language of histone and DNA modifications. Biochim. Biophys. Acta. 2014, 1839:627-643.
6. Petruk S., et al. TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell 2012, 150:922-933.
7. Misteli T. The cell biology of genomes: bringing the double helix to life. Cell 2013, 152:1209-1212.
8. Kouzarides T. Chromatin modifications and their function. Cell 2007, 128:693-705.
9. Daxinger L., Whitelaw E. Transgenerational epigenetic inheritance: more questions than answers. Genome Res. 2010, 20:1623-1628.
10. Heard E., Martienssen R.A. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 2014, 157:95-109.
11. Sanchez-Freire V., et al. Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Nat. Protoc. 2012, 7:829-838.
12. White A.K., et al. High-throughput microfluidic single-cell RT-qPCR. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:13999-14004.
13. Tang F., et al. RNA-seq analysis to capture the transcriptome landscape of a single cell. Nat. Protoc. 2010, 5:516-535.
14. Wu A.R., et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods 2014, 11:41-46.
15. Burton A., et al. Single-cell profiling of epigenetic modifiers identifies PRDM14 as an inducer of cell fate in the mammalian embryo. Cell Rep. 2013, 5:687-701.
16. Fatica A., Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat. Rev. Genet. 2014, 15:7-21.
17. Dekker J., et al. Capturing chromosome conformation. Science 2002, 295:1306-1311.
18. Zhao Z., et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 2006, 38:1341-1347.
19. Simonis M., et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 2006, 38:1348-1354.
20. Dostie J., et al. Chromosome Conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006, 16:1299-1309.
21. van Berkum N.L., et al. Hi-C: a method to study the three-dimensional architecture of genomes. J. Vis. Exp. 2010, 10.3791/1869.
22. Belton J.M., et al. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 2012, 58:268-276.
23. Nora E.P., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012, 485:381-385.
24. Tsai C.L., et al. Higher order chromatin structure at the X-inactivation center via looping DNA. Dev. Biol. 2008, 319:416-425.
25. Sexton T., et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 2012, 148:458-472.
26. Jin F., et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 2013, 503:290-294.
27. Nagano T., et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 2013, 502:59-64.
28. Hernandez H.G., et al. Optimizing methodologies for PCR-based DNA methylation analysis. Biotechniques 2013, 55:181-197.
29. Laird P.W. Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet. 2010, 11:191-203.
30. Guo H., et al. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res. 2013, 23:2126-2135.
31. Smallwood S.A., et al. Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 2014, 11:817-820.
32. Kantlehner M., et al. A high-throughput DNA methylation analysis of a single cell. Nucleic Acids Res. 2011, 39:e44.
33. Lorthongpanich C., et al. Single-cell DNA-methylation analysis reveals epigenetic chimerism in preimplantation embryos. Science 2013, 341:1110-1112.
34. Jessen W.J., et al. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat. Struct. Mol. Biol. 2006, 13:256-263.
35. Kelly T.K., et al. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 2012, 22:2497-2506.
36. Small E.C., et al. Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:E2462-E2471.
37. Gilfillan G.D., et al. Limitations and possibilities of low cell number ChIP-seq. BMC Genomics 2012, 13:645.
38. van Steensel B., Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nat. Biotechnol. 2000, 18:424-428.
39. Chaumeil J., et al. Combined immunofluorescence, RNA fluorescent in situ hybridization, and DNA fluorescent in situ hybridization to study chromatin changes, transcriptional activity, nuclear organization, and X-chromosome inactivation. Methods Mol. Biol. 2008, 463:297-308.
40. Li Y., et al. Sequence-specific microscopic visualization of DNA methylation status at satellite repeats in individual cell nuclei and chromosomes. Nucleic Acids Res. 2013, 41:e186.
41. Nuovo G.J., et al. In situ detection of the hypermethylation-induced inactivation of the p16 gene as an early event in oncogenesis. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:12754-12759.
42. Gomez D., et al. Detection of histone modifications at specific gene loci in single cells in histological sections. Nat. Methods 2013, 10:171-177.
43. Veening J.W., et al. Bet-hedging and epigenetic inheritance in bacterial cell development. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:4393-4398.
44. Rais Y., et al. Deterministic direct reprogramming of somatic cells to pluripotency. Nature 2013, 502:65-70.
45. Hathaway N.A., et al. Dynamics and memory of heterochromatin in living cells. Cell 2012, 149:1447-1460.
46. Hayashi-Takanaka Y., et al. Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling. Nucleic Acids Res. 2011, 39:6475-6488.
47. Rothbauer U., et al. Targeting and tracing antigens in live cells with fluorescent nanobodies. Nat. Methods 2006, 3:887-889.
48. Sato Y., et al. Genetically encoded system to track histone modification in vivo. Sci. Rep. 2013, 3:2436.
49. Yamagata K. DNA methylation profiling using live-cell imaging. Methods 2010, 52:259-266.
50. Sasaki K., et al. Real-time imaging of histone H4 hyperacetylation in living cells. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:16257-16262.
51. Sasaki K., et al. Development of live-cell imaging probes for monitoring histone modifications. Bioorg. Med. Chem. 2012, 20:1887-1892.
52. Kind J., et al. Single-cell dynamics of genome-nuclear lamina interactions. Cell 2013, 153:178-192.
53. Lleres D., et al. Quantitative analysis of chromatin compaction in living cells using FLIM-FRET. J. Cell Biol. 2009, 187:481-496.
54. Doyle E.L., et al. TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol. 2013, 23:390-398.
55. Jinek M., et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
56. Truong K., Ikura M. The use of FRET imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo. Curr. Opin. Struct. Biol. 2001, 11:573-578.
57. Chen B., et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 2013, 155:1479-1491.
58. Remy I., Michnick S.W. Application of protein-fragment complementation assays in cell biology. Biotechniques 2007, 42:137. 139, 141 passim.
59. Raser J.M., O'Shea E.K. Noise in gene expression: origins, consequences, and control. Science 2005, 309:2010-2013.
60. Torres-Padilla M.E., Chambers I. Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage. Development 2014, 141:2173-2181.
61. Torres-Padilla M.E. Generating different epigenotypes. Reprod. Biomed. Online 2013, 27:624-628.
62. Dekker J., et al. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 2013, 14:390-403.
63. Mensaert K., et al. Next-generation technologies and data analytical approaches for epigenomics. Environ. Mol. Mutagen. 2014, 55:155-170.
64. Sims D., et al. Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet. 2014, 15:121-132.
65. Miyanari Y., et al. Live visualization of chromatin dynamics with fluorescent TALEs. Nat. Struct. Mol. Biol. 2013, 20:1321-1324.
66. Piyasena M.E., Graves S.W. The intersection of flow cytometry with microfluidics and microfabrication. Lab Chip 2014, 14:1044-1059.
67. Bonn S., et al. Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat. Protoc. 2012, 7:978-994.
68. Behringer R., et al. Disaggregating cleavage-stage embryos and the inner cell mass of blastocysts into individual cells. Manipulating the Mouse Embryo: A Laboratory Manual 2014, 547-548. CSH Press. 4th edn.
69. Decarlo K., et al. Laser capture microdissection: methods and applications. Methods Mol. Biol. 2011, 755:1-15.
70. Yin H., Marshall D. Microfluidics for single cell analysis. Curr. Opin. Biotechnol. 2012, 23:110-119.
71. Microfluidics for Biological Applications 2008, Springer. W.C. Tian, E. Finehout (Eds.).
72. Autebert J., et al. Microfluidic: an innovative tool for efficient cell sorting. Methods 2012, 57:297-307.
73. Crane M.M., et al. Microfluidics-enabled phenotyping, imaging, and screening of multicellular organisms. Lab Chip 2010, 10:1509-1517.
74. Mehling M., Tay S. Microfluidic cell culture. Curr. Opin. Biotechnol. 2014, 25:95-102.
75. Charvin G., et al. Long-term imaging in microfluidic devices. Methods Mol. Biol. 2010, 591:229-242.
76. Denervaud N., et al. A chemostat array enables the spatio-temporal analysis of the yeast proteome. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:15842-15847.
77. Unger M.A., et al. Monolithic microfabricated valves and pumps by multilayer soft lithography. Science 2000, 288:113-116.
78. Mazutis L., et al. Single-cell analysis and sorting using droplet-based microfluidics. Nat. Protoc. 2013, 8:870-891.