A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

Nature Methods

Volumn 14, Issue 6, 2017, Pages 629-635

  Diao, Yarui ^a   Fang, Rongxin ^a,b   Li, Bin ^a   Meng, Zhipeng ^c,d   Yu, Juntao ^a,e   Qiu, Yunjiang ^a,b   Lin, Kimberly C ^c,d   Huang, Hui ^a,b   Liu, Tristin ^a   Marina, Ryan J ^b   Jung, Inkyung ^f   Shen, Yin ^g   Guan, Kun Liang ^c,d   Ren, Bing ^a,d,h  

^a LUDWIG INSTITUTE FOR CANCER RESEARCH   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c San Diego   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^e UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^f Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; DEOXYRIBONUCLEASE; OCTAMER TRANSCRIPTION FACTOR 4;

ARTICLE; CONTROLLED STUDY; EMBRYO; ENHANCER REGION; FUNCTIONAL ASSESSMENT; GENE DELETION; GENE LOCUS; GENETIC IDENTIFICATION; GENETIC SCREENING; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; HUMAN EMBRYONIC STEM CELL; MOLECULAR GENETICS; PRIORITY JOURNAL; PROMOTER REGION; ALGORITHM; CELL CULTURE; CHROMOSOMAL MAPPING; DNA SEQUENCE; EMBRYONIC STEM CELL; GENE EXPRESSION REGULATION; GENETICS; PHYSIOLOGY; PROCEDURES; REGULATORY SEQUENCE; SINGLE CELL ANALYSIS;

ALGORITHMS; CELLS, CULTURED; CHROMOSOME MAPPING; EMBRYONIC STEM CELLS; GENE EXPRESSION REGULATION; GENETIC TESTING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS;

EID: 85017510953     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.4264     Document Type: Article

References (60)

1. Gerstein, M.B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
2. Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012).
3. Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134-1148 (2013).
4. Roadmap Epigenomics Consortium. et al. Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015).
5. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
6. Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
7. Thurman, R.E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
8. Farh, K.K. et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337-343 (2015).
9. Gjoneska, E. et al. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature 518, 365-369 (2015).
10. Canver, M.C. et al. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527, 192-197 (2015).
11. Korkmaz, G. et al. Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9. Nat. Biotechnol. 34, 192-198 (2016).
12. Rajagopal, N. et al. High-throughput mapping of regulatory DNA. Nat. Biotechnol. 34, 167-174 (2016).
13. Diao, Y. et al. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Res. 26, 397-405 (2016).
14. Sanjana, N.E. et al. High-resolution interrogation of functional elements in the noncoding genome. Science 353, 1545-1549 (2016).
15. Fulco, C.P. et al. Systematic mapping of functional enhancer-promoter connections with CRISPR interference. Science 354, 769-773 (2016).
16. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
17. Mojica, F.J., Diez-Villasenor, C., Garcia-Martinez, J., Almendros, C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 155, 733-740 (2009).
18. Sternberg, S.H., Redding, S., Jinek, M., Greene, E.C., Doudna, J.A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67 (2014).
19. Zwaka, T.P., Thomson, J.A. Homologous recombination in human embryonic stem cells. Nat. Biotechnol. 21, 319-321 (2003).
20. Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 15, 554 (2014).
21. Ware, C.B. et al. Derivation of naive human embryonic stem cells. Proc. Natl. Acad. Sci. USA 111, 4484-4489 (2014).
22. Buenrostro, J.D., Giresi, P.G., Zaba, L.C., Chang, H.Y., Greenleaf, W.J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013).
23. Ghirlando, R., Felsenfeld, G. CTCF: Making the right connections. Genes Dev. 30, 881-891 (2016).
24. Dixon, J.R., Gorkin, D.U., Ren, B. Chromatin domains: The unit of chromosome organization. Mol. Cell 62, 668-680 (2016).
25. Yan, J. et al. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 154, 801-813 (2013).
26. MacArthur, S. et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 10, R80 (2009).
27. Yip, K.Y. et al. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 13, R48 (2012).
28. Chandra, T. et al. Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol. Cell 47, 203-214 (2012).
29. Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-947 (2013).
30. Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84-98 (2012).
31. Engreitz, J.M. et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature 539, 452-455 (2016).
32. Chia, N.Y. et al. A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature 468, 316-320 (2010).
33. Rogakou, E.P., Boon, C., Redon, C., Bonner, W.M. Megabase chromatin domains involved in DNA double-strand breaks in vivo. J. Cell Biol. 146, 905-916 (1999).
34. Downs, J.A., Lowndes, N.F., Jackson, S.P. A role for Saccharomyces cerevisiae histone H2A in DNA repair. Nature 408, 1001-1004 (2000).
35. Burma, S., Chen, B.P., Murphy, M., Kurimasa, A., Chen, D.J. ATM phosphorylates histone H2AX in response to DNA double-strand breaks. J. Biol. Chem. 276, 42462-42467 (2001).
36. Dixon, J.R. et al. Chromatin architecture reorganization during stem cell differentiation. Nature 518, 331-336 (2015).
37. Core, L.J. et al. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat. Genet. 46, 1311-1320 (2014).
38. Paralkar, V.R. et al. Unlinking an lncRNA from its associated cis element. Mol. Cell 62, 104-110 (2016).
39. Handoko, L. et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat. Genet. 43, 630-638 (2011).
40. DeMare, L.E. et al. The genomic landscape of cohesin-associated chromatin interactions. Genome Res. 23, 1224-1234 (2013).
41. Kieffer-Kwon, K.R. et al. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155, 1507-1520 (2013).
42. Ji, X. et al. 3D chromosome regulatory landscape of human pluripotent cells. Cell Stem Cell 18, 262-275 (2016).
43. Tang, Z. et al. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. Cell 163, 1611-1627 (2015).
44. Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290-294 (2013).
45. Rao, S.S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665-1680 (2014).
46. Dixon, J.R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376-380 (2012).
47. Arnold, C.D. et al. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339, 1074-1077 (2013).
48. Thakore, P.I. et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12, 1143-1149 (2015).
49. Diao, Y., Fang, R., Li, B., Ren, B. A dual sgRNA mediated tiling-deletion based genetic screen to identify regulatory DNA sequence in mammalian cells. Protoc. exch. http://dx.doi.org/10.1038/protex.2017.037 (2017).
50. Langmead, B., Trapnell, C., Pop, M., Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
51. Wu, X., Kriz, A.J., Sharp, P.A. Target specificity of the CRISPR-Cas9 system. Quant. Biol. 2, 59-70 (2014)
52. Meng, Z. et al. Berbamine inhibits the growth of liver cancer cells and cancer-initiating cells by targeting Ca2+/calmodulin-dependent protein kinase II. Mol. Cancer Ther. 12, 2067-2077 (2013).
53. Kolde, R., Laur, S., Adler, P., Vilo, J. Robust rank aggregation for gene list integration and meta-analysis. Bioinformatics 28, 573-580 (2012).
54. Rajagopal, N. et al. RFECS: A random-forest based algorithm for enhancer identification from chromatin state. PLoS Comput. Biol. 9, e1002968 (2013).
55. Quinlan, A.R., Hall, I.M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
56. Kelley, M.L., Strezoska, Ž., He, K., Vermeulen, A., Smith, Av. Versatility of chemically synthesized guide RNAs for CRISPR-Cas9 genome editing. J. Biotechnol. 233, 74-83 (2016).
57. Heintzman, N.D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318 (2007).
58. Diao, Y. et al. Pax3/7BP is a Pax7-A nd Pax3-binding protein that regulates the proliferation of muscle precursor cells by an epigenetic mechanism. Cell Stem Cell 11, 231-241 (2012).
59. Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
60. Ramírez, F. et al. deepTools2: A next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160-W165 (2016).